Variant report

Variant	rs6717723
Chromosome Location	chr2:99756930-99756931
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	E2F4	chr2:99756641-99757193	MCF10A-Er-Src	breast:	n/a	chr2:99756720-99756729
2	HCFC1	chr2:99756684-99758952	Hela-S3	cervix:	n/a	n/a
3	RFX5	chr2:99756928-99758310	Hela-S3	cervix:	n/a	chr2:99758068-99758082
4	POLR2A	chr2:99756780-99758458	MCF10A-Er-Src	breast:	n/a	n/a
5	SIN3A	chr2:99756764-99758620	H1-hESC	embryonic stem cell:	n/a	chr2:99757378-99757391
6	MXI1	chr2:99756468-99759006	SK-N-SH	brain:	n/a	chr2:99757257-99757272
7	STAT3	chr2:99756768-99757265	MCF10A-Er-Src	breast:	n/a	chr2:99757211-99757219
8	TBP	chr2:99756750-99758236	Hela-S3	cervix:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr2:99754836..99757247-chr2:99953707..99955496,2	MCF-7	breast:
2	chr2:99755178..99760444-chr2:99795813..99800130,7	MCF-7	breast:
3	chr2:99756129..99759101-chr2:99952738..99954734,2	MCF-7	breast:
4	chr2:99754528..99760418-chr2:99769364..99773305,11	K562	blood:
5	chr2:99755030..99760884-chr2:99769021..99772906,10	K562	blood:
6	chr2:99756639..99759461-chr2:99768691..99772730,10	MCF-7	breast:
7	chr2:99756618..99760530-chr2:99796957..99801063,7	MCF-7	breast:

Variant related genes	Relation type
C2orf15	TF binding region
ENSG00000273045	TF binding region
ENSG00000241962	Chromatin interaction
ENSG00000115514	Chromatin interaction
ENSG00000144182	Chromatin interaction
ENSG00000273155	Chromatin interaction
ENSG00000158417	Chromatin interaction
ENSG00000185414	Chromatin interaction
ENSG00000158411	Chromatin interaction
ENSG00000135951	Chromatin interaction

Extended variants
information (count: 163 )
Associated
traits (count: 12 )

rSNPs within LD-proxies of this variant (count:160)

rs_ID	r²[population]
rs10165534	0.85[ASN][1000 genomes]
rs10179043	1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[YRI][hapmap];0.87[ASN][1000 genomes]
rs10190421	1.00[CHB][hapmap];1.00[JPT][hapmap];0.97[YRI][hapmap]
rs10196680	0.85[ASN][1000 genomes]
rs1044575	0.85[AMR][1000 genomes];0.91[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs10865029	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.97[YRI][hapmap];0.95[AFR][1000 genomes];0.91[AMR][1000 genomes];0.90[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs11123761	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[AMR][1000 genomes];0.90[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs11123762	0.95[AFR][1000 genomes];0.91[AMR][1000 genomes];0.90[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs11123763	0.98[AFR][1000 genomes];0.93[AMR][1000 genomes];0.91[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11123764	0.93[AMR][1000 genomes];0.90[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11123765	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.97[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11123766	0.82[AFR][1000 genomes];0.91[AMR][1000 genomes];0.94[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11123770	0.88[EUR][1000 genomes]
rs1133977	0.92[CEU][hapmap];0.89[EUR][1000 genomes]
rs1133978	0.89[EUR][1000 genomes]
rs11674894	0.88[CEU][hapmap];0.85[EUR][1000 genomes]
rs11677247	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.97[YRI][hapmap];1.00[AFR][1000 genomes];0.93[AMR][1000 genomes];0.93[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11677321	0.87[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs11678456	0.91[AMR][1000 genomes];0.89[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs11683107	0.92[CEU][hapmap];0.93[EUR][1000 genomes]
rs11683188	0.88[CEU][hapmap];0.89[EUR][1000 genomes]
rs11684507	0.98[AFR][1000 genomes];0.86[AMR][1000 genomes];0.84[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs11684610	0.92[AFR][1000 genomes];0.88[AMR][1000 genomes];0.82[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs11685759	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11688004	0.92[CEU][hapmap];0.89[EUR][1000 genomes]
rs11689265	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs11692336	0.89[EUR][1000 genomes]
rs11692669	0.84[EUR][1000 genomes]
rs11692699	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[YRI][hapmap];0.94[AFR][1000 genomes];0.91[AMR][1000 genomes];0.90[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs11693427	0.92[AFR][1000 genomes];0.93[AMR][1000 genomes];0.91[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs11695379	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[YRI][hapmap];0.96[AFR][1000 genomes];0.93[AMR][1000 genomes];0.91[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs11695751	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[YRI][hapmap];0.91[AFR][1000 genomes];0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs11883676	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[YRI][hapmap];0.86[AMR][1000 genomes];0.92[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs11890338	0.98[AFR][1000 genomes];0.93[AMR][1000 genomes];0.93[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs11895749	0.89[EUR][1000 genomes]
rs11900670	0.88[AFR][1000 genomes];0.91[AMR][1000 genomes];0.90[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs12464710	0.86[AFR][1000 genomes];0.82[ASN][1000 genomes]
rs12467679	0.85[ASN][1000 genomes]
rs12468807	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs12473029	1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[YRI][hapmap];0.87[ASN][1000 genomes]
rs12477754	0.85[ASN][1000 genomes]
rs12477978	0.86[AFR][1000 genomes];0.84[ASN][1000 genomes]
rs12613624	0.92[CEU][hapmap];0.89[EUR][1000 genomes]
rs12619780	0.86[AFR][1000 genomes];0.88[EUR][1000 genomes]
rs12621007	0.92[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs12987548	0.88[EUR][1000 genomes]
rs12991189	0.83[EUR][1000 genomes]
rs12992218	1.00[AFR][1000 genomes];0.92[AMR][1000 genomes];0.93[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12992930	0.86[AMR][1000 genomes];0.92[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs12995473	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[AMR][1000 genomes];0.93[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12999417	0.96[CEU][hapmap];0.86[CHB][hapmap];0.88[JPT][hapmap];0.88[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs13000731	0.90[EUR][1000 genomes]
rs13004491	0.91[AFR][1000 genomes];0.93[AMR][1000 genomes];0.88[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs13008171	0.92[CEU][hapmap];0.89[EUR][1000 genomes]
rs13008496	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[YRI][hapmap];0.87[AFR][1000 genomes];0.82[ASN][1000 genomes]
rs13009147	1.00[CEU][hapmap];0.85[CHB][hapmap];1.00[JPT][hapmap];0.85[AMR][1000 genomes];0.90[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs13012481	0.86[AFR][1000 genomes];0.90[AMR][1000 genomes];0.92[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs13018891	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[YRI][hapmap];0.83[AFR][1000 genomes];0.93[AMR][1000 genomes];0.93[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs13020339	0.90[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs13022329	0.94[AFR][1000 genomes];0.91[AMR][1000 genomes];0.90[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs13023479	0.85[AFR][1000 genomes];0.81[EUR][1000 genomes]
rs13023501	0.85[EUR][1000 genomes]
rs13023744	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs13026928	0.82[AMR][1000 genomes];0.92[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs13030961	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs13031919	0.82[EUR][1000 genomes]
rs13033012	0.92[CEU][hapmap];0.90[EUR][1000 genomes]
rs13035311	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[AMR][1000 genomes];0.90[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs1349778	1.00[CHB][hapmap];1.00[JPT][hapmap];0.85[ASN][1000 genomes]
rs1349779	1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[YRI][hapmap];0.86[AFR][1000 genomes];0.87[ASN][1000 genomes]
rs13798	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.87[AMR][1000 genomes];0.91[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs1453561	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs1453562	1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[YRI][hapmap]
rs1453563	0.92[CEU][hapmap];0.89[EUR][1000 genomes]
rs1580068	1.00[CHB][hapmap];1.00[JPT][hapmap];0.97[YRI][hapmap];0.86[AFR][1000 genomes];0.85[ASN][1000 genomes]
rs17708218	1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[YRI][hapmap];0.90[AFR][1000 genomes];0.88[ASN][1000 genomes]
rs17759607	0.92[CEU][hapmap];0.89[EUR][1000 genomes]
rs1993230	1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[YRI][hapmap];0.85[AFR][1000 genomes];0.88[ASN][1000 genomes]
rs2045057	1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[YRI][hapmap];0.85[AFR][1000 genomes];0.88[ASN][1000 genomes]
rs2171359	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[YRI][hapmap];0.85[AMR][1000 genomes];0.91[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2171362	0.90[AFR][1000 genomes];0.84[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs2309524	1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[YRI][hapmap];0.82[AFR][1000 genomes];0.88[ASN][1000 genomes]
rs2309581	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[YRI][hapmap];0.91[AMR][1000 genomes];0.92[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2516827	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.97[YRI][hapmap];1.00[AFR][1000 genomes];0.91[AMR][1000 genomes];0.93[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2516828	0.91[AMR][1000 genomes];0.93[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2516829	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[AMR][1000 genomes];0.93[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2516830	0.92[CEU][hapmap];0.91[EUR][1000 genomes]
rs2516832	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AFR][1000 genomes];0.88[AMR][1000 genomes];0.93[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2516833	0.91[EUR][1000 genomes]
rs2516834	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.97[YRI][hapmap];0.93[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2516835	0.92[CEU][hapmap];0.92[EUR][1000 genomes]
rs2516836	0.96[AFR][1000 genomes];0.87[AMR][1000 genomes];0.90[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2632260	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.97[YRI][hapmap];0.98[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2632261	0.88[AMR][1000 genomes];0.93[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2632277	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2632283	0.92[CEU][hapmap];0.92[EUR][1000 genomes]
rs2632284	0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2964969	0.88[AMR][1000 genomes];0.92[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2969379	0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34252185	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs34272114	0.89[EUR][1000 genomes]
rs34766932	0.93[AMR][1000 genomes];0.89[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs35461437	0.88[AMR][1000 genomes];0.85[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs36071868	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4324365	1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[YRI][hapmap]
rs4340581	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.97[YRI][hapmap];0.96[AFR][1000 genomes];0.98[AMR][1000 genomes];0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4347885	0.89[EUR][1000 genomes]
rs4402818	0.91[AMR][1000 genomes];0.90[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs4588238	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[YRI][hapmap];0.83[AFR][1000 genomes];0.93[AMR][1000 genomes];0.90[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4622780	1.00[CHB][hapmap];1.00[JPT][hapmap];0.85[ASN][1000 genomes]
rs4850897	0.92[CEU][hapmap];0.91[EUR][1000 genomes]
rs4851184	1.00[CHB][hapmap];1.00[JPT][hapmap];0.97[YRI][hapmap]
rs4851187	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[YRI][hapmap];0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4851188	0.92[CEU][hapmap];0.89[EUR][1000 genomes]
rs6542852	0.82[ASN][1000 genomes]
rs6542858	0.83[AFR][1000 genomes];0.85[ASN][1000 genomes]
rs6542863	0.95[AFR][1000 genomes];0.91[AMR][1000 genomes];0.90[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs6542864	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[YRI][hapmap];0.91[AMR][1000 genomes];0.90[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs6542865	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[YRI][hapmap];0.81[AFR][1000 genomes];0.93[AMR][1000 genomes];0.93[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6542866	0.92[CEU][hapmap];0.92[EUR][1000 genomes]
rs6542868	0.92[CEU][hapmap];0.91[EUR][1000 genomes]
rs6542869	0.90[AMR][1000 genomes];0.91[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6542870	0.86[AMR][1000 genomes];0.92[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs6704766	1.00[CHB][hapmap];1.00[JPT][hapmap];0.97[YRI][hapmap];0.86[AFR][1000 genomes];0.85[ASN][1000 genomes]
rs6708576	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[AMR][1000 genomes];0.91[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs6708878	0.91[EUR][1000 genomes]
rs6712704	0.95[AFR][1000 genomes];0.91[AMR][1000 genomes];0.90[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs6717729	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[YRI][hapmap];0.93[AMR][1000 genomes];0.94[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6726618	0.95[AFR][1000 genomes];0.87[AMR][1000 genomes];0.87[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs6727749	0.92[CEU][hapmap];0.91[EUR][1000 genomes]
rs6733285	0.92[CEU][hapmap]
rs6736064	0.86[AFR][1000 genomes];0.85[ASN][1000 genomes]
rs6739579	0.91[AMR][1000 genomes];0.90[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs6741772	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs6741773	0.88[AMR][1000 genomes];0.84[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs6743355	0.92[AFR][1000 genomes];0.91[AMR][1000 genomes];0.90[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs6751927	0.90[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[YRI][hapmap];0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6753063	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[YRI][hapmap];0.86[AMR][1000 genomes];0.92[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs6753650	0.88[AFR][1000 genomes];0.82[EUR][1000 genomes]
rs6756650	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[YRI][hapmap];0.86[AMR][1000 genomes];0.92[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs6757019	1.00[CHB][hapmap];1.00[JPT][hapmap];0.97[YRI][hapmap]
rs6757661	0.85[AMR][1000 genomes];0.92[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs6759354	0.85[ASN][1000 genomes]
rs720228	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[YRI][hapmap];0.91[AFR][1000 genomes];0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs720229	0.92[CEU][hapmap];0.88[EUR][1000 genomes]
rs7349217	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.87[AMR][1000 genomes];0.89[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7558004	0.85[AMR][1000 genomes];0.91[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7558239	1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[YRI][hapmap];0.84[AFR][1000 genomes];0.82[ASN][1000 genomes]
rs7572660	0.91[AMR][1000 genomes];0.92[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7577477	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.97[YRI][hapmap];0.94[AFR][1000 genomes];0.91[AMR][1000 genomes];0.90[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7584809	0.94[AFR][1000 genomes];0.91[AMR][1000 genomes];0.88[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs7604557	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7605843	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.85[AMR][1000 genomes];0.91[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7608938	0.91[EUR][1000 genomes]
rs8179690	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[YRI][hapmap];0.85[AMR][1000 genomes];0.91[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs896886	1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[YRI][hapmap];0.86[AFR][1000 genomes];0.85[ASN][1000 genomes]
rs9308816	1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[YRI][hapmap];0.85[ASN][1000 genomes]
rs972768	1.00[CHB][hapmap];1.00[JPT][hapmap];0.97[YRI][hapmap];0.82[AFR][1000 genomes];0.88[ASN][1000 genomes]
rs9808541	1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[YRI][hapmap];0.82[AFR][1000 genomes];0.80[ASN][1000 genomes]
rs9941561	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[AMR][1000 genomes];0.93[EUR][1000 genomes];0.98[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv431424	chr2:99652682-100494682	Flanking Active TSS Enhancers Strong transcription Weak transcription ZNF genes & repeats Transcr. at gene 5' and 3' Genic enhancers Active TSS Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	49 gene(s)	inside rSNPs	diseases
2	nsv1013507	chr2:99729047-99861692	Weak transcription Strong transcription Enhancers Active TSS Flanking Active TSS Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	20 gene(s)	inside rSNPs	diseases
3	nsv535839	chr2:99742621-99793747	Weak transcription Active TSS Strong transcription Flanking Active TSS Enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Genic enhancers Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	15 gene(s)	inside rSNPs	diseases

mRNA abundance (count:12)

SNP	Gene	Cis/trans	Tissue	Source
rs6717723	TSGA10	Cis_1M	lymphoblastoid	RTeQTL
rs6717723	MITD1	Cis_1M	lymphoblastoid	RTeQTL
rs6717723	TSGA10	cis	Esophagus Mucosa	GTEx
rs6717723	TSGA10	cis	multi-tissue	Pritchard
rs6717723	LIPT1	Cis_1M	lymphoblastoid	RTeQTL
rs6717723	LIPT1	cis	uninvolved skin	skin_eQTL
rs6717723	TSGA10	cis	Lymphoblastoid	GTEx
rs6717723	LIPT1	cis	normal skin	skin_eQTL
rs6717723	TSGA10	cis	Skin Sun Exposed Lower leg	GTEx
rs6717723	LIPT1	cis	lesional skin	skin_eQTL
rs6717723	TSGA10	cis	Thyroid	GTEx
rs6717723	TSGA10	cis	lung	GTEx

Chromatin state (count:93 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:99742800-99757200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
2	chr2:99743200-99757000	Weak transcription	Small Intestine	intestine
3	chr2:99756200-99757000	Enhancers	Primary T helper cells PMA-I stimulated	--
4	chr2:99756200-99757000	Enhancers	Primary T killer naive cells fromperipheralblood	blood
5	chr2:99756400-99757000	Flanking Bivalent TSS/Enh	iPS-20b Cell Line	embryonic stem cell
6	chr2:99756400-99757000	Flanking Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
7	chr2:99756400-99757000	Bivalent Enhancer	Primary monocytes fromperipheralblood	blood
8	chr2:99756400-99757000	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
9	chr2:99756400-99758400	Active TSS	Foreskin Keratinocyte Primary Cells skin02	Skin
10	chr2:99756400-99758800	Active TSS	Pancreatic Islets	Pancreatic Islet
11	chr2:99756600-99757000	Flanking Active TSS	H9 Derived Neuron Cultured Cells	ES cell derived
12	chr2:99756600-99757000	Flanking Active TSS	Breast Myoepithelial Primary Cells	Breast
13	chr2:99756600-99757000	Enhancers	Primary neutrophils fromperipheralblood	blood
14	chr2:99756600-99757000	Enhancers	Stomach Mucosa	stomach
15	chr2:99756600-99757000	Flanking Active TSS	GM12878-XiMat	blood
16	chr2:99756600-99757000	Flanking Active TSS	Hela-S3	cervix
17	chr2:99756600-99757000	Enhancers	HSMM	muscle
18	chr2:99756600-99757200	Active TSS	HepG2	liver
19	chr2:99756600-99758000	Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
20	chr2:99756600-99758200	Active TSS	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
21	chr2:99756600-99758200	Active TSS	Foreskin Keratinocyte Primary Cells skin03	Skin
22	chr2:99756600-99758200	Active TSS	Duodenum Smooth Muscle	Duodenum
23	chr2:99756600-99758200	Active TSS	HMEC	breast
24	chr2:99756600-99758200	Active TSS	NHEK	skin
25	chr2:99756600-99758600	Active TSS	A549	lung
26	chr2:99756600-99758800	Active TSS	ES-I3 Cell Line	embryonic stem cell
27	chr2:99756600-99758800	Active TSS	Ganglion Eminence derived primary cultured neurospheres	brain
28	chr2:99756600-99758800	Active TSS	Fetal Intestine Large	intestine
29	chr2:99756600-99759000	Active TSS	H1 Cell Line	embryonic stem cell
30	chr2:99756600-99759000	Active TSS	HUES6 Cell Line	embryonic stem cell
31	chr2:99756600-99759000	Active TSS	Fetal Kidney	kidney
32	chr2:99756800-99757000	Flanking Bivalent TSS/Enh	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
33	chr2:99756800-99757000	Flanking Active TSS	iPS-15b Cell Line	embryonic stem cell
34	chr2:99756800-99757000	Flanking Active TSS	iPS-18 Cell Line	embryonic stem cell
35	chr2:99756800-99757000	Flanking Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
36	chr2:99756800-99757000	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
37	chr2:99756800-99757000	Enhancers	Primary T cells fromperipheralblood	blood
38	chr2:99756800-99757000	Flanking Active TSS	Primary hematopoietic stem cells	blood
39	chr2:99756800-99757000	Enhancers	Primary T helper naive cells from peripheral blood	blood
40	chr2:99756800-99757000	Flanking Active TSS	Primary T killer memory cells from peripheral blood	blood
41	chr2:99756800-99757000	Flanking Active TSS	Cortex derived primary cultured neurospheres	brain
42	chr2:99756800-99757000	Enhancers	Primary mononuclear cells fromperipheralblood	Blood
43	chr2:99756800-99757000	Flanking Active TSS	Brain Angular Gyrus	brain
44	chr2:99756800-99757000	Flanking Active TSS	Brain Cingulate Gyrus	brain
45	chr2:99756800-99757000	Flanking Active TSS	Brain Substantia Nigra	brain
46	chr2:99756800-99757000	Flanking Active TSS	Colon Smooth Muscle	Colon
47	chr2:99756800-99757000	Active TSS	Duodenum Mucosa	Duodenum
48	chr2:99756800-99757000	Active TSS	Fetal Stomach	stomach
49	chr2:99756800-99757000	Enhancers	Placenta Amnion	Placenta Amnion
50	chr2:99756800-99757000	Enhancers	Skeletal Muscle Female	skeletal muscle

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links