Variant report

Variant	rs1781931
Chromosome Location	chr10:5197881-5197882
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	chr10:5196320..5198098-chr10:5207185..5208709,2	MCF-7	breast:

Extended variants
information (count: 80 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:57)

rs_ID	r²[population]
rs10160019	0.95[CEU][hapmap];0.87[CHB][hapmap];0.82[EUR][1000 genomes]
rs10904429	0.90[EUR][1000 genomes]
rs10904430	0.81[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs11252940	0.95[CEU][hapmap];0.93[CHB][hapmap];0.82[EUR][1000 genomes]
rs11252942	0.95[CEU][hapmap];0.93[CHB][hapmap];0.82[EUR][1000 genomes]
rs11252943	0.95[CEU][hapmap];0.93[CHB][hapmap];0.82[EUR][1000 genomes]
rs11252944	0.94[CEU][hapmap];0.92[CHB][hapmap];0.82[EUR][1000 genomes]
rs11252945	0.95[CEU][hapmap];0.93[CHB][hapmap];0.82[EUR][1000 genomes]
rs11252946	0.91[CEU][hapmap];0.82[EUR][1000 genomes]
rs11252947	0.82[EUR][1000 genomes]
rs11252948	0.82[EUR][1000 genomes]
rs11252949	0.82[EUR][1000 genomes]
rs11252950	0.90[CEU][hapmap];0.92[CHB][hapmap];0.81[EUR][1000 genomes]
rs11252951	0.86[CEU][hapmap];0.93[CHB][hapmap];0.82[EUR][1000 genomes]
rs11252985	0.82[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs11253009	0.82[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs11499158	0.90[AFR][1000 genomes];0.89[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs11499185	0.87[EUR][1000 genomes]
rs12242350	0.95[CEU][hapmap];0.93[CHB][hapmap];0.82[EUR][1000 genomes]
rs12244584	0.82[EUR][1000 genomes]
rs12244591	0.82[EUR][1000 genomes]
rs12255333	0.83[AFR][1000 genomes];0.87[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs12259827	1.00[CEU][hapmap];0.92[CHB][hapmap];0.89[JPT][hapmap];0.82[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs12263243	0.81[EUR][1000 genomes]
rs12264305	0.89[EUR][1000 genomes]
rs12769666	0.82[EUR][1000 genomes]
rs12782982	0.95[CEU][hapmap];0.93[CHB][hapmap];0.92[YRI][hapmap];0.81[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs17155732	0.82[EUR][1000 genomes]
rs17173403	1.00[CEU][hapmap];0.93[CHB][hapmap];0.81[CHD][hapmap];0.94[TSI][hapmap];0.82[EUR][1000 genomes]
rs1889456	0.84[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs1937920	0.89[EUR][1000 genomes]
rs1937921	0.89[EUR][1000 genomes]
rs2154306	0.95[CEU][hapmap];0.93[CHB][hapmap];0.82[EUR][1000 genomes]
rs2154307	0.95[CEU][hapmap];0.93[CHB][hapmap];0.82[EUR][1000 genomes]
rs2186172	0.81[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs2186173	0.82[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs2186174	0.82[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs2245191	1.00[CEU][hapmap];0.94[TSI][hapmap];0.81[EUR][1000 genomes]
rs2275928	0.93[CHB][hapmap];0.87[CHD][hapmap]
rs2398183	0.84[AFR][1000 genomes];0.94[AMR][1000 genomes];0.91[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs2398202	0.81[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs2398203	0.89[AFR][1000 genomes];0.89[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs34277279	0.80[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs41460145	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.93[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs4880709	0.93[CHB][hapmap];0.92[JPT][hapmap]
rs60725680	0.89[EUR][1000 genomes]
rs7068685	0.89[EUR][1000 genomes]
rs7070041	0.84[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs7086771	0.87[CHB][hapmap];0.91[CHD][hapmap];0.92[JPT][hapmap]
rs7089831	0.85[AFR][1000 genomes];0.97[AMR][1000 genomes];0.95[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs7094666	0.86[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs7904863	1.00[CEU][hapmap];0.93[CHB][hapmap];0.91[JPT][hapmap];0.92[YRI][hapmap];0.81[EUR][1000 genomes]
rs7921327	0.93[CHB][hapmap];0.92[JPT][hapmap]
rs915136	0.94[AFR][1000 genomes];0.84[AMR][1000 genomes];0.87[ASN][1000 genomes]
rs9329316	0.95[CEU][hapmap];0.93[CHB][hapmap];0.82[EUR][1000 genomes]
rs9731807	0.81[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs9888062	0.82[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:23 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv894792	chr10:4832920-5498724	Enhancers Weak transcription Flanking Active TSS Active TSS Genic enhancers ZNF genes & repeats Strong transcription Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	47 gene(s)	inside rSNPs	diseases
2	nsv948794	chr10:4863093-5227382	Enhancers Strong transcription Flanking Active TSS Weak transcription Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	18 gene(s)	inside rSNPs	diseases
3	nsv1045155	chr10:4872239-5211318	Enhancers Weak transcription Active TSS Strong transcription Transcr. at gene 5' and 3' Genic enhancers Flanking Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	18 gene(s)	inside rSNPs	diseases
4	nsv869470	chr10:4878904-5203685	Weak transcription Enhancers Active TSS Flanking Active TSS Flanking Bivalent TSS/Enh Strong transcription ZNF genes & repeats Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	18 gene(s)	inside rSNPs	diseases
5	nsv466713	chr10:4901798-5319679	Active TSS Enhancers Weak transcription ZNF genes & repeats Flanking Active TSS Genic enhancers Strong transcription Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	23 gene(s)	inside rSNPs	diseases
6	nsv549881	chr10:4901798-5319679	Enhancers Weak transcription Genic enhancers Strong transcription Active TSS Flanking Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	23 gene(s)	inside rSNPs	diseases
7	nsv534685	chr10:4914018-5853324	Weak transcription Enhancers Flanking Active TSS Strong transcription Bivalent Enhancer Active TSS Genic enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	68 gene(s)	inside rSNPs	diseases
8	nsv1050246	chr10:4927428-5211318	Enhancers Weak transcription Flanking Active TSS Active TSS ZNF genes & repeats Strong transcription Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	17 gene(s)	inside rSNPs	diseases
9	nsv549882	chr10:4943518-5203864	Weak transcription Flanking Active TSS Enhancers Strong transcription Transcr. at gene 5' and 3' Active TSS Genic enhancers ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	16 gene(s)	inside rSNPs	diseases
10	esv2763913	chr10:4961021-5321407	Enhancers Flanking Active TSS 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	22 gene(s)	inside rSNPs	diseases
11	nsv1039386	chr10:5008383-5348491	Weak transcription Strong transcription Enhancers Active TSS Genic enhancers Flanking Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	24 gene(s)	inside rSNPs	diseases
12	nsv1036566	chr10:5037926-5261426	Enhancers Weak transcription Flanking Active TSS Active TSS Genic enhancers Strong transcription Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	13 gene(s)	inside rSNPs	diseases
13	nsv549883	chr10:5037926-5275762	Active TSS Enhancers Weak transcription Genic enhancers Strong transcription Flanking Active TSS ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	14 gene(s)	inside rSNPs	diseases
14	nsv1047484	chr10:5076258-5261482	Enhancers Strong transcription Flanking Active TSS Genic enhancers Weak transcription ZNF genes & repeats Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases
15	nsv1036291	chr10:5076258-5456234	Weak transcription Enhancers Strong transcription Flanking Active TSS Active TSS Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	23 gene(s)	inside rSNPs	diseases
16	nsv540465	chr10:5108345-5261482	ZNF genes & repeats Enhancers Flanking Active TSS Weak transcription Strong transcription Genic enhancers Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
17	nsv540467	chr10:5114577-5225365	Weak transcription Enhancers Strong transcription Flanking Active TSS Active TSS Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
18	nsv540468	chr10:5114577-5261482	Active TSS Enhancers Strong transcription Weak transcription Flanking Active TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
19	nsv540469	chr10:5120774-5225365	Weak transcription Enhancers Active TSS Strong transcription ZNF genes & repeats Genic enhancers Flanking Active TSS Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
20	nsv540470	chr10:5120774-5261482	Flanking Active TSS Active TSS Weak transcription Enhancers Strong transcription Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3' Genic enhancers Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
21	nsv540471	chr10:5133561-5261482	Strong transcription Flanking Active TSS Active TSS Weak transcription Enhancers Transcr. at gene 5' and 3' Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
22	nsv540472	chr10:5133561-5284334	Enhancers Weak transcription Active TSS Flanking Bivalent TSS/Enh Flanking Active TSS Genic enhancers ZNF genes & repeats Strong transcription Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
23	nsv1048081	chr10:5149144-5321395	Weak transcription Flanking Active TSS Enhancers Strong transcription ZNF genes & repeats Genic enhancers Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	12 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs1781931	CALML3	cis	cerebellum	SCAN
rs1781931	IL2RA	cis	lymphoblastoid	seeQTL

Chromatin state (count:5 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr10:5194400-5206600	Strong transcription	Liver	Liver
2	chr10:5196800-5198800	Enhancers	HMEC	breast
3	chr10:5197000-5198000	Strong transcription	Adipose Nuclei	Adipose
4	chr10:5197000-5198200	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
5	chr10:5197800-5198600	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin

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