Variant report

Variant	rs3812139
Chromosome Location	chr6:86196990-86196991
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 121 )
Associated
traits (count: 5 )

rSNPs within LD-proxies of this variant (count:112)

rs_ID	r²[population]
rs1000632	0.81[ASN][1000 genomes]
rs1000633	0.81[ASN][1000 genomes]
rs1000634	0.81[ASN][1000 genomes]
rs11508041	0.82[ASN][1000 genomes]
rs11963844	0.82[ASN][1000 genomes]
rs11968230	0.82[ASN][1000 genomes]
rs11968238	0.82[ASN][1000 genomes]
rs12055597	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.84[YRI][hapmap];0.81[ASN][1000 genomes]
rs12524836	1.00[CHB][hapmap];0.86[JPT][hapmap];0.85[ASN][1000 genomes]
rs12528808	1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs12662033	1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[ASN][1000 genomes]
rs12664908	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[AMR][1000 genomes];0.99[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs1322401	0.81[ASN][1000 genomes]
rs1570310	0.81[ASN][1000 genomes]
rs1570311	1.00[CHB][hapmap];0.87[CHD][hapmap];1.00[JPT][hapmap];0.82[ASN][1000 genomes]
rs1590279	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs2208722	0.81[ASN][1000 genomes]
rs2229524	0.84[AFR][1000 genomes];0.91[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs2295890	0.82[ASN][1000 genomes]
rs3812137	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.82[MEX][hapmap];1.00[TSI][hapmap];0.82[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4144166	0.87[ASN][1000 genomes]
rs4144167	1.00[CHB][hapmap];1.00[JPT][hapmap];0.84[ASN][1000 genomes]
rs4327657	0.96[AFR][1000 genomes];0.91[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs4373339	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.87[ASN][1000 genomes]
rs4400191	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.87[ASN][1000 genomes]
rs4458647	1.00[CHB][hapmap];0.87[CHD][hapmap];1.00[JPT][hapmap];0.82[ASN][1000 genomes]
rs4463232	0.82[ASN][1000 genomes]
rs4487548	1.00[CHB][hapmap];0.87[CHD][hapmap];1.00[JPT][hapmap];0.82[ASN][1000 genomes]
rs4565270	1.00[CHB][hapmap];1.00[JPT][hapmap];0.87[ASN][1000 genomes]
rs4571538	0.82[ASN][1000 genomes]
rs494688	0.85[JPT][hapmap]
rs59797285	0.82[ASN][1000 genomes]
rs6900270	1.00[ASW][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[LWK][hapmap];1.00[MKK][hapmap];1.00[YRI][hapmap];0.91[AFR][1000 genomes];0.91[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs6902638	1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[ASN][1000 genomes]
rs6902904	1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs6910543	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.93[ASN][1000 genomes]
rs6913634	1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs6923017	0.81[ASN][1000 genomes]
rs6930790	1.00[CEU][hapmap];1.00[CHB][hapmap];0.94[GIH][hapmap];0.86[JPT][hapmap];0.82[AMR][1000 genomes];0.96[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs6942065	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.87[ASN][1000 genomes]
rs73751215	0.82[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7744309	1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[ASN][1000 genomes]
rs7745560	1.00[CHB][hapmap];0.87[CHD][hapmap];1.00[JPT][hapmap]
rs7746186	0.87[ASN][1000 genomes]
rs7749600	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.81[ASN][1000 genomes]
rs7749745	0.81[ASN][1000 genomes]
rs7752105	0.93[ASN][1000 genomes]
rs7753022	0.80[ASW][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.85[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.88[TSI][hapmap];0.90[ASN][1000 genomes]
rs7753936	0.81[ASN][1000 genomes]
rs7753950	0.81[ASN][1000 genomes]
rs7754559	0.81[ASN][1000 genomes]
rs7771187	1.00[CHB][hapmap];1.00[JPT][hapmap];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7771366	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.87[ASN][1000 genomes]
rs7772233	0.82[ASN][1000 genomes]
rs7775788	0.81[ASN][1000 genomes]
rs9294336	0.82[ASN][1000 genomes]
rs9342039	0.82[ASN][1000 genomes]
rs9344519	0.81[ASN][1000 genomes]
rs9344520	0.81[ASN][1000 genomes]
rs9344521	0.81[ASN][1000 genomes]
rs9344522	0.81[ASN][1000 genomes]
rs9344523	0.82[ASN][1000 genomes]
rs9344524	0.82[ASN][1000 genomes]
rs9344525	0.82[ASN][1000 genomes]
rs9344526	0.82[ASN][1000 genomes]
rs9344527	0.87[ASN][1000 genomes]
rs9344528	1.00[CHB][hapmap];0.85[JPT][hapmap];0.87[ASN][1000 genomes]
rs9344529	0.87[ASN][1000 genomes]
rs9344530	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9344538	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.81[ASN][1000 genomes]
rs9351063	0.93[ASN][1000 genomes]
rs9353312	0.82[ASN][1000 genomes]
rs9353313	0.82[ASN][1000 genomes]
rs9353314	0.82[ASN][1000 genomes]
rs9353315	0.82[ASN][1000 genomes]
rs9353316	0.82[ASN][1000 genomes]
rs9353317	0.82[ASN][1000 genomes]
rs9353319	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.82[AMR][1000 genomes];0.93[ASN][1000 genomes]
rs9353321	0.93[ASN][1000 genomes]
rs9353323	0.81[ASN][1000 genomes]
rs9353324	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap]
rs9359654	0.82[ASN][1000 genomes]
rs9359655	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.87[ASN][1000 genomes]
rs9359656	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[AMR][1000 genomes];0.94[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs9362211	0.81[ASN][1000 genomes]
rs9362213	0.81[ASN][1000 genomes]
rs9362215	0.81[ASN][1000 genomes]
rs9362216	0.82[ASN][1000 genomes]
rs9362217	0.82[ASN][1000 genomes]
rs9362218	0.82[ASN][1000 genomes]
rs9362219	0.82[ASN][1000 genomes]
rs9362220	0.82[ASN][1000 genomes]
rs9362221	0.82[ASN][1000 genomes]
rs9362223	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9362224	1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs9362225	0.91[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs9362226	0.93[ASN][1000 genomes]
rs9444353	0.93[ASN][1000 genomes]
rs9450274	0.82[ASN][1000 genomes]
rs9450278	1.00[CHB][hapmap];0.87[CHD][hapmap];1.00[JPT][hapmap];0.82[ASN][1000 genomes]
rs9450279	0.82[ASN][1000 genomes]
rs9450280	1.00[CHB][hapmap];1.00[JPT][hapmap];0.87[ASN][1000 genomes]
rs9450286	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.82[MEX][hapmap];0.88[TSI][hapmap];0.82[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9450289	0.82[AMR][1000 genomes];0.93[ASN][1000 genomes]
rs9450294	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.93[ASN][1000 genomes]
rs9450295	0.93[ASN][1000 genomes]
rs9450300	0.93[ASN][1000 genomes]
rs9450304	0.81[ASN][1000 genomes]
rs9450307	1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[ASN][1000 genomes]
rs9450308	1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[ASN][1000 genomes]
rs9450309	0.81[ASN][1000 genomes]
rs9450313	1.00[CHB][hapmap];1.00[JPT][hapmap]

Variant overlapped rSNPs/rCNVs (count:9 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1017418	chr6:85344786-86259540	Flanking Bivalent TSS/Enh Bivalent Enhancer Genic enhancers Enhancers Bivalent/Poised TSS Strong transcription Weak transcription Active TSS Flanking Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	26 gene(s)	inside rSNPs	diseases
2	nsv538347	chr6:85344786-86259540	Weak transcription Enhancers Bivalent/Poised TSS Active TSS Flanking Active TSS Strong transcription Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	26 gene(s)	inside rSNPs	diseases
3	nsv1022445	chr6:85972678-86392968	Enhancers Weak transcription Flanking Active TSS ZNF genes & repeats Strong transcription Transcr. at gene 5' and 3' Genic enhancers Bivalent/Poised TSS Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	136 gene(s)	inside rSNPs	diseases
4	nsv538349	chr6:85972678-86392968	Active TSS Enhancers Weak transcription Strong transcription Genic enhancers Flanking Active TSS ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	136 gene(s)	inside rSNPs	diseases
5	esv3326486	chr6:86020165-86292456	Weak transcription Genic enhancers Strong transcription Enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Active TSS Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	15 gene(s)	inside rSNPs	diseases
6	esv3435075	chr6:86052235-86271910	Strong transcription Weak transcription Active TSS Flanking Active TSS Enhancers Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	15 gene(s)	inside rSNPs	diseases
7	nsv463937	chr6:86114766-86264374	Enhancers Weak transcription Strong transcription Flanking Active TSS Bivalent/Poised TSS Genic enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	14 gene(s)	inside rSNPs	diseases
8	nsv604092	chr6:86114766-86264374	Genic enhancers Flanking Active TSS Strong transcription Weak transcription Bivalent/Poised TSS Enhancers Flanking Bivalent TSS/Enh Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	14 gene(s)	inside rSNPs	diseases
9	nsv520112	chr6:86144875-86247759	Weak transcription Strong transcription Enhancers Transcr. at gene 5' and 3' Flanking Active TSS Genic enhancers Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	12 gene(s)	inside rSNPs	diseases

mRNA abundance (count:5)

SNP	Gene	Cis/trans	Tissue	Source
rs3812139	C6orf160	cis	multi-tissue	Pritchard
rs3812139	RIPPLY2	cis	cerebellum	SCAN
rs3812139	NT5E	cis	parietal	SCAN
rs3812139	NT5E	cis	Thyroid	GTEx
rs3812139	NT5E	cis	lymphoblastoid	seeQTL

Chromatin state (count:60 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:86176800-86242600	Weak transcription	Gastric	stomach
2	chr6:86178800-86206800	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
3	chr6:86186800-86206200	Weak transcription	Lung	lung
4	chr6:86186800-86211000	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
5	chr6:86189200-86197800	Enhancers	Placenta	Placenta
6	chr6:86191400-86200200	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
7	chr6:86192600-86207000	Weak transcription	Brain Hippocampus Middle	brain
8	chr6:86192800-86198000	Weak transcription	Ovary	ovary
9	chr6:86192800-86199200	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
10	chr6:86192800-86200200	Weak transcription	Psoas Muscle	Psoas
11	chr6:86192800-86205000	Weak transcription	GM12878-XiMat	blood
12	chr6:86192800-86221400	Weak transcription	Brain Substantia Nigra	brain
13	chr6:86193000-86199000	Weak transcription	Primary T cells from cord blood	blood
14	chr6:86193000-86199200	Weak transcription	NH-A	brain
15	chr6:86193000-86199400	Weak transcription	Colon Smooth Muscle	Colon
16	chr6:86193000-86199800	Strong transcription	NHEK	skin
17	chr6:86193000-86200200	Weak transcription	Hela-S3	cervix
18	chr6:86193000-86203800	Weak transcription	HepG2	liver
19	chr6:86193000-86204400	Weak transcription	Adipose Nuclei	Adipose
20	chr6:86193000-86221200	Weak transcription	A549	lung
21	chr6:86193200-86198800	Weak transcription	Skeletal Muscle Female	skeletal muscle
22	chr6:86193200-86199000	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
23	chr6:86193200-86199200	Strong transcription	HMEC	breast
24	chr6:86193200-86200200	Strong transcription	Osteobl	bone
25	chr6:86193200-86203400	Strong transcription	NHLF	lung
26	chr6:86193200-86204400	Strong transcription	Muscle Satellite Cultured Cells	--
27	chr6:86193200-86212200	Weak transcription	Brain Anterior Caudate	brain
28	chr6:86193400-86197600	Weak transcription	Rectal Smooth Muscle	rectum
29	chr6:86193400-86199800	Strong transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
30	chr6:86193400-86208600	Weak transcription	HUVEC	blood vessel
31	chr6:86193400-86219800	Weak transcription	Brain Cingulate Gyrus	brain
32	chr6:86193600-86200200	Strong transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
33	chr6:86193800-86200200	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
34	chr6:86194000-86204000	Weak transcription	HSMMtube	muscle
35	chr6:86194800-86200000	Strong transcription	HSMM	muscle
36	chr6:86194800-86206000	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
37	chr6:86194800-86206000	Strong transcription	NHDF-Ad	bronchial
38	chr6:86195000-86197200	Weak transcription	Fetal Stomach	stomach
39	chr6:86195000-86197800	Strong transcription	Foreskin Fibroblast Primary Cells skin02	Skin
40	chr6:86195000-86211800	Weak transcription	Duodenum Smooth Muscle	Duodenum
41	chr6:86195000-86219800	Weak transcription	Brain Angular Gyrus	brain
42	chr6:86195200-86200200	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
43	chr6:86195400-86200200	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
44	chr6:86195600-86197800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
45	chr6:86195600-86198800	Strong transcription	Foreskin Fibroblast Primary Cells skin01	Skin
46	chr6:86195600-86199000	Weak transcription	Rectal Mucosa Donor 29	rectum
47	chr6:86195800-86198800	Weak transcription	Fetal Muscle Trunk	muscle
48	chr6:86196000-86198200	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
49	chr6:86196000-86200600	Strong transcription	Aorta	Aorta
50	chr6:86196200-86202400	Strong transcription	Liver	Liver

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