Variant report

Variant	rs12676009
Chromosome Location	chr8:100582666-100582667
allele	A/C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 117 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:102)

rs_ID	r²[population]
rs1039448	0.82[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs10955207	0.89[AFR][1000 genomes];0.93[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs10955208	0.85[AMR][1000 genomes]
rs10955213	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs10955214	1.00[JPT][hapmap]
rs10955215	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[YRI][hapmap];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs11986595	0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12234903	0.90[AMR][1000 genomes]
rs12541387	0.90[ASN][1000 genomes]
rs12542214	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs12544095	0.90[ASN][1000 genomes]
rs12544691	0.85[ASN][1000 genomes]
rs12549477	1.00[JPT][hapmap]
rs12550617	0.83[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12676915	1.00[JPT][hapmap]
rs12678012	0.94[ASN][1000 genomes]
rs12681244	0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs1386374	0.88[ASN][1000 genomes]
rs1386377	0.90[ASN][1000 genomes]
rs1388657	1.00[JPT][hapmap]
rs1487022	1.00[JPT][hapmap]
rs1545959	1.00[JPT][hapmap]
rs16897430	1.00[JPT][hapmap]
rs16897435	1.00[JPT][hapmap]
rs16897440	1.00[JPT][hapmap]
rs16897530	0.82[ASN][1000 genomes]
rs1788152	0.83[ASN][1000 genomes]
rs1788157	0.83[ASN][1000 genomes]
rs2035619	0.90[ASN][1000 genomes]
rs2046936	0.87[AFR][1000 genomes];0.85[AMR][1000 genomes]
rs2084556	0.83[ASN][1000 genomes]
rs2280061	0.97[ASN][1000 genomes]
rs2510200	0.83[ASN][1000 genomes]
rs3099853	0.81[ASN][1000 genomes]
rs3103102	0.85[AFR][1000 genomes];0.99[AMR][1000 genomes];0.96[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs3103698	1.00[JPT][hapmap]
rs3103702	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.87[YRI][hapmap];0.82[AFR][1000 genomes];0.95[AMR][1000 genomes];0.92[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs3103713	0.89[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs3103715	0.84[AFR][1000 genomes];0.93[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs3103716	0.91[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs3105167	0.81[AFR][1000 genomes];0.85[AMR][1000 genomes]
rs3105178	0.94[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.84[AFR][1000 genomes];0.83[AMR][1000 genomes]
rs3105179	0.91[AMR][1000 genomes]
rs3105180	0.82[AMR][1000 genomes]
rs3105182	0.84[AFR][1000 genomes];0.90[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs3105183	0.84[AFR][1000 genomes];0.91[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs3105184	0.81[AFR][1000 genomes];0.91[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs3105188	0.84[AFR][1000 genomes];0.93[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs3105189	0.85[AFR][1000 genomes];0.92[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs3105196	0.81[AFR][1000 genomes];0.91[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs3105197	0.87[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs3105200	0.81[AFR][1000 genomes];0.95[AMR][1000 genomes];0.92[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs3105202	0.83[AFR][1000 genomes];0.96[AMR][1000 genomes];0.94[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs3110407	0.85[AFR][1000 genomes];0.85[AMR][1000 genomes]
rs3134147	0.95[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs3134148	0.90[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs3134149	0.85[AFR][1000 genomes];0.96[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs3134151	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.87[YRI][hapmap];0.82[AFR][1000 genomes];0.95[AMR][1000 genomes];0.90[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs3134153	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.83[YRI][hapmap];0.82[AFR][1000 genomes];0.96[AMR][1000 genomes];0.94[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs3134154	0.81[AFR][1000 genomes];0.96[AMR][1000 genomes];0.94[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs3134157	0.96[AMR][1000 genomes];0.93[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs3134160	0.94[AMR][1000 genomes];0.92[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs3134165	0.96[AMR][1000 genomes];0.95[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs3134169	0.86[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs3134170	0.87[AFR][1000 genomes];0.99[AMR][1000 genomes];0.97[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs3134171	0.91[JPT][hapmap]
rs3134172	0.81[AFR][1000 genomes];0.91[AMR][1000 genomes]
rs3134186	0.82[AMR][1000 genomes]
rs3134187	0.87[AFR][1000 genomes];0.95[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs3134299	0.82[AFR][1000 genomes];0.91[AMR][1000 genomes]
rs3134301	1.00[JPT][hapmap]
rs3134302	0.82[AFR][1000 genomes];0.91[AMR][1000 genomes]
rs3134304	0.85[AFR][1000 genomes];0.88[AMR][1000 genomes]
rs34237216	0.82[AMR][1000 genomes]
rs4735615	0.91[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4735619	0.81[AFR][1000 genomes];0.99[AMR][1000 genomes];0.97[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs4735620	0.84[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4735627	0.92[ASN][1000 genomes]
rs56174158	0.95[AFR][1000 genomes];0.99[AMR][1000 genomes];0.97[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs56193096	0.81[AFR][1000 genomes];0.92[AMR][1000 genomes];0.98[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs57636892	0.90[ASN][1000 genomes]
rs59375661	0.92[ASN][1000 genomes]
rs61097926	0.97[ASN][1000 genomes]
rs6468690	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.93[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6468691	1.00[JPT][hapmap]
rs6985574	0.90[ASN][1000 genomes]
rs6986467	1.00[JPT][hapmap]
rs7009315	1.00[JPT][hapmap]
rs717365	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs721995	0.92[ASN][1000 genomes]
rs72674642	0.86[AFR][1000 genomes];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs72674644	0.86[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs72674651	0.86[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs72674675	0.97[ASN][1000 genomes]
rs72674676	0.90[ASN][1000 genomes]
rs72674678	0.92[ASN][1000 genomes]
rs72674698	0.90[ASN][1000 genomes]
rs72676204	0.90[ASN][1000 genomes]
rs72676222	0.85[ASN][1000 genomes]
rs7825783	0.90[ASN][1000 genomes]
rs957539	0.90[AMR][1000 genomes]
rs965657	0.86[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:15 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv524617	chr8:100032844-100717925	ZNF genes & repeats Strong transcription Enhancers Weak transcription Flanking Active TSS Active TSS Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	26 gene(s)	inside rSNPs	diseases
2	nsv1020614	chr8:100046692-100594092	ZNF genes & repeats Weak transcription Strong transcription Enhancers Flanking Active TSS Bivalent/Poised TSS Active TSS Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	22 gene(s)	inside rSNPs	diseases
3	nsv1022914	chr8:100190356-100720313	Weak transcription Strong transcription Enhancers Flanking Active TSS ZNF genes & repeats Genic enhancers Active TSS Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	18 gene(s)	inside rSNPs	diseases
4	nsv539695	chr8:100190356-100720313	Weak transcription Strong transcription Enhancers ZNF genes & repeats Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	18 gene(s)	inside rSNPs	diseases
5	nsv891226	chr8:100295634-100708595	Strong transcription Enhancers Weak transcription Genic enhancers ZNF genes & repeats Flanking Active TSS Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA	15 gene(s)	inside rSNPs	diseases
6	nsv891227	chr8:100295634-100743556	Weak transcription ZNF genes & repeats Enhancers Strong transcription Flanking Active TSS Active TSS Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA	15 gene(s)	inside rSNPs	diseases
7	nsv1019256	chr8:100336249-100852803	Weak transcription Strong transcription Enhancers Genic enhancers ZNF genes & repeats Active TSS Bivalent Enhancer Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA	18 gene(s)	inside rSNPs	diseases
8	nsv539698	chr8:100336249-100852803	Strong transcription Weak transcription Enhancers ZNF genes & repeats Active TSS Flanking Active TSS Bivalent Enhancer Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA	18 gene(s)	inside rSNPs	diseases
9	esv2758167	chr8:100404151-100838624	Enhancers Weak transcription Strong transcription Active TSS ZNF genes & repeats Flanking Active TSS Genic enhancers Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA	15 gene(s)	inside rSNPs	diseases
10	esv2759633	chr8:100404151-100838624	Weak transcription Strong transcription Enhancers ZNF genes & repeats Flanking Active TSS Genic enhancers Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA	15 gene(s)	inside rSNPs	diseases
11	nsv933879	chr8:100417371-100622310	Weak transcription Enhancers Strong transcription Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Flanking Active TSS Bivalent Enhancer Genic enhancers Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA	9 gene(s)	inside rSNPs	diseases
12	nsv1029616	chr8:100442135-100796643	Strong transcription Weak transcription Enhancers ZNF genes & repeats Active TSS Genic enhancers Flanking Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA	11 gene(s)	inside rSNPs	diseases
13	nsv1023922	chr8:100474230-100702005	Enhancers Strong transcription Weak transcription Genic enhancers ZNF genes & repeats Flanking Active TSS Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA	7 gene(s)	inside rSNPs	diseases
14	nsv831408	chr8:100523523-100721507	Weak transcription Flanking Active TSS Enhancers Strong transcription ZNF genes & repeats Active TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA	7 gene(s)	inside rSNPs	diseases
15	nsv1033795	chr8:100557344-100666640	Weak transcription Strong transcription Enhancers Flanking Active TSS ZNF genes & repeats Active TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs12676009	ARHGEF12	trans	lymphoblastoid	RTeQTL

Chromatin state (count:38 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr8:100516400-100589000	Weak transcription	Primary T cells fromperipheralblood	blood
2	chr8:100534800-100595800	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
3	chr8:100536200-100596000	Weak transcription	Breast Myoepithelial Primary Cells	Breast
4	chr8:100550400-100596000	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
5	chr8:100550400-100597600	Weak transcription	Dnd41	blood
6	chr8:100555400-100588200	Weak transcription	Primary monocytes fromperipheralblood	blood
7	chr8:100559400-100596000	Weak transcription	Sigmoid Colon	Sigmoid Colon
8	chr8:100560000-100596000	Weak transcription	Duodenum Smooth Muscle	Duodenum
9	chr8:100560200-100596000	Weak transcription	Fetal Intestine Large	intestine
10	chr8:100560400-100583600	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
11	chr8:100560400-100583600	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
12	chr8:100560400-100596600	Weak transcription	Fetal Lung	lung
13	chr8:100560400-100619600	Weak transcription	Rectal Mucosa Donor 31	rectum
14	chr8:100560600-100588000	Weak transcription	Rectal Mucosa Donor 29	rectum
15	chr8:100565400-100597600	Weak transcription	Fetal Muscle Leg	muscle
16	chr8:100567800-100596600	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
17	chr8:100569600-100589000	Weak transcription	Monocytes-CD14+_RO01746	blood
18	chr8:100570000-100589600	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
19	chr8:100570400-100595200	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
20	chr8:100570400-100596000	Weak transcription	Primary hematopoietic stem cells	blood
21	chr8:100570400-100596000	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
22	chr8:100570600-100595800	Weak transcription	Primary T helper cells PMA-I stimulated	--
23	chr8:100570600-100596000	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
24	chr8:100570600-100596200	Weak transcription	Primary T helper cells fromperipheralblood	blood
25	chr8:100571200-100588800	Weak transcription	Primary B cells from peripheral blood	blood
26	chr8:100575400-100592600	Weak transcription	Fetal Stomach	stomach
27	chr8:100576800-100588000	Weak transcription	Primary B cells from cord blood	blood
28	chr8:100576800-100596000	Weak transcription	Left Ventricle	heart
29	chr8:100577200-100593600	Weak transcription	Primary T cells from cord blood	blood
30	chr8:100577200-100596000	Weak transcription	Primary hematopoietic stem cells short term culture	blood
31	chr8:100577200-100596000	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
32	chr8:100577400-100592600	Weak transcription	Fetal Intestine Small	intestine
33	chr8:100581800-100612400	Weak transcription	HSMMtube	muscle
34	chr8:100582000-100584000	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
35	chr8:100582000-100600400	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
36	chr8:100582000-100610400	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
37	chr8:100582400-100586400	Weak transcription	NHDF-Ad	bronchial
38	chr8:100582600-100589600	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell

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