Variant report

Variant	rs11161643
Chromosome Location	chr1:86083571-86083572
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	chr1:86046852..86049403-chr1:86080324..86084474,3	K562	blood:

Variant related genes	Relation type
ENSG00000142871	Chromatin interaction

Extended variants
information (count: 61 )
Associated
traits (count: 5 )

rSNPs within LD-proxies of this variant (count:58)

rs_ID	r²[population]
rs1047892	0.85[CEU][hapmap];0.95[CHB][hapmap];0.91[CHD][hapmap];0.80[GIH][hapmap];1.00[JPT][hapmap];0.91[TSI][hapmap];0.81[EUR][1000 genomes]
rs1047893	0.85[CEU][hapmap];0.86[JPT][hapmap];0.82[TSI][hapmap]
rs1047895	1.00[ASW][hapmap];0.93[CEU][hapmap];0.95[CHB][hapmap];0.88[CHD][hapmap];0.80[GIH][hapmap];1.00[JPT][hapmap];0.86[MKK][hapmap];0.86[TSI][hapmap];0.92[YRI][hapmap];0.80[EUR][1000 genomes]
rs10518350	0.86[JPT][hapmap]
rs10782553	0.87[CEU][hapmap];0.83[JPT][hapmap];0.98[AMR][1000 genomes];0.95[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs10873709	0.90[ASN][1000 genomes]
rs10873710	0.93[ASW][hapmap];0.86[CHB][hapmap];0.95[CHD][hapmap];0.86[JPT][hapmap];0.89[LWK][hapmap];0.96[MEX][hapmap];0.89[TSI][hapmap];0.91[AMR][1000 genomes];0.90[ASN][1000 genomes]
rs1094359	0.94[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs11161641	0.90[ASN][1000 genomes]
rs11161645	0.93[ASW][hapmap];1.00[CHB][hapmap];0.98[CHD][hapmap];0.91[GIH][hapmap];1.00[JPT][hapmap];0.80[MEX][hapmap];0.99[ASN][1000 genomes]
rs11578464	0.93[ASW][hapmap];1.00[CEU][hapmap];0.86[CHB][hapmap];0.95[CHD][hapmap];0.86[JPT][hapmap];0.89[LWK][hapmap];1.00[MEX][hapmap];0.94[MKK][hapmap];1.00[TSI][hapmap];0.82[AFR][1000 genomes];0.97[AMR][1000 genomes];0.95[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs12128916	0.93[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.81[EUR][1000 genomes]
rs12566746	0.85[CEU][hapmap];0.86[JPT][hapmap]
rs1539444	0.85[CEU][hapmap];0.86[JPT][hapmap];0.86[TSI][hapmap]
rs1764285	0.93[CEU][hapmap];0.95[CHB][hapmap];0.91[CHD][hapmap];0.81[GIH][hapmap];1.00[JPT][hapmap];0.93[TSI][hapmap];0.85[EUR][1000 genomes]
rs1764288	0.82[EUR][1000 genomes]
rs1764289	0.82[EUR][1000 genomes]
rs1764291	0.93[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.84[EUR][1000 genomes]
rs1764292	0.93[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.84[EUR][1000 genomes]
rs1764299	0.93[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.86[YRI][hapmap];0.85[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs1775988	1.00[ASW][hapmap];0.93[CEU][hapmap];0.95[CHB][hapmap];0.91[CHD][hapmap];0.81[GIH][hapmap];1.00[JPT][hapmap];0.86[MKK][hapmap];0.93[TSI][hapmap];0.83[EUR][1000 genomes]
rs1775990	0.88[CEU][hapmap];0.95[CHB][hapmap];0.94[JPT][hapmap];0.82[EUR][1000 genomes]
rs1928626	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2389970	1.00[ASW][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];1.00[JPT][hapmap];0.92[MEX][hapmap];0.85[MKK][hapmap];0.86[YRI][hapmap];0.89[AMR][1000 genomes];0.99[ASN][1000 genomes]
rs2785081	0.90[CHB][hapmap];1.00[JPT][hapmap];0.81[EUR][1000 genomes]
rs2995537	0.93[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.85[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs34448540	0.89[AMR][1000 genomes];0.97[ASN][1000 genomes]
rs373787	0.93[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.81[EUR][1000 genomes]
rs3753786	0.85[CEU][hapmap];0.86[JPT][hapmap];0.84[TSI][hapmap]
rs3767162	0.86[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs414618	1.00[CHB][hapmap];0.93[CHD][hapmap];1.00[JPT][hapmap]
rs418979	0.93[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap]
rs419409	0.80[EUR][1000 genomes]
rs434853	0.80[EUR][1000 genomes]
rs447446	0.80[EUR][1000 genomes]
rs4912441	0.81[EUR][1000 genomes]
rs4949915	0.86[CHB][hapmap];0.90[JPT][hapmap];0.87[AMR][1000 genomes];0.91[ASN][1000 genomes]
rs61783617	0.81[EUR][1000 genomes]
rs6667094	0.81[EUR][1000 genomes]
rs6672312	0.85[CEU][hapmap];0.86[JPT][hapmap];0.84[TSI][hapmap]
rs6689925	0.92[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs6697535	0.85[CEU][hapmap];0.86[JPT][hapmap]
rs6699497	0.86[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs709801	0.95[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs7520491	0.85[CEU][hapmap];0.81[EUR][1000 genomes]
rs7532758	0.93[CEU][hapmap];0.95[CHB][hapmap];0.91[CHD][hapmap];0.80[GIH][hapmap];1.00[JPT][hapmap];0.93[TSI][hapmap];0.81[EUR][1000 genomes]
rs821379	0.86[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs821381	0.86[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs821386	0.92[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.91[YRI][hapmap];0.86[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs821389	1.00[ASW][hapmap];0.93[CEU][hapmap];0.95[CHB][hapmap];0.95[CHD][hapmap];0.81[GIH][hapmap];1.00[JPT][hapmap];0.84[MKK][hapmap];0.98[TSI][hapmap];0.86[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs821393	0.95[CHB][hapmap];1.00[JPT][hapmap];0.86[YRI][hapmap];0.90[AMR][1000 genomes];0.95[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs821394	0.94[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs821396	0.94[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs821401	0.86[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs843969	0.94[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs9324154	0.83[EUR][1000 genomes]
rs952837	0.93[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.92[YRI][hapmap];0.86[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs9700177	0.80[AFR][1000 genomes];0.86[EUR][1000 genomes];0.83[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:5)

SNP	Gene	Cis/trans	Tissue	Source
rs11161643	ZNHIT6	cis	lymphoblastoid	seeQTL
rs11161643	LOC339524	cis	cerebellum	SCAN
rs11161643	ZNHIT6	cis	lung	GTEx
rs11161643	ZNHIT6	cis	Adipose Subcutaneous	GTEx
rs11161643	C1orf181	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:35 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:86079200-86085200	Weak transcription	Hela-S3	cervix
2	chr1:86079200-86086400	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
3	chr1:86079200-86087800	Weak transcription	Left Ventricle	heart
4	chr1:86079200-86094400	Weak transcription	Pancreas	Pancrea
5	chr1:86079400-86084200	Enhancers	NHDF-Ad	bronchial
6	chr1:86081200-86083800	Enhancers	Placenta Amnion	Placenta Amnion
7	chr1:86081600-86084600	Enhancers	Foreskin Fibroblast Primary Cells skin02	Skin
8	chr1:86082000-86083800	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
9	chr1:86082000-86086400	Weak transcription	Duodenum Smooth Muscle	Duodenum
10	chr1:86082200-86084200	Enhancers	Fetal Muscle Leg	muscle
11	chr1:86082200-86086800	Weak transcription	Fetal Heart	heart
12	chr1:86082200-86086800	Weak transcription	Fetal Intestine Small	intestine
13	chr1:86082200-86087600	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
14	chr1:86082400-86084200	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
15	chr1:86082400-86085400	Weak transcription	Aorta	Aorta
16	chr1:86082400-86086800	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
17	chr1:86082400-86087200	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
18	chr1:86082600-86084200	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
19	chr1:86082600-86084400	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
20	chr1:86082600-86085200	Weak transcription	Fetal Stomach	stomach
21	chr1:86083000-86083800	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
22	chr1:86083000-86083800	Enhancers	Brain Anterior Caudate	brain
23	chr1:86083000-86083800	Enhancers	Brain Cingulate Gyrus	brain
24	chr1:86083000-86083800	Enhancers	Stomach Smooth Muscle	stomach
25	chr1:86083000-86084000	Enhancers	Muscle Satellite Cultured Cells	--
26	chr1:86083000-86084000	Enhancers	HSMM	muscle
27	chr1:86083000-86084000	Enhancers	NH-A	brain
28	chr1:86083000-86084000	Enhancers	NHLF	lung
29	chr1:86083000-86084000	Enhancers	Osteobl	bone
30	chr1:86083200-86083600	Enhancers	Brain Hippocampus Middle	brain
31	chr1:86083200-86083600	Enhancers	Brain Substantia Nigra	brain
32	chr1:86083200-86083600	Enhancers	HSMMtube	muscle
33	chr1:86083200-86086600	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
34	chr1:86083400-86083800	Enhancers	Brain Inferior Temporal Lobe	brain
35	chr1:86083400-86086800	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell

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