Variant report

Variant	rs12142010
Chromosome Location	chr1:176016410-176016411
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr1:176015298..176018054-chr1:176018508..176020268,2	K562	blood:

Extended variants
information (count: 44 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:40)

rs_ID	r²[population]
rs10494497	1.00[CEU][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs12119366	0.92[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs12121832	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[GIH][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.92[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs12123116	0.85[AMR][1000 genomes]
rs12125119	0.85[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs12125192	0.88[CEU][hapmap];1.00[AFR][1000 genomes];0.92[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs12125328	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[GIH][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.85[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs12127204	1.00[CEU][hapmap];0.92[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs12127719	0.92[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs12128099	1.00[CEU][hapmap];0.92[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs12128327	1.00[CEU][hapmap];1.00[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs12129466	0.96[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs12129873	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[GIH][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.87[MKK][hapmap];1.00[TSI][hapmap];0.86[AFR][1000 genomes];0.92[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs12130538	0.92[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs12132072	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[GIH][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];1.00[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs12133268	0.92[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs12133310	1.00[CEU][hapmap];0.81[EUR][1000 genomes]
rs12133701	0.86[AFR][1000 genomes];1.00[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs12134392	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[GIH][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];0.86[AFR][1000 genomes];0.92[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs12134984	0.92[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs12135045	0.86[AFR][1000 genomes];0.92[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs12137136	1.00[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs12139160	0.89[CEU][hapmap];0.92[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs12140631	0.92[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs12141054	0.92[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs12142461	1.00[CEU][hapmap];0.92[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs12143425	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[GIH][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.85[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs12144612	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[GIH][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];0.85[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs12144692	0.87[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs12144806	1.00[CEU][hapmap];0.86[AFR][1000 genomes];0.92[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs12145452	0.85[CEU][hapmap];0.92[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs12145703	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[GIH][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.85[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs12145778	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[GIH][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];0.86[AFR][1000 genomes];0.92[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs12146072	0.85[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs1330863	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[GIH][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.92[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs16849475	1.00[CEU][hapmap];0.86[AFR][1000 genomes];0.92[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs28770189	0.85[AMR][1000 genomes]
rs4400573	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[GIH][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];0.86[AFR][1000 genomes];0.92[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs56230548	1.00[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs7349083	1.00[AFR][1000 genomes];0.92[AMR][1000 genomes];0.86[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	esv1823794	chr1:175869554-176311778	Enhancers ZNF genes & repeats Strong transcription Weak transcription Active TSS Bivalent Enhancer Genic enhancers Flanking Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	33 gene(s)	inside rSNPs	diseases
2	nsv872561	chr1:175949646-176092167	Weak transcription Strong transcription ZNF genes & repeats Enhancers Genic enhancers Active TSS Flanking Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
3	nsv872562	chr1:175949646-176141866	Weak transcription Enhancers Strong transcription ZNF genes & repeats Genic enhancers Flanking Active TSS Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
4	nsv872563	chr1:175949646-176184625	Weak transcription ZNF genes & repeats Strong transcription Flanking Active TSS Enhancers Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	23 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:87 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:175957800-176022000	Weak transcription	Primary T helper naive cells from peripheral blood	blood
2	chr1:175976800-176046000	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
3	chr1:175978200-176050600	Weak transcription	Aorta	Aorta
4	chr1:175978400-176017800	Strong transcription	Monocytes-CD14+_RO01746	blood
5	chr1:175978400-176069000	Weak transcription	Primary T killer memory cells from peripheral blood	blood
6	chr1:175979600-176045400	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
7	chr1:175980200-176028000	Weak transcription	K562	blood
8	chr1:175989800-176036400	Weak transcription	Pancreas	Pancrea
9	chr1:175994200-176065200	Weak transcription	Psoas Muscle	Psoas
10	chr1:175999000-176017000	Strong transcription	Primary monocytes fromperipheralblood	blood
11	chr1:176003800-176021400	Weak transcription	Osteobl	bone
12	chr1:176004000-176018200	Weak transcription	Hela-S3	cervix
13	chr1:176004000-176021200	Weak transcription	A549	lung
14	chr1:176004000-176026400	Weak transcription	Small Intestine	intestine
15	chr1:176004000-176036400	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
16	chr1:176004200-176039800	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
17	chr1:176006000-176045200	Weak transcription	GM12878-XiMat	blood
18	chr1:176006200-176049000	Weak transcription	HSMM	muscle
19	chr1:176007600-176020200	Weak transcription	Fetal Heart	heart
20	chr1:176007800-176020400	Weak transcription	Fetal Brain Female	brain
21	chr1:176007800-176066400	Weak transcription	Fetal Brain Male	brain
22	chr1:176008200-176019000	Weak transcription	Fetal Kidney	kidney
23	chr1:176008200-176019000	Weak transcription	Pancreatic Islets	Pancreatic Islet
24	chr1:176009800-176016800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
25	chr1:176010200-176048000	Weak transcription	Rectal Mucosa Donor 31	rectum
26	chr1:176010400-176019200	Weak transcription	NHDF-Ad	bronchial
27	chr1:176010400-176066000	Weak transcription	Muscle Satellite Cultured Cells	--
28	chr1:176010800-176018400	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
29	chr1:176012000-176018600	Weak transcription	Fetal Muscle Trunk	muscle
30	chr1:176012200-176024200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
31	chr1:176012200-176028200	Weak transcription	Fetal Intestine Small	intestine
32	chr1:176012200-176044800	Weak transcription	Fetal Stomach	stomach
33	chr1:176012200-176045200	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
34	chr1:176012200-176045200	Weak transcription	Esophagus	oesophagus
35	chr1:176012200-176045200	Weak transcription	Fetal Lung	lung
36	chr1:176012400-176016800	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
37	chr1:176012400-176017000	Weak transcription	Duodenum Mucosa	Duodenum
38	chr1:176012400-176019400	Weak transcription	Brain Anterior Caudate	brain
39	chr1:176012400-176019400	Weak transcription	Fetal Thymus	thymus
40	chr1:176012400-176024000	Weak transcription	Sigmoid Colon	Sigmoid Colon
41	chr1:176012400-176029200	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
42	chr1:176012400-176036400	Weak transcription	Fetal Muscle Leg	muscle
43	chr1:176012400-176036400	Weak transcription	Gastric	stomach
44	chr1:176012400-176036400	Weak transcription	Left Ventricle	heart
45	chr1:176012400-176036400	Weak transcription	Spleen	Spleen
46	chr1:176012400-176045400	Weak transcription	Rectal Mucosa Donor 29	rectum
47	chr1:176012400-176045800	Weak transcription	Brain Hippocampus Middle	brain
48	chr1:176012400-176048200	Weak transcription	Ovary	ovary
49	chr1:176012400-176048200	Weak transcription	Thymus	Thymus
50	chr1:176012400-176062800	Weak transcription	Lung	lung

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