Variant report

Variant	rs821396
Chromosome Location	chr1:86102956-86102957
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 71 )
Associated
traits (count: 6 )

rSNPs within LD-proxies of this variant (count:68)

rs_ID	r²[population]
rs1047892	0.93[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.81[MEX][hapmap];0.93[TSI][hapmap];0.86[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs1047893	0.92[CEU][hapmap];0.82[CHD][hapmap];0.81[GIH][hapmap];0.86[JPT][hapmap];0.85[TSI][hapmap]
rs1047895	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.93[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.95[LWK][hapmap];0.86[MEX][hapmap];0.94[MKK][hapmap];0.89[TSI][hapmap];0.93[YRI][hapmap];0.88[AFR][1000 genomes];0.85[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs10518350	0.83[CHB][hapmap];0.86[JPT][hapmap]
rs10782553	0.82[CEU][hapmap];0.83[JPT][hapmap];0.90[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs10873709	0.81[ASN][1000 genomes]
rs10873710	0.93[ASW][hapmap];0.82[CHB][hapmap];0.91[CHD][hapmap];0.86[JPT][hapmap];0.81[MKK][hapmap];0.86[TSI][hapmap];0.81[ASN][1000 genomes]
rs10873716	0.85[CEU][hapmap]
rs1094359	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11161641	0.81[ASN][1000 genomes]
rs11161643	1.00[ASW][hapmap];0.93[CEU][hapmap];0.95[CHB][hapmap];0.95[CHD][hapmap];0.81[GIH][hapmap];1.00[JPT][hapmap];0.92[MKK][hapmap];0.98[TSI][hapmap];0.86[YRI][hapmap];0.94[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs11161645	0.93[ASW][hapmap];0.95[CHB][hapmap];0.93[CHD][hapmap];1.00[JPT][hapmap];0.92[ASN][1000 genomes]
rs11161651	0.85[CEU][hapmap]
rs11578464	0.93[ASW][hapmap];0.93[CEU][hapmap];0.82[CHB][hapmap];0.91[CHD][hapmap];0.86[JPT][hapmap];0.94[MKK][hapmap];0.98[TSI][hapmap];0.90[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs12128916	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[AMR][1000 genomes];0.86[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs12566746	0.92[CEU][hapmap];0.86[JPT][hapmap]
rs1539444	0.93[CEU][hapmap];0.82[CHD][hapmap];0.81[GIH][hapmap];0.86[JPT][hapmap];0.89[TSI][hapmap];0.81[EUR][1000 genomes]
rs1764285	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.95[MEX][hapmap];0.95[TSI][hapmap];0.90[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs1764288	0.90[AFR][1000 genomes];0.81[AMR][1000 genomes];0.87[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs1764289	0.87[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs1764291	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.83[AMR][1000 genomes];0.89[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs1764292	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs1764299	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];0.83[AMR][1000 genomes];0.90[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs1775988	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.81[LWK][hapmap];1.00[MEX][hapmap];0.94[MKK][hapmap];0.95[TSI][hapmap];0.83[AMR][1000 genomes];0.88[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs1775990	0.96[CEU][hapmap];0.90[CHB][hapmap];0.94[JPT][hapmap];0.87[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs1928626	0.84[AFR][1000 genomes];0.94[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2389969	0.82[MKK][hapmap]
rs2389970	1.00[ASW][hapmap];0.95[CHB][hapmap];0.93[CHD][hapmap];1.00[JPT][hapmap];0.90[ASN][1000 genomes]
rs2785081	0.95[CHB][hapmap];1.00[JPT][hapmap];0.86[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs2995537	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[YRI][hapmap];0.97[AFR][1000 genomes];0.88[AMR][1000 genomes];0.90[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs34448540	0.91[ASN][1000 genomes]
rs373787	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs3753786	0.93[CEU][hapmap];0.82[CHD][hapmap];0.81[GIH][hapmap];0.86[JPT][hapmap];0.87[TSI][hapmap];0.80[EUR][1000 genomes]
rs3753789	0.85[CEU][hapmap]
rs3753790	0.85[CEU][hapmap]
rs3767162	0.99[AFR][1000 genomes];0.90[AMR][1000 genomes];0.91[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs414618	0.95[CHB][hapmap];0.88[CHD][hapmap];0.81[GIH][hapmap];1.00[JPT][hapmap];0.81[ASN][1000 genomes]
rs418979	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.85[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs419409	0.84[AFR][1000 genomes];0.81[AMR][1000 genomes];0.85[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs424205	0.84[AFR][1000 genomes];0.81[AMR][1000 genomes];0.84[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs434853	0.85[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs447446	0.85[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs4912441	0.86[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs4949911	0.82[MKK][hapmap]
rs4949915	0.82[CHB][hapmap];0.90[JPT][hapmap];0.82[ASN][1000 genomes]
rs61783617	0.90[AFR][1000 genomes];0.81[AMR][1000 genomes];0.86[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs6667094	0.86[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs6672312	0.93[CEU][hapmap];0.82[CHD][hapmap];0.81[GIH][hapmap];0.86[JPT][hapmap];0.87[TSI][hapmap]
rs6689168	0.84[CEU][hapmap]
rs6689925	0.97[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6697535	0.93[CEU][hapmap];0.86[JPT][hapmap]
rs6699497	0.92[AFR][1000 genomes];0.90[AMR][1000 genomes];0.91[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs709801	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7520491	0.92[CEU][hapmap];0.84[EUR][1000 genomes]
rs7532758	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.95[MEX][hapmap];0.95[TSI][hapmap];0.86[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs821379	0.96[AFR][1000 genomes];0.91[AMR][1000 genomes];0.91[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs821381	0.99[AFR][1000 genomes];0.91[AMR][1000 genomes];0.91[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs821386	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[YRI][hapmap];0.97[AFR][1000 genomes];0.93[AMR][1000 genomes];0.91[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs821389	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.95[LWK][hapmap];1.00[MEX][hapmap];0.92[MKK][hapmap];1.00[TSI][hapmap];0.87[YRI][hapmap];0.99[AFR][1000 genomes];0.95[AMR][1000 genomes];0.91[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs821391	0.88[AFR][1000 genomes]
rs821393	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.93[AFR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs821394	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs821395	0.86[AFR][1000 genomes];0.81[ASN][1000 genomes]
rs821401	0.99[AFR][1000 genomes];0.95[AMR][1000 genomes];0.91[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs843969	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9324154	0.93[AFR][1000 genomes];0.86[AMR][1000 genomes];0.88[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs952837	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[YRI][hapmap];0.91[AFR][1000 genomes];0.84[AMR][1000 genomes];0.91[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs9700177	0.95[AFR][1000 genomes];0.90[AMR][1000 genomes];0.91[EUR][1000 genomes];0.92[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	nsv1006994	chr1:85454304-86327679	Active TSS Enhancers Weak transcription Flanking Active TSS Strong transcription Flanking Bivalent TSS/Enh Genic enhancers ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	72 gene(s)	inside rSNPs	diseases
2	esv3391173	chr1:86005637-86337469	Enhancers Flanking Active TSS Active TSS Bivalent Enhancer Weak transcription Transcr. at gene 5' and 3' Strong transcription Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	40 gene(s)	inside rSNPs	diseases
3	nsv1000290	chr1:86078495-86105379	Weak transcription Enhancers ZNF genes & repeats Bivalent Enhancer Strong transcription Flanking Active TSS Bivalent/Poised TSS Active TSS Genic enhancers Flanking Bivalent TSS/Enh	Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases

mRNA abundance (count:6)

SNP	Gene	Cis/trans	Tissue	Source
rs821396	ZNHIT6	cis	Artery Aorta	GTEx
rs821396	ZNHIT6	cis	Adipose Subcutaneous	GTEx
rs821396	ZNHIT6	cis	lung	GTEx
rs821396	ZNHIT6	cis	Esophagus Muscularis	GTEx
rs821396	ZNHIT6	cis	lymphoblastoid	seeQTL
rs821396	LOC339524	cis	cerebellum	SCAN

Chromatin state (count:96 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:86083800-86103200	Weak transcription	Brain Cingulate Gyrus	brain
2	chr1:86088400-86103000	Weak transcription	Brain Hippocampus Middle	brain
3	chr1:86088600-86103000	Weak transcription	NHEK	skin
4	chr1:86089400-86103000	Weak transcription	Brain Inferior Temporal Lobe	brain
5	chr1:86091200-86103200	Weak transcription	Brain Angular Gyrus	brain
6	chr1:86091800-86107600	Weak transcription	Colonic Mucosa	Colon
7	chr1:86094000-86118600	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
8	chr1:86094800-86103200	Weak transcription	Small Intestine	intestine
9	chr1:86095000-86103200	Weak transcription	Fetal Heart	heart
10	chr1:86095200-86103000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
11	chr1:86095200-86103000	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
12	chr1:86095200-86103000	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
13	chr1:86095200-86103000	Weak transcription	Gastric	stomach
14	chr1:86095200-86103000	Weak transcription	Ovary	ovary
15	chr1:86095200-86103000	Weak transcription	Skeletal Muscle Male	skeletal muscle
16	chr1:86095200-86103000	Weak transcription	Spleen	Spleen
17	chr1:86095200-86104200	Weak transcription	Psoas Muscle	Psoas
18	chr1:86095200-86104400	Weak transcription	Right Ventricle	heart
19	chr1:86095400-86103000	Weak transcription	HUES6 Cell Line	embryonic stem cell
20	chr1:86095400-86103000	Weak transcription	Breast Myoepithelial Primary Cells	Breast
21	chr1:86095400-86103000	Weak transcription	Brain Anterior Caudate	brain
22	chr1:86095400-86103000	Weak transcription	Skeletal Muscle Female	skeletal muscle
23	chr1:86095400-86107600	Weak transcription	iPS-15b Cell Line	embryonic stem cell
24	chr1:86095400-86119000	Weak transcription	Rectal Smooth Muscle	rectum
25	chr1:86095400-86134800	Weak transcription	Placenta Amnion	Placenta Amnion
26	chr1:86095600-86103000	Weak transcription	Fetal Lung	lung
27	chr1:86095600-86103800	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
28	chr1:86095600-86104000	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
29	chr1:86095600-86104000	Weak transcription	HUES48 Cell Line	embryonic stem cell
30	chr1:86095600-86117000	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
31	chr1:86095800-86103000	Weak transcription	HSMMtube	muscle
32	chr1:86095800-86103200	Weak transcription	iPS-20b Cell Line	embryonic stem cell
33	chr1:86096000-86103000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
34	chr1:86096000-86104000	Weak transcription	ES-I3 Cell Line	embryonic stem cell
35	chr1:86096200-86103400	Weak transcription	HUES64 Cell Line	embryonic stem cell
36	chr1:86096200-86103800	Weak transcription	HepG2	liver
37	chr1:86096200-86115600	Weak transcription	NH-A	brain
38	chr1:86096400-86103000	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
39	chr1:86096400-86103000	Weak transcription	NHDF-Ad	bronchial
40	chr1:86096400-86104800	Weak transcription	Muscle Satellite Cultured Cells	--
41	chr1:86096600-86103200	Weak transcription	Primary T helper naive cells from peripheral blood	blood
42	chr1:86097200-86103000	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
43	chr1:86099800-86103800	Strong transcription	Primary T cells from cord blood	blood
44	chr1:86100200-86103000	Strong transcription	Left Ventricle	heart
45	chr1:86101000-86107600	ZNF genes & repeats	Primary hematopoietic stem cells G-CSF-mobilized Male	--
46	chr1:86101200-86103000	Strong transcription	Foreskin Fibroblast Primary Cells skin01	Skin
47	chr1:86101200-86103000	Strong transcription	Liver	Liver
48	chr1:86101200-86103000	Weak transcription	Pancreas	Pancrea
49	chr1:86101200-86106600	ZNF genes & repeats	Primary hematopoietic stem cells	blood
50	chr1:86101400-86103600	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin

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