Variant report

Variant	rs540170
Chromosome Location	chr11:59880038-59880039
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr11:59878766..59880591-chr11:59882568..59884421,2	K562	blood:

Extended variants
information (count: 91 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:88)

rs_ID	r²[population]
rs107903	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.85[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs10897009	0.83[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs11230147	0.85[CEU][hapmap];0.86[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs11230153	0.85[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs11230155	0.85[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs11230160	0.84[CEU][hapmap];0.88[GIH][hapmap]
rs11230161	0.85[CEU][hapmap];0.91[GIH][hapmap]
rs1125357	0.85[CEU][hapmap];0.86[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs11600716	0.84[CEU][hapmap];0.84[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs11605427	0.82[CEU][hapmap]
rs12226022	0.86[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs12453	0.82[CEU][hapmap]
rs1286182	0.81[YRI][hapmap]
rs1303615	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.95[MEX][hapmap];1.00[TSI][hapmap];0.88[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1303617	0.81[YRI][hapmap]
rs1303621	1.00[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.95[MEX][hapmap];1.00[TSI][hapmap];0.88[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1441586	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];0.86[MEX][hapmap];0.91[TSI][hapmap];0.82[AMR][1000 genomes];0.93[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs17528859	0.85[CEU][hapmap];0.82[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs17529983	0.85[CEU][hapmap];0.84[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs17602572	0.82[CEU][hapmap]
rs1786137	0.94[AMR][1000 genomes];0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1813217	0.82[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs2070970	0.85[CEU][hapmap];0.82[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs2165525	0.86[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs2278867	0.81[CEU][hapmap]
rs2583471	0.85[CEU][hapmap];0.82[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs2583476	0.81[CEU][hapmap];0.82[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs2847655	0.85[CEU][hapmap];0.83[TSI][hapmap];0.80[EUR][1000 genomes]
rs2847663	0.85[CEU][hapmap];0.83[EUR][1000 genomes]
rs2847664	0.82[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs2847666	0.85[CEU][hapmap];0.83[TSI][hapmap]
rs2847667	0.96[CEU][hapmap]
rs2847668	0.85[CEU][hapmap];0.82[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs2855017	0.85[CEU][hapmap];0.82[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs476722	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[YRI][hapmap]
rs483629	0.89[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs485682	0.81[YRI][hapmap]
rs487997	0.99[AFR][1000 genomes];0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4939311	0.85[CEU][hapmap];0.93[GIH][hapmap];0.83[TSI][hapmap];0.86[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs4939312	0.85[CEU][hapmap];0.95[GIH][hapmap];0.81[TSI][hapmap];0.86[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs4939314	0.85[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs502419	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.99[AFR][1000 genomes];0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs502581	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.98[TSI][hapmap];0.94[AMR][1000 genomes];0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs504272	0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs510518	0.91[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs512495	0.81[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs514266	0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs516478	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.83[AFR][1000 genomes];0.94[AMR][1000 genomes];0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs521952	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[AMR][1000 genomes];0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs525794	1.00[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.95[MEX][hapmap];0.98[TSI][hapmap];0.87[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs534273	0.86[YRI][hapmap];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs555635	1.00[CEU][hapmap];0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs556917	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[AMR][1000 genomes];0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs55847558	0.86[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs563803	0.95[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs564912	0.96[CEU][hapmap];0.88[AMR][1000 genomes];0.99[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs569046	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs574695	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];0.99[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs574704	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.86[YRI][hapmap];0.83[AFR][1000 genomes];0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs574798	0.82[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs576483	0.81[YRI][hapmap]
rs580064	1.00[ASW][hapmap];0.89[CEU][hapmap];0.98[LWK][hapmap];0.88[MKK][hapmap];0.95[YRI][hapmap];0.98[AFR][1000 genomes];0.83[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs580817	0.99[AFR][1000 genomes];0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs581133	0.82[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.84[LWK][hapmap];1.00[MEX][hapmap];0.98[TSI][hapmap];0.86[YRI][hapmap];0.82[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs583296	1.00[ASW][hapmap];1.00[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[TSI][hapmap];0.95[YRI][hapmap]
rs583791	0.93[CEU][hapmap];0.89[JPT][hapmap];0.80[TSI][hapmap];0.83[EUR][1000 genomes]
rs595481	1.00[CEU][hapmap];0.86[YRI][hapmap]
rs602396	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.85[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs606588	1.00[CEU][hapmap];1.00[CHB][hapmap];0.93[JPT][hapmap];0.94[YRI][hapmap]
rs610932	0.93[CEU][hapmap];0.88[CHD][hapmap];0.89[JPT][hapmap];0.87[MEX][hapmap];0.83[TSI][hapmap];0.87[EUR][1000 genomes]
rs617135	0.88[CHD][hapmap];0.89[JPT][hapmap];0.87[MEX][hapmap]
rs617916	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs61901691	0.83[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs624663	0.92[CEU][hapmap];0.88[JPT][hapmap];0.83[EUR][1000 genomes]
rs631853	0.93[CEU][hapmap];0.89[JPT][hapmap];0.84[EUR][1000 genomes]
rs632185	0.93[CEU][hapmap];0.83[JPT][hapmap];0.81[MEX][hapmap];0.82[EUR][1000 genomes]
rs634475	0.84[EUR][1000 genomes]
rs636147	0.89[CEU][hapmap];0.89[JPT][hapmap];0.81[EUR][1000 genomes]
rs652354	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.87[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs662196	0.93[CEU][hapmap];0.89[JPT][hapmap];0.80[TSI][hapmap];0.84[EUR][1000 genomes]
rs667897	0.88[CHD][hapmap];0.89[JPT][hapmap];0.86[MEX][hapmap]
rs684961	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs688030	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs7124974	0.83[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs7933202	0.82[CEU][hapmap]
rs7935829	0.82[CEU][hapmap]
rs920573	0.85[CEU][hapmap];0.91[GIH][hapmap];0.82[MEX][hapmap];0.86[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs983392	0.81[AMR][1000 genomes];0.83[EUR][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	nsv832173	chr11:59788884-59940560	Enhancers Weak transcription Flanking Active TSS ZNF genes & repeats Active TSS Genic enhancers Bivalent Enhancer Strong transcription Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases
2	nsv468579	chr11:59814287-59975400	Enhancers Active TSS Bivalent Enhancer Flanking Active TSS Weak transcription Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
3	nsv555150	chr11:59814287-59975400	Weak transcription Strong transcription Active TSS Enhancers Flanking Active TSS ZNF genes & repeats Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs540170	SLC43A3	cis	parietal	SCAN
rs540170	GNG3	cis	parietal	SCAN
rs540170	FAM111A	cis	parietal	SCAN

Chromatin state (count:11 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr11:59877000-59880200	Weak transcription	Small Intestine	intestine
2	chr11:59877000-59880800	Weak transcription	Fetal Intestine Large	intestine
3	chr11:59877000-59885000	Weak transcription	Monocytes-CD14+_RO01746	blood
4	chr11:59877000-59885800	Weak transcription	Primary monocytes fromperipheralblood	blood
5	chr11:59878800-59882200	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
6	chr11:59879200-59882400	Enhancers	Fetal Intestine Small	intestine
7	chr11:59879400-59897600	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
8	chr11:59879800-59888200	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
9	chr11:59880000-59881000	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
10	chr11:59880000-59881000	Weak transcription	Ovary	ovary
11	chr11:59880000-59883600	Weak transcription	K562	blood

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links