Variant report

Variant	rs12086634
Chromosome Location	chr1:209880259-209880260
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr1:209879551..209882258-chr1:209882693..209884984,3	K562	blood:
2	chr1:209873397..209875484-chr1:209878580..209881106,2	K562	blood:

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-G0S2-3	chr1:209879660-209880325	NONHSAT009228
2	lnc-G0S2-3	chr1:209880184-209880325	NONHSAT009229

Extended variants
information (count: 81 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:77)

rs_ID	r²[population]
rs1000282	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs1000283	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs10157973	0.87[EUR][1000 genomes]
rs10863783	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10863785	0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs11119327	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11119328	0.85[AFR][1000 genomes];0.84[AMR][1000 genomes];0.80[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11119330	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11119331	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11119332	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11119336	0.88[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs11485195	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11487866	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11487867	0.85[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs11806703	0.99[AFR][1000 genomes];0.89[AMR][1000 genomes];0.98[ASN][1000 genomes]
rs11807619	0.99[AFR][1000 genomes];0.92[AMR][1000 genomes];0.99[ASN][1000 genomes]
rs11808690	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11811440	0.99[AFR][1000 genomes];0.89[AMR][1000 genomes];0.98[ASN][1000 genomes]
rs12030655	0.86[EUR][1000 genomes]
rs12034758	0.84[AFR][1000 genomes];0.96[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs12059226	0.84[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs12060420	0.84[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs12060922	0.84[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs12090931	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12094117	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12116437	0.80[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs12120361	0.83[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs12129718	0.91[EUR][1000 genomes]
rs12138452	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs1337531	0.90[EUR][1000 genomes]
rs1415542	0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs1415544	0.91[EUR][1000 genomes]
rs1474654	0.99[AFR][1000 genomes];0.92[AMR][1000 genomes];0.80[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1474655	0.99[AFR][1000 genomes];0.92[AMR][1000 genomes];0.80[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs17389184	0.81[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs17389198	0.96[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs1999826	0.92[EUR][1000 genomes]
rs2064148	0.90[EUR][1000 genomes]
rs2205985	0.89[EUR][1000 genomes]
rs2236903	0.90[EUR][1000 genomes]
rs2272867	0.94[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs2282738	0.88[EUR][1000 genomes]
rs2282739	0.90[EUR][1000 genomes]
rs2282741	0.90[EUR][1000 genomes]
rs2884090	0.90[EUR][1000 genomes]
rs3765240	0.92[EUR][1000 genomes]
rs3766618	0.85[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs3766619	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs3817821	0.84[EUR][1000 genomes]
rs4314885	0.89[EUR][1000 genomes]
rs4844891	0.90[EUR][1000 genomes]
rs61820570	0.99[AFR][1000 genomes];0.92[AMR][1000 genomes];0.80[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs627670	0.85[EUR][1000 genomes]
rs6540550	0.87[EUR][1000 genomes]
rs6540551	0.87[EUR][1000 genomes]
rs6540552	0.85[EUR][1000 genomes]
rs6540553	0.85[EUR][1000 genomes]
rs6665715	0.84[EUR][1000 genomes]
rs6672256	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs667681	0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs6679099	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs6679405	0.85[EUR][1000 genomes]
rs6702301	0.87[EUR][1000 genomes]
rs6752	0.84[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs679846	0.83[EUR][1000 genomes]
rs7521461	0.85[EUR][1000 genomes]
rs7532324	0.85[EUR][1000 genomes]
rs7539852	0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs7548781	0.91[EUR][1000 genomes]
rs7555978	0.87[EUR][1000 genomes]
rs909710	0.90[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs932335	0.90[AMR][1000 genomes];1.00[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs9430012	0.86[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs9430014	0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs9430015	0.90[EUR][1000 genomes]
rs9430016	0.92[EUR][1000 genomes]
rs9430017	0.96[AMR][1000 genomes];0.88[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv999901	chr1:209600631-210205379	Flanking Active TSS Enhancers Weak transcription Active TSS Bivalent Enhancer Strong transcription Flanking Bivalent TSS/Enh ZNF genes & repeats Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	76 gene(s)	inside rSNPs	diseases
2	nsv1014034	chr1:209759648-210501731	Enhancers Weak transcription Flanking Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer Strong transcription Active TSS Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	45 gene(s)	inside rSNPs	diseases
3	nsv873139	chr1:209828955-210050794	Active TSS Enhancers Weak transcription Bivalent Enhancer Genic enhancers Strong transcription Flanking Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	27 gene(s)	inside rSNPs	diseases
4	nsv1004343	chr1:209879304-209909385	Enhancers Weak transcription Genic enhancers Flanking Active TSS Strong transcription ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3' Active TSS	TF binding region Chromatin interactive region lncRNA miRNA target site	3 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:22 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:209875200-209882400	Enhancers	Brain Substantia Nigra	brain
2	chr1:209877400-209882600	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
3	chr1:209878400-209880800	Weak transcription	Brain Germinal Matrix	brain
4	chr1:209878400-209881800	Weak transcription	Breast Myoepithelial Primary Cells	Breast
5	chr1:209878600-209881200	Weak transcription	Brain Anterior Caudate	brain
6	chr1:209878600-209881400	Weak transcription	Brain Inferior Temporal Lobe	brain
7	chr1:209878600-209888200	Weak transcription	Brain Angular Gyrus	brain
8	chr1:209878800-209880400	Weak transcription	NHLF	lung
9	chr1:209878800-209893400	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
10	chr1:209879000-209881400	Weak transcription	Brain Cingulate Gyrus	brain
11	chr1:209879200-209880400	Flanking Active TSS	Liver	Liver
12	chr1:209879400-209880800	Weak transcription	Brain Hippocampus Middle	brain
13	chr1:209879400-209881000	Weak transcription	Adipose Nuclei	Adipose
14	chr1:209879600-209880600	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
15	chr1:209880000-209880600	Enhancers	Gastric	stomach
16	chr1:209880000-209881000	Genic enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
17	chr1:209880000-209881200	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
18	chr1:209880000-209881400	Enhancers	HMEC	breast
19	chr1:209880200-209881000	Enhancers	HUVEC	blood vessel
20	chr1:209880200-209881400	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
21	chr1:209880200-209881400	Enhancers	NHEK	skin
22	chr1:209880200-209881800	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin

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