Variant report

Variant	rs6712686
Chromosome Location	chr2:173562687-173562688
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr2:173558154..173560301-chr2:173561566..173564675,4	MCF-7	breast:
2	chr2:173561632..173563652-chr2:173565236..173567735,2	MCF-7	breast:

Extended variants
information (count: 89 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:86)

rs_ID	r²[population]
rs10166107	0.82[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10172894	1.00[CHB][hapmap];0.95[ASN][1000 genomes]
rs10178654	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs10180021	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs10188207	0.95[ASN][1000 genomes]
rs10188540	0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs10190099	0.80[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs10198425	0.83[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs10198426	0.83[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs10198546	0.83[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs10199472	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs10201129	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs10202550	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs10205076	0.80[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs10205126	0.95[ASN][1000 genomes]
rs10208151	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs10209860	0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10210195	0.82[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs10210546	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs11887454	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs11887904	0.80[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs11888564	0.83[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11890159	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs11891071	0.83[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11894913	0.82[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11895461	1.00[CEU][hapmap];1.00[CHB][hapmap];0.86[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs11897396	0.83[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs11898565	0.91[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs11899594	0.82[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs11902043	0.83[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs11904366	1.00[JPT][hapmap]
rs12328591	0.83[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs12328781	0.83[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs12329241	0.83[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs12693005	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs13007707	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs13384609	0.80[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs13385403	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs13385676	0.86[AMR][1000 genomes];0.99[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs13387816	0.80[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs13389072	0.82[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13392808	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs13394924	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs13400719	0.83[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs13408965	0.83[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs13411408	0.81[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs13415156	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs13417334	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs13417913	0.83[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs13420845	0.82[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs13422388	0.80[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs13423248	0.83[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs13425350	0.80[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs13427701	0.80[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs13427921	0.82[TSI][hapmap];0.80[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs13428122	0.82[EUR][1000 genomes]
rs13432176	0.82[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs1451447	0.83[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs16860696	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs16860697	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs17299956	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs17702263	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs17706710	1.00[CHB][hapmap]
rs1869922	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs2167374	0.83[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs28541707	0.81[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs28670307	0.80[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs28690076	0.82[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs3816536	0.91[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[ASN][1000 genomes]
rs57104776	0.80[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs59648896	0.95[ASN][1000 genomes]
rs62168072	0.81[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs62169318	0.86[AMR][1000 genomes];0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs62169319	0.80[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs62169322	0.83[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs62169323	0.86[ASN][1000 genomes]
rs62169324	0.83[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62169325	0.83[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62169326	0.95[ASN][1000 genomes]
rs6717366	0.83[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6717851	1.00[ASN][1000 genomes]
rs6723872	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs6724116	0.83[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs6741433	0.83[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6752257	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs6757567	0.95[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	nsv533927	chr2:173161637-173796894	Active TSS Enhancers Bivalent/Poised TSS Genic enhancers ZNF genes & repeats Strong transcription Weak transcription Bivalent Enhancer Flanking Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	44 gene(s)	inside rSNPs	diseases
2	esv2760591	chr2:173396905-173719520	Flanking Active TSS Weak transcription Enhancers ZNF genes & repeats Genic enhancers Strong transcription Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	29 gene(s)	inside rSNPs	diseases
3	nsv583665	chr2:173460640-173643087	Enhancers ZNF genes & repeats Strong transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Genic enhancers Weak transcription Active TSS Flanking Active TSS Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	17 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs6712686	RAPGEF4	cis	cerebellum	SCAN
rs6712686	HOXD11	cis	parietal	SCAN
rs6712686	LOC440925	cis	parietal	SCAN

Chromatin state (count:28 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:173556800-173564600	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
2	chr2:173558800-173563000	Weak transcription	Rectal Smooth Muscle	rectum
3	chr2:173559000-173563000	Weak transcription	Primary hematopoietic stem cells short term culture	blood
4	chr2:173560600-173565400	Weak transcription	Esophagus	oesophagus
5	chr2:173561800-173563600	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
6	chr2:173561800-173563600	Enhancers	NHDF-Ad	bronchial
7	chr2:173561800-173563800	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
8	chr2:173561800-173564400	Enhancers	NHEK	skin
9	chr2:173561800-173564400	Enhancers	NHLF	lung
10	chr2:173562000-173563400	Enhancers	HSMM	muscle
11	chr2:173562000-173563600	Enhancers	Osteobl	bone
12	chr2:173562000-173564000	Enhancers	Foreskin Fibroblast Primary Cells skin02	Skin
13	chr2:173562000-173564200	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
14	chr2:173562000-173564200	Enhancers	HMEC	breast
15	chr2:173562000-173564400	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
16	chr2:173562200-173563800	Enhancers	NH-A	brain
17	chr2:173562400-173562800	Flanking Active TSS	Muscle Satellite Cultured Cells	--
18	chr2:173562400-173562800	Enhancers	A549	lung
19	chr2:173562400-173563200	Enhancers	Placenta Amnion	Placenta Amnion
20	chr2:173562400-173563400	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
21	chr2:173562400-173563600	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
22	chr2:173562400-173563600	Enhancers	Hela-S3	cervix
23	chr2:173562400-173563600	Enhancers	HUVEC	blood vessel
24	chr2:173562600-173563200	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
25	chr2:173562600-173563400	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
26	chr2:173562600-173563400	Enhancers	Primary monocytes fromperipheralblood	blood
27	chr2:173562600-173563400	Enhancers	Primary T helper cells PMA-I stimulated	--
28	chr2:173562600-173563800	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung

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