Variant report

Variant	rs7172677
Chromosome Location	chr15:75424593-75424594
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 78 )
Associated
traits (count: 5 )

rSNPs within LD-proxies of this variant (count:71)

rs_ID	r²[population]
rs1021382	0.85[AMR][1000 genomes];0.94[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10775208	0.94[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10851877	0.82[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs10851878	0.83[AMR][1000 genomes];0.92[ASN][1000 genomes]
rs11072525	0.95[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.97[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11072526	0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs11072528	0.86[AMR][1000 genomes];0.98[ASN][1000 genomes]
rs11638746	0.86[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs12102035	0.91[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12442392	0.86[AMR][1000 genomes];0.98[ASN][1000 genomes]
rs12442410	0.83[AMR][1000 genomes];0.98[ASN][1000 genomes]
rs12910348	0.83[AMR][1000 genomes];0.96[ASN][1000 genomes]
rs12914536	0.86[AMR][1000 genomes];0.98[ASN][1000 genomes]
rs12917185	0.82[AMR][1000 genomes];0.98[ASN][1000 genomes]
rs12917304	0.92[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs1602360	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[YRI][hapmap];0.93[AFR][1000 genomes];0.97[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1806793	0.93[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1806794	0.89[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1806795	0.95[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs2029519	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];0.94[MEX][hapmap];0.90[TSI][hapmap];0.85[AMR][1000 genomes];0.94[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2029520	0.83[AMR][1000 genomes];0.92[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2415158	0.92[ASN][1000 genomes]
rs2415159	0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs28767543	0.94[AMR][1000 genomes];0.89[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs34511319	0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4243032	1.00[AFR][1000 genomes];0.95[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4334268	0.92[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs4421941	0.86[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs4479194	0.91[AMR][1000 genomes];0.94[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4480765	0.82[AMR][1000 genomes];0.96[ASN][1000 genomes]
rs4886420	0.83[ASN][1000 genomes]
rs4886422	1.00[AFR][1000 genomes];0.92[AMR][1000 genomes];0.92[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4886658	0.85[AMR][1000 genomes];0.94[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs4886661	0.91[AMR][1000 genomes];0.94[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4886667	0.83[AMR][1000 genomes];0.98[ASN][1000 genomes]
rs4886668	0.89[CHB][hapmap];0.92[JPT][hapmap];0.96[ASN][1000 genomes]
rs4886669	0.96[ASN][1000 genomes]
rs55662404	0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs58201389	0.94[ASN][1000 genomes]
rs59390721	0.86[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs6495153	0.86[AMR][1000 genomes];0.98[ASN][1000 genomes]
rs6495154	0.83[AMR][1000 genomes];0.98[ASN][1000 genomes]
rs6495155	0.86[AMR][1000 genomes];0.98[ASN][1000 genomes]
rs6495158	0.88[CHB][hapmap];1.00[JPT][hapmap];0.96[ASN][1000 genomes]
rs7162055	0.93[ASN][1000 genomes]
rs7162376	0.92[ASN][1000 genomes]
rs7163083	0.86[AMR][1000 genomes];0.98[ASN][1000 genomes]
rs7166695	0.86[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs7168020	0.90[ASN][1000 genomes]
rs7169545	0.98[ASN][1000 genomes]
rs7169867	0.98[ASN][1000 genomes]
rs7172205	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7177528	0.82[AMR][1000 genomes];0.94[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs7178005	0.86[AMR][1000 genomes];0.98[ASN][1000 genomes]
rs7178625	0.81[AMR][1000 genomes];0.98[ASN][1000 genomes]
rs7178784	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7179426	0.85[AMR][1000 genomes];0.98[ASN][1000 genomes]
rs7179436	1.00[AFR][1000 genomes];0.95[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs7181933	0.82[AFR][1000 genomes];0.85[AMR][1000 genomes];0.98[ASN][1000 genomes]
rs72730601	0.89[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs8025412	0.86[ASW][hapmap];0.89[CHB][hapmap];0.94[CHD][hapmap];0.86[GIH][hapmap];1.00[JPT][hapmap];0.89[MEX][hapmap];0.82[AMR][1000 genomes];0.98[ASN][1000 genomes]
rs8026273	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.85[AMR][1000 genomes];0.94[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs8027552	0.81[AMR][1000 genomes];0.83[ASN][1000 genomes]
rs8027604	0.89[CHB][hapmap];1.00[CHD][hapmap];0.86[GIH][hapmap];1.00[JPT][hapmap];0.89[MEX][hapmap];0.96[ASN][1000 genomes]
rs8028146	0.92[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs8029756	0.86[AMR][1000 genomes];0.97[ASN][1000 genomes]
rs8029760	0.86[AMR][1000 genomes];0.98[ASN][1000 genomes]
rs8032208	0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs8033754	0.86[AMR][1000 genomes];0.98[ASN][1000 genomes]
rs8035588	0.82[AFR][1000 genomes];0.80[AMR][1000 genomes];0.89[ASN][1000 genomes]
rs8035789	0.96[AFR][1000 genomes];0.90[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:7 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv569993	chr15:75242155-75483752	Enhancers Weak transcription Flanking Active TSS Active TSS Strong transcription Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	72 gene(s)	inside rSNPs	diseases
2	nsv457205	chr15:75336729-75447773	Weak transcription Enhancers Flanking Active TSS ZNF genes & repeats Strong transcription Genic enhancers Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases
3	nsv569994	chr15:75336729-75447773	Genic enhancers Weak transcription Enhancers ZNF genes & repeats Strong transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Flanking Active TSS Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases
4	nsv904383	chr15:75382542-75520378	Weak transcription Genic enhancers Enhancers Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer Strong transcription Flanking Active TSS Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	42 gene(s)	inside rSNPs	diseases
5	esv1796196	chr15:75389382-75531124	Weak transcription Active TSS Bivalent Enhancer Enhancers Flanking Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Strong transcription Transcr. at gene 5' and 3' Genic enhancers Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	42 gene(s)	inside rSNPs	diseases
6	nsv1039713	chr15:75394213-75674389	Weak transcription Enhancers Flanking Active TSS Bivalent Enhancer Active TSS Genic enhancers Bivalent/Poised TSS Strong transcription Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	96 gene(s)	inside rSNPs	diseases
7	nsv1037713	chr15:75401213-75665304	Weak transcription Enhancers Strong transcription Flanking Active TSS Active TSS Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3' Genic enhancers Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	96 gene(s)	inside rSNPs	diseases

Variant related diseases (count:1)

Disease	PMID	Source
Systemic lupus erythematosus and Systemic sclerosis	23740937	GWAS catalog

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs7172677	CYP11A1	cis	cerebellum	SCAN
rs7172677	ISLR2	cis	lymphoblastoid	seeQTL
rs7172677	ULK3	cis	multi-tissue	Pritchard
rs7172677	STRA6	cis	cerebellum	SCAN

Chromatin state (count:18 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:75401200-75430600	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
2	chr15:75412800-75433600	Weak transcription	Aorta	Aorta
3	chr15:75415000-75425400	Enhancers	Primary monocytes fromperipheralblood	blood
4	chr15:75417800-75430600	Weak transcription	ES-I3 Cell Line	embryonic stem cell
5	chr15:75421800-75424600	Enhancers	Primary B cells from cord blood	blood
6	chr15:75422000-75424600	Enhancers	Hela-S3	cervix
7	chr15:75423400-75431600	Weak transcription	Lung	lung
8	chr15:75423800-75425000	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
9	chr15:75423800-75425200	Enhancers	Monocytes-CD14+_RO01746	blood
10	chr15:75424000-75425000	Enhancers	GM12878-XiMat	blood
11	chr15:75424000-75425600	Enhancers	Primary neutrophils fromperipheralblood	blood
12	chr15:75424000-75427800	Weak transcription	Primary hematopoietic stem cells short term culture	blood
13	chr15:75424000-75427800	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
14	chr15:75424000-75428000	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
15	chr15:75424000-75428400	Weak transcription	Primary hematopoietic stem cells	blood
16	chr15:75424200-75424600	Weak transcription	Rectal Mucosa Donor 29	rectum
17	chr15:75424400-75425200	Enhancers	HepG2	liver
18	chr15:75424400-75428400	Weak transcription	Primary B cells from peripheral blood	blood

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