Variant report

Variant	rs2965180
Chromosome Location	chr19:19491973-19491974
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	FOXA1	chr19:19491893-19492169	HepG2	liver:	n/a	chr19:19492003-19492018
2	FOXA2	chr19:19491896-19492103	HepG2	liver:	n/a	n/a
3	KAP1	chr19:19491880-19492455	U2OS	brain:	n/a	n/a
4	TCF12	chr19:19491785-19492018	GM12878	blood:	n/a	n/a
5	GATA3	chr19:19491865-19492259	T-47D	breast:	n/a	n/a
6	FOXA1	chr19:19491776-19492230	HepG2	liver:	n/a	chr19:19492003-19492018
7	FOXA1	chr19:19491856-19492264	HepG2	liver:	n/a	chr19:19492003-19492018
8	RUNX3	chr19:19491756-19492130	GM12878	blood:	n/a	n/a
9	FOXA1	chr19:19491889-19492165	T-47D	breast:	n/a	chr19:19492003-19492018
10	FOXA1	chr19:19491782-19492292	T-47D	breast:	n/a	chr19:19492003-19492018
11	CTCF	chr19:19491961-19491975	LNCaP	prostate:	n/a	n/a
12	ATF1	chr19:19491918-19492265	K562	blood:	n/a	n/a
13	FOXA1	chr19:19491880-19492228	HepG2	liver:	n/a	chr19:19492003-19492018

No.	Distal block	Cell Line	Cell type
1	chr19:19490798..19493427-chr19:19502651..19505000,2	K562	blood:
2	chr19:19491673..19504307-chr19:19513999..19523684,33	K562	blood:
3	chr19:19491648..19493907-chr19:19494746..19496356,2	MCF-7	breast:
4	chr19:19483095..19487397-chr19:19491404..19494790,5	K562	blood:

Variant related genes	Relation type
GATAD2A	TF binding region
ENSG00000167491	Chromatin interaction

Extended variants
information (count: 140 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:137)

rs_ID	r²[population]
rs1000237	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[AFR][1000 genomes];0.95[AMR][1000 genomes];0.91[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs1009136	1.00[CEU][hapmap];0.85[JPT][hapmap];0.94[LWK][hapmap];0.91[MEX][hapmap];0.84[MKK][hapmap];0.88[TSI][hapmap];0.88[YRI][hapmap]
rs1010207	0.92[CEU][hapmap];0.85[JPT][hapmap];1.00[YRI][hapmap]
rs10282	1.00[ASW][hapmap];0.96[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];0.89[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];0.96[YRI][hapmap];0.83[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs10401193	0.94[CHB][hapmap];0.94[CHD][hapmap];0.94[JPT][hapmap]
rs10402308	1.00[CHB][hapmap];0.94[CHD][hapmap];0.84[ASN][1000 genomes]
rs10402451	0.87[AFR][1000 genomes];0.81[AMR][1000 genomes];0.84[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs10402627	0.83[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs10405625	0.87[AFR][1000 genomes];0.93[AMR][1000 genomes];0.89[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs10410664	0.88[AFR][1000 genomes];0.93[AMR][1000 genomes];0.91[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs10414830	0.94[ASW][hapmap];0.96[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.95[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.87[AFR][1000 genomes];0.93[AMR][1000 genomes];0.90[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs10419912	1.00[ASW][hapmap];0.96[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.87[AFR][1000 genomes];0.83[AMR][1000 genomes];0.84[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs10422819	0.94[ASW][hapmap];0.96[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];0.89[LWK][hapmap];0.92[MEX][hapmap];0.92[MKK][hapmap];0.97[TSI][hapmap];0.96[YRI][hapmap];0.82[AMR][1000 genomes];0.84[ASN][1000 genomes]
rs1047361	0.83[AFR][1000 genomes];0.81[AMR][1000 genomes];0.84[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs1054284	0.89[ASW][hapmap];0.96[CEU][hapmap];0.94[CHB][hapmap];0.94[CHD][hapmap];0.87[GIH][hapmap];0.94[JPT][hapmap];0.96[MEX][hapmap];0.97[TSI][hapmap];0.92[YRI][hapmap];0.83[EUR][1000 genomes]
rs1054930	0.84[ASN][1000 genomes]
rs1063966	1.00[ASW][hapmap];0.96[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];0.89[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];0.96[YRI][hapmap];0.81[AFR][1000 genomes];0.81[AMR][1000 genomes];0.83[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs11669516	0.92[CHB][hapmap];0.93[JPT][hapmap];0.82[ASN][1000 genomes]
rs12460764	0.83[AMR][1000 genomes]
rs12972397	0.94[CHB][hapmap];0.94[JPT][hapmap];0.82[ASN][1000 genomes]
rs12973258	0.94[CHB][hapmap];0.97[CHD][hapmap];0.94[JPT][hapmap];0.91[ASN][1000 genomes]
rs12975119	0.92[AFR][1000 genomes];0.89[AMR][1000 genomes];0.88[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs12977524	0.94[CHB][hapmap];0.94[CHD][hapmap];0.94[JPT][hapmap];0.82[ASN][1000 genomes]
rs12977937	0.82[AMR][1000 genomes]
rs12985655	0.83[AMR][1000 genomes]
rs13964	1.00[CEU][hapmap];1.00[YRI][hapmap];0.84[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs1469712	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.94[AFR][1000 genomes];0.93[AMR][1000 genomes];0.94[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs1469713	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.94[AFR][1000 genomes];0.92[AMR][1000 genomes];0.88[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs15622	1.00[CEU][hapmap];1.00[LWK][hapmap];0.96[MEX][hapmap];0.90[MKK][hapmap];0.90[TSI][hapmap];1.00[YRI][hapmap];0.84[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs17288409	0.90[ASN][1000 genomes]
rs1808653	0.87[AMR][1000 genomes];0.85[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs1858999	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1865034	0.83[AFR][1000 genomes];0.81[AMR][1000 genomes];0.84[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2074088	0.89[AFR][1000 genomes];0.82[AMR][1000 genomes];0.83[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2074089	1.00[CEU][hapmap];0.97[LWK][hapmap];0.91[MEX][hapmap];0.90[MKK][hapmap];0.90[TSI][hapmap];1.00[YRI][hapmap];0.83[AMR][1000 genomes]
rs2074090	1.00[CEU][hapmap];0.97[LWK][hapmap];0.91[MEX][hapmap];0.90[MKK][hapmap];0.90[TSI][hapmap];1.00[YRI][hapmap];0.83[AMR][1000 genomes]
rs2074091	0.83[AMR][1000 genomes]
rs2074296	0.83[CEU][hapmap];0.91[MEX][hapmap];0.90[TSI][hapmap]
rs2074303	0.92[CEU][hapmap];0.80[JPT][hapmap];0.83[LWK][hapmap];0.91[MEX][hapmap];0.90[TSI][hapmap];0.92[YRI][hapmap]
rs2074550	0.92[CEU][hapmap];0.80[JPT][hapmap];0.92[LWK][hapmap];0.91[MEX][hapmap];0.90[TSI][hapmap];0.92[YRI][hapmap]
rs2082421	0.84[EUR][1000 genomes]
rs2099334	0.87[AFR][1000 genomes];0.93[AMR][1000 genomes];0.89[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2163804	0.94[CHB][hapmap];0.94[CHD][hapmap];0.94[JPT][hapmap];0.82[ASN][1000 genomes]
rs2163805	0.82[ASN][1000 genomes]
rs2269873	0.92[CEU][hapmap];0.80[JPT][hapmap];0.92[LWK][hapmap];0.91[MEX][hapmap];0.90[TSI][hapmap];0.92[YRI][hapmap]
rs2285627	1.00[CEU][hapmap];0.92[MEX][hapmap];0.84[TSI][hapmap];0.81[AMR][1000 genomes]
rs2288852	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[YRI][hapmap];0.83[AFR][1000 genomes];0.83[AMR][1000 genomes];0.84[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2301669	0.83[AMR][1000 genomes]
rs2301784	0.92[CEU][hapmap];0.80[JPT][hapmap];0.91[YRI][hapmap]
rs2301786	0.92[CEU][hapmap];0.85[JPT][hapmap];1.00[YRI][hapmap]
rs2304098	0.87[ASW][hapmap];0.96[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];0.89[LWK][hapmap];1.00[MEX][hapmap];0.89[MKK][hapmap];0.97[TSI][hapmap];0.96[YRI][hapmap];0.81[AMR][1000 genomes];0.84[ASN][1000 genomes]
rs2315025	0.85[JPT][hapmap];0.80[AMR][1000 genomes]
rs2315279	0.93[AFR][1000 genomes];0.95[AMR][1000 genomes];0.94[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2315281	0.93[AFR][1000 genomes];0.95[AMR][1000 genomes];0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2315283	0.86[AFR][1000 genomes];0.86[AMR][1000 genomes];0.84[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2315610	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.87[AFR][1000 genomes];0.83[AMR][1000 genomes];0.84[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs28478453	0.81[ASN][1000 genomes]
rs2872878	0.81[AFR][1000 genomes]
rs2905421	0.96[CEU][hapmap];1.00[LWK][hapmap];0.88[MEX][hapmap];0.89[MKK][hapmap];0.86[TSI][hapmap];1.00[YRI][hapmap]
rs2905423	0.83[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs2905424	0.81[ASW][hapmap];1.00[CEU][hapmap];0.85[JPT][hapmap];1.00[LWK][hapmap];0.96[MEX][hapmap];0.90[MKK][hapmap];0.90[TSI][hapmap];1.00[YRI][hapmap];0.87[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs2905425	1.00[CEU][hapmap];0.85[JPT][hapmap];0.88[EUR][1000 genomes]
rs2905427	0.80[EUR][1000 genomes]
rs2905430	0.87[AFR][1000 genomes];0.90[AMR][1000 genomes];0.84[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2905431	0.92[AFR][1000 genomes];0.95[AMR][1000 genomes];0.95[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2905432	0.84[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs2905435	0.85[AFR][1000 genomes];0.91[AMR][1000 genomes];0.89[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2916069	0.95[AFR][1000 genomes];0.96[AMR][1000 genomes];0.92[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2916073	0.95[AFR][1000 genomes];0.92[AMR][1000 genomes];0.89[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2916074	1.00[ASW][hapmap];0.92[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];0.96[MEX][hapmap];1.00[MKK][hapmap];0.97[TSI][hapmap];1.00[YRI][hapmap];0.95[AFR][1000 genomes];0.92[AMR][1000 genomes];0.89[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2916076	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[YRI][hapmap];0.93[AFR][1000 genomes];0.92[AMR][1000 genomes];0.88[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2965175	0.87[AFR][1000 genomes];0.91[AMR][1000 genomes];0.87[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2965182	0.90[AFR][1000 genomes];0.92[AMR][1000 genomes];0.87[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2965183	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[YRI][hapmap];0.93[AFR][1000 genomes];0.92[AMR][1000 genomes];0.88[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2965185	1.00[ASW][hapmap];0.84[CEU][hapmap];1.00[LWK][hapmap];0.94[MKK][hapmap];0.81[TSI][hapmap];1.00[YRI][hapmap];0.94[AFR][1000 genomes]
rs2965188	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.95[AFR][1000 genomes];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2965189	1.00[ASW][hapmap];0.92[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];0.96[MEX][hapmap];1.00[MKK][hapmap];0.97[TSI][hapmap];1.00[YRI][hapmap];0.95[AFR][1000 genomes];0.95[AMR][1000 genomes];0.92[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2965191	0.83[AMR][1000 genomes]
rs2965193	0.96[CEU][hapmap];1.00[LWK][hapmap];0.91[MEX][hapmap];0.90[MKK][hapmap];0.90[TSI][hapmap];1.00[YRI][hapmap]
rs2965198	1.00[CEU][hapmap];0.85[JPT][hapmap];1.00[YRI][hapmap];0.87[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs2965199	0.86[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs2965200	0.81[EUR][1000 genomes]
rs34277109	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.98[MKK][hapmap];0.97[TSI][hapmap];1.00[YRI][hapmap];0.95[AFR][1000 genomes];0.99[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34538000	0.89[AFR][1000 genomes];0.88[AMR][1000 genomes];0.89[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs34647936	0.82[ASN][1000 genomes]
rs35418933	0.95[AFR][1000 genomes];0.98[AMR][1000 genomes];0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs3752151	0.89[ASW][hapmap];0.96[CEU][hapmap];0.94[CHB][hapmap];0.94[CHD][hapmap];0.87[GIH][hapmap];0.94[JPT][hapmap];0.82[LWK][hapmap];0.96[MEX][hapmap];0.97[TSI][hapmap];0.92[YRI][hapmap];0.83[EUR][1000 genomes]
rs3764567	0.96[CEU][hapmap];0.87[MEX][hapmap];0.88[TSI][hapmap]
rs3794990	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.87[AFR][1000 genomes];0.81[AMR][1000 genomes];0.84[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs3794993	0.94[ASW][hapmap];0.96[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];0.89[LWK][hapmap];1.00[MEX][hapmap];0.95[MKK][hapmap];1.00[TSI][hapmap];0.96[YRI][hapmap];0.83[AFR][1000 genomes];0.81[AMR][1000 genomes];0.84[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs4808198	0.87[AMR][1000 genomes];0.93[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs4808199	0.94[CHB][hapmap];0.94[CHD][hapmap];0.94[JPT][hapmap];0.82[ASN][1000 genomes]
rs4808200	1.00[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.83[AMR][1000 genomes];0.91[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs4808202	0.91[AMR][1000 genomes];0.89[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs4808203	0.96[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.83[AMR][1000 genomes];0.89[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs4808208	0.94[ASW][hapmap];0.96[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];0.86[LWK][hapmap];0.91[MEX][hapmap];0.92[MKK][hapmap];0.97[TSI][hapmap];0.96[YRI][hapmap];0.81[ASN][1000 genomes]
rs4808931	0.84[YRI][hapmap]
rs4808950	0.87[ASN][1000 genomes]
rs4808955	0.82[AMR][1000 genomes];0.90[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs4808957	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.87[AFR][1000 genomes];0.91[AMR][1000 genomes];0.89[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs4808959	0.96[CEU][hapmap];1.00[CHB][hapmap];0.94[JPT][hapmap];0.92[YRI][hapmap];0.82[AFR][1000 genomes];0.92[AMR][1000 genomes];0.87[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs4808960	0.94[CHB][hapmap];0.94[JPT][hapmap];0.82[ASN][1000 genomes]
rs4808961	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.86[AFR][1000 genomes];0.87[AMR][1000 genomes];0.90[ASN][1000 genomes]
rs4808964	1.00[ASW][hapmap];0.96[CEU][hapmap];0.89[CHB][hapmap];0.94[CHD][hapmap];0.87[GIH][hapmap];0.94[JPT][hapmap];0.89[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];0.97[TSI][hapmap];0.96[YRI][hapmap];0.83[AFR][1000 genomes];0.83[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs4808965	1.00[ASW][hapmap];0.96[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];0.89[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];0.96[YRI][hapmap];0.84[ASN][1000 genomes]
rs4808967	0.87[ASW][hapmap];0.96[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];0.89[LWK][hapmap];0.96[MEX][hapmap];0.95[MKK][hapmap];1.00[TSI][hapmap];0.96[YRI][hapmap];0.81[AMR][1000 genomes];0.84[ASN][1000 genomes]
rs60003758	0.82[ASN][1000 genomes]
rs60321073	0.90[ASN][1000 genomes]
rs62135552	0.82[AMR][1000 genomes]
rs6511026	0.92[CEU][hapmap];0.80[JPT][hapmap];0.92[LWK][hapmap];0.91[MEX][hapmap];0.90[TSI][hapmap];0.92[YRI][hapmap]
rs6511032	0.86[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs6511036	0.94[CHB][hapmap];0.94[JPT][hapmap];0.81[ASN][1000 genomes]
rs6511038	0.86[AFR][1000 genomes];0.84[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs67720221	0.81[AMR][1000 genomes]
rs6909	1.00[ASW][hapmap];0.96[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];0.89[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];0.96[YRI][hapmap];0.83[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs7245983	0.96[CEU][hapmap];1.00[CHB][hapmap];0.90[JPT][hapmap];0.84[ASN][1000 genomes]
rs7246748	0.83[AMR][1000 genomes]
rs7247309	0.81[AMR][1000 genomes]
rs7250893	0.86[ASN][1000 genomes]
rs7252888	0.94[CHB][hapmap];0.94[CHD][hapmap];0.94[JPT][hapmap]
rs7253807	0.84[ASN][1000 genomes]
rs7254230	1.00[CEU][hapmap];0.85[JPT][hapmap];0.83[AMR][1000 genomes]
rs7254748	0.92[CEU][hapmap];1.00[YRI][hapmap]
rs7256149	0.83[AFR][1000 genomes];0.93[AMR][1000 genomes];0.88[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs735273	0.92[CEU][hapmap];0.80[JPT][hapmap];1.00[LWK][hapmap];0.91[MEX][hapmap];0.90[MKK][hapmap];0.90[TSI][hapmap];0.92[YRI][hapmap]
rs747050	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.87[AFR][1000 genomes];0.82[AMR][1000 genomes];0.84[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs751856	0.83[AFR][1000 genomes];0.83[AMR][1000 genomes];0.84[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs751858	0.86[ASN][1000 genomes]
rs754255	0.82[ASN][1000 genomes]
rs769267	0.81[ASW][hapmap];1.00[CEU][hapmap];1.00[LWK][hapmap];0.91[MEX][hapmap];0.90[MKK][hapmap];0.88[TSI][hapmap];1.00[YRI][hapmap];0.81[AMR][1000 genomes]
rs8101499	0.82[ASN][1000 genomes]
rs8103197	1.00[CEU][hapmap];1.00[YRI][hapmap];0.83[AMR][1000 genomes]
rs8103496	0.92[CEU][hapmap];0.80[JPT][hapmap];0.92[LWK][hapmap];0.91[MEX][hapmap];0.90[TSI][hapmap];0.92[YRI][hapmap]
rs8108647	0.85[JPT][hapmap]
rs892021	0.91[CEU][hapmap];1.00[CHB][hapmap];0.94[JPT][hapmap];0.92[YRI][hapmap];0.85[AFR][1000 genomes];0.81[AMR][1000 genomes];0.83[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs892022	0.96[CEU][hapmap];0.94[CHB][hapmap];0.94[JPT][hapmap];0.92[YRI][hapmap];0.81[EUR][1000 genomes]
rs9917108	0.87[AFR][1000 genomes];0.93[AMR][1000 genomes];0.89[EUR][1000 genomes];0.89[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	nsv911303	chr19:19256870-19505087	Flanking Active TSS Weak transcription Strong transcription Enhancers Genic enhancers Bivalent/Poised TSS Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	39 gene(s)	inside rSNPs	diseases
2	nsv911305	chr19:19303802-19663850	Genic enhancers Weak transcription Enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Strong transcription Active TSS ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	60 gene(s)	inside rSNPs	diseases
3	nsv1056419	chr19:19421218-19510611	Flanking Active TSS Enhancers Transcr. at gene 5' and 3' Weak transcription Genic enhancers Strong transcription Active TSS Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	28 gene(s)	inside rSNPs	diseases

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs2965180	DDX49	cis	cerebellum	SCAN
rs2965180	GATAD2A	cis	parietal	SCAN
rs2965180	IL12RB1	cis	parietal	SCAN
rs2965180	TM6SF2	cis	cerebellum	SCAN

Chromatin state (count:60 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr19:19478800-19495800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
2	chr19:19482600-19493200	Enhancers	Primary monocytes fromperipheralblood	blood
3	chr19:19486400-19495400	Weak transcription	Primary B cells from peripheral blood	blood
4	chr19:19486400-19495600	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
5	chr19:19488200-19492400	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
6	chr19:19488800-19492800	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
7	chr19:19488800-19495400	Weak transcription	H9 Cell Line	embryonic stem cell
8	chr19:19488800-19495400	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
9	chr19:19488800-19495400	Weak transcription	Primary hematopoietic stem cells short term culture	blood
10	chr19:19488800-19495400	Weak transcription	Fetal Muscle Leg	muscle
11	chr19:19488800-19495400	Weak transcription	Gastric	stomach
12	chr19:19489000-19492800	Weak transcription	ES-I3 Cell Line	embryonic stem cell
13	chr19:19489000-19495200	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
14	chr19:19489000-19495200	Weak transcription	Duodenum Smooth Muscle	Duodenum
15	chr19:19489000-19495200	Weak transcription	A549	lung
16	chr19:19489000-19495400	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
17	chr19:19489000-19495400	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
18	chr19:19489000-19495400	Weak transcription	Primary neutrophils fromperipheralblood	blood
19	chr19:19489000-19495400	Weak transcription	Adipose Nuclei	Adipose
20	chr19:19489000-19495400	Weak transcription	Colon Smooth Muscle	Colon
21	chr19:19489000-19495400	Weak transcription	Skeletal Muscle Male	skeletal muscle
22	chr19:19489000-19495400	Weak transcription	Hela-S3	cervix
23	chr19:19489000-19495400	Weak transcription	Osteobl	bone
24	chr19:19489000-19495600	Weak transcription	Muscle Satellite Cultured Cells	--
25	chr19:19489000-19495600	Weak transcription	Brain Cingulate Gyrus	brain
26	chr19:19489000-19495600	Weak transcription	Fetal Lung	lung
27	chr19:19489200-19492400	Enhancers	Placenta	Placenta
28	chr19:19489200-19494800	Weak transcription	Fetal Muscle Trunk	muscle
29	chr19:19489200-19495200	Weak transcription	Rectal Smooth Muscle	rectum
30	chr19:19489200-19495400	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
31	chr19:19489200-19495400	Weak transcription	Duodenum Mucosa	Duodenum
32	chr19:19489200-19495400	Weak transcription	NHEK	skin
33	chr19:19489200-19495600	Weak transcription	Breast Myoepithelial Primary Cells	Breast
34	chr19:19489200-19495600	Weak transcription	HMEC	breast
35	chr19:19489200-19496000	Weak transcription	Spleen	Spleen
36	chr19:19489400-19495600	Weak transcription	Cortex derived primary cultured neurospheres	brain
37	chr19:19489600-19492000	Weak transcription	K562	blood
38	chr19:19489600-19492800	Enhancers	Rectal Mucosa Donor 31	rectum
39	chr19:19489800-19493000	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
40	chr19:19489800-19495200	Weak transcription	Fetal Heart	heart
41	chr19:19490800-19492000	Weak transcription	Brain Substantia Nigra	brain
42	chr19:19490800-19495200	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
43	chr19:19490800-19495600	Weak transcription	Placenta Amnion	Placenta Amnion
44	chr19:19491000-19492000	Enhancers	Sigmoid Colon	Sigmoid Colon
45	chr19:19491000-19495400	Weak transcription	Brain Hippocampus Middle	brain
46	chr19:19491200-19495400	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
47	chr19:19491400-19492000	Enhancers	Colonic Mucosa	Colon
48	chr19:19491400-19494800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
49	chr19:19491600-19492200	Enhancers	Lung	lung
50	chr19:19491600-19493200	Enhancers	Stomach Mucosa	stomach

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links