Variant report

Variant	rs6837991
Chromosome Location	chr4:142558755-142558756
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 42 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:34)

rs_ID	r²[population]
rs10028670	0.89[EUR][1000 genomes]
rs1040257	0.95[CEU][hapmap];0.89[EUR][1000 genomes]
rs11100722	0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11100723	0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11100724	0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12508955	0.95[CEU][hapmap];0.86[EUR][1000 genomes]
rs13111860	0.86[EUR][1000 genomes]
rs1476326	0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1493024	0.86[EUR][1000 genomes]
rs1519550	0.86[EUR][1000 genomes]
rs1519552	0.95[CEU][hapmap];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1519553	0.95[CEU][hapmap];1.00[CHD][hapmap];0.91[GIH][hapmap];0.92[MEX][hapmap];0.87[TSI][hapmap];0.89[EUR][1000 genomes]
rs1589241	1.00[CEU][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[MEX][hapmap];0.97[TSI][hapmap];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1607592	0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1607593	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1850853	0.89[EUR][1000 genomes]
rs2087849	0.95[CEU][hapmap];0.88[EUR][1000 genomes]
rs2254514	0.87[EUR][1000 genomes]
rs2322262	1.00[ASW][hapmap];0.95[CEU][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.97[LWK][hapmap];1.00[MEX][hapmap];0.93[MKK][hapmap];0.97[TSI][hapmap];1.00[YRI][hapmap];0.94[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4956404	0.95[CEU][hapmap];1.00[CHD][hapmap];0.91[GIH][hapmap];0.92[MEX][hapmap];0.87[TSI][hapmap];0.89[EUR][1000 genomes]
rs4956407	0.95[CEU][hapmap];0.87[EUR][1000 genomes]
rs6537058	1.00[CEU][hapmap];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6816210	0.95[CEU][hapmap];0.85[EUR][1000 genomes]
rs6841454	0.95[CEU][hapmap];1.00[CHD][hapmap];0.91[GIH][hapmap];0.92[MEX][hapmap];0.87[TSI][hapmap];0.89[EUR][1000 genomes]
rs6842194	0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7661408	0.86[EUR][1000 genomes]
rs7665842	0.85[EUR][1000 genomes]
rs7688250	0.95[CEU][hapmap];1.00[CHD][hapmap];0.91[GIH][hapmap];0.92[MEX][hapmap];0.87[TSI][hapmap];0.89[EUR][1000 genomes]
rs7698675	0.95[CEU][hapmap];0.87[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9683566	0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9684235	0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs970327	0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs970328	0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs990851	1.00[CEU][hapmap];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:8 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv880172	chr4:142355535-142565089	Enhancers Weak transcription Active TSS Flanking Active TSS Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh Strong transcription Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
2	nsv880173	chr4:142355535-142666106	Enhancers Weak transcription Flanking Active TSS Strong transcription Flanking Bivalent TSS/Enh Active TSS Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
3	nsv830094	chr4:142411738-142567788	Weak transcription Flanking Active TSS Enhancers Flanking Bivalent TSS/Enh Active TSS Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
4	esv3401979	chr4:142434442-142803321	Weak transcription Enhancers ZNF genes & repeats Active TSS Flanking Active TSS Bivalent Enhancer Strong transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
5	nsv1018949	chr4:142451823-142732365	Enhancers Weak transcription Strong transcription Active TSS Bivalent/Poised TSS Bivalent Enhancer Flanking Active 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	3 gene(s)	inside rSNPs	diseases
6	nsv1030822	chr4:142487721-142706053	Enhancers ZNF genes & repeats Weak transcription Flanking Active TSS Active TSS Strong transcription Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
7	nsv1027004	chr4:142487721-143007320	Weak transcription Enhancers Active TSS Flanking Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Strong transcription Bivalent Enhancer Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
8	nsv498005	chr4:142515689-143502988	Enhancers Weak transcription Flanking Active TSS Strong transcription Flanking Bivalent TSS/Enh Active TSS ZNF genes & repeats Genic enhancers Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs6837991	IL15	cis	multi-tissue	Pritchard
rs6837991	MED9	trans	parietal	SCAN

Chromatin state (count:83 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:142556800-142560000	Active TSS	NHDF-Ad	bronchial
2	chr4:142557000-142558800	Bivalent/Poised TSS	HUES48 Cell Line	embryonic stem cell
3	chr4:142557000-142558800	Bivalent/Poised TSS	iPS-20b Cell Line	embryonic stem cell
4	chr4:142557000-142558800	Active TSS	Foreskin Fibroblast Primary Cells skin02	Skin
5	chr4:142557000-142558800	Active TSS	Brain Cingulate Gyrus	brain
6	chr4:142557000-142558800	Active TSS	Stomach Mucosa	stomach
7	chr4:142557000-142559000	Active TSS	Skeletal Muscle Female	skeletal muscle
8	chr4:142557000-142559000	Active TSS	Thymus	Thymus
9	chr4:142557000-142559200	Active TSS	Right Ventricle	heart
10	chr4:142557000-142559600	Active TSS	HSMM	muscle
11	chr4:142557000-142559800	Active TSS	NHLF	lung
12	chr4:142557000-142560000	Active TSS	Aorta	Aorta
13	chr4:142557000-142560000	Active TSS	Rectal Mucosa Donor 29	rectum
14	chr4:142557000-142560000	Active TSS	Right Atrium	heart
15	chr4:142557000-142561200	Active TSS	Duodenum Smooth Muscle	Duodenum
16	chr4:142557200-142558800	Bivalent/Poised TSS	ES-I3 Cell Line	embryonic stem cell
17	chr4:142557200-142558800	Bivalent/Poised TSS	iPS-15b Cell Line	embryonic stem cell
18	chr4:142557200-142558800	Bivalent/Poised TSS	iPS-18 Cell Line	embryonic stem cell
19	chr4:142557200-142558800	Flanking Active TSS	Primary hematopoietic stem cells short term culture	blood
20	chr4:142557200-142558800	Active TSS	Primary T killer memory cells from peripheral blood	blood
21	chr4:142557200-142559000	Bivalent/Poised TSS	HUES6 Cell Line	embryonic stem cell
22	chr4:142557200-142559000	Active TSS	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
23	chr4:142557200-142559000	Active TSS	Psoas Muscle	Psoas
24	chr4:142557200-142559000	Active TSS	Rectal Smooth Muscle	rectum
25	chr4:142557200-142559200	Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
26	chr4:142557200-142560600	Active TSS	GM12878-XiMat	blood
27	chr4:142557200-142560800	Active TSS	A549	lung
28	chr4:142557400-142558800	Active TSS	Muscle Satellite Cultured Cells	--
29	chr4:142557400-142559200	Active TSS	Skeletal Muscle Male	skeletal muscle
30	chr4:142557400-142559400	Active TSS	Hela-S3	cervix
31	chr4:142557400-142560000	Active TSS	Stomach Smooth Muscle	stomach
32	chr4:142557600-142558800	Active TSS	Fetal Intestine Small	intestine
33	chr4:142557600-142559000	Active TSS	IMR90 fetal lung fibroblasts Cell Line	lung
34	chr4:142558000-142558800	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Female	--
35	chr4:142558000-142559000	Flanking Active TSS	Adipose Nuclei	Adipose
36	chr4:142558200-142558800	Flanking Active TSS	Primary T helper memory cells from peripheral blood 1	blood
37	chr4:142558200-142558800	Flanking Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
38	chr4:142558200-142558800	Bivalent/Poised TSS	Brain Anterior Caudate	brain
39	chr4:142558200-142558800	Flanking Active TSS	Brain Hippocampus Middle	brain
40	chr4:142558200-142558800	Flanking Active TSS	NHEK	skin
41	chr4:142558200-142559000	Flanking Active TSS	Liver	Liver
42	chr4:142558400-142558800	Flanking Active TSS	Primary T cells from cord blood	blood
43	chr4:142558400-142558800	Flanking Active TSS	Primary hematopoietic stem cells	blood
44	chr4:142558400-142558800	Flanking Active TSS	Primary T helper memory cells from peripheral blood 2	blood
45	chr4:142558400-142558800	Flanking Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
46	chr4:142558400-142558800	Active TSS	Foreskin Keratinocyte Primary Cells skin02	Skin
47	chr4:142558400-142558800	Flanking Active TSS	Duodenum Mucosa	Duodenum
48	chr4:142558400-142558800	Flanking Active TSS	Rectal Mucosa Donor 31	rectum
49	chr4:142558400-142558800	Flanking Active TSS	NH-A	brain
50	chr4:142558400-142559000	Flanking Active TSS	HUVEC	blood vessel

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