Variant report

Variant	rs7839363
Chromosome Location	chr8:62474645-62474646
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 48 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:38)

rs_ID	r²[population]
rs10086389	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs10086644	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[YRI][hapmap];0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs10101416	0.87[CHB][hapmap];0.84[JPT][hapmap];0.81[ASN][1000 genomes]
rs10109999	0.81[ASN][1000 genomes]
rs10113272	0.81[ASN][1000 genomes]
rs11774171	0.87[CHB][hapmap];0.91[CHD][hapmap];0.84[JPT][hapmap];0.94[MEX][hapmap];0.88[TSI][hapmap]
rs11984530	0.80[ASN][1000 genomes]
rs1320081	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs13253460	0.87[CHB][hapmap];0.84[JPT][hapmap];0.84[ASN][1000 genomes]
rs16918881	0.87[CHB][hapmap];0.87[MEX][hapmap]
rs16927435	0.95[CHB][hapmap];0.83[JPT][hapmap];0.85[ASN][1000 genomes]
rs16927470	0.87[CHB][hapmap];0.86[CHD][hapmap];0.84[JPT][hapmap];0.93[MEX][hapmap];0.88[TSI][hapmap];0.81[ASN][1000 genomes]
rs16927479	0.81[ASN][1000 genomes]
rs2350617	0.93[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.97[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];0.95[YRI][hapmap];1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2350618	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs34344679	0.81[ASN][1000 genomes]
rs3802286	0.93[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.97[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs3922836	0.80[ASN][1000 genomes]
rs4400380	0.93[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];0.96[GIH][hapmap];1.00[JPT][hapmap];0.97[LWK][hapmap];0.94[MEX][hapmap];0.96[MKK][hapmap];0.91[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4416815	0.87[CHB][hapmap];0.86[CHD][hapmap];0.84[JPT][hapmap];0.88[MEX][hapmap];0.88[TSI][hapmap]
rs4510853	0.87[CHB][hapmap];0.84[JPT][hapmap];0.81[ASN][1000 genomes]
rs4737587	0.87[CHB][hapmap];0.84[JPT][hapmap];0.81[ASN][1000 genomes]
rs56007602	0.81[AMR][1000 genomes];0.88[ASN][1000 genomes]
rs6471958	0.93[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.97[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6471959	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs67210846	0.81[ASN][1000 genomes]
rs6984604	0.93[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.97[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];0.95[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7005455	0.87[CHB][hapmap];0.84[JPT][hapmap]
rs7009762	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7011243	0.83[CHB][hapmap];0.84[CHD][hapmap];0.84[JPT][hapmap];0.88[MEX][hapmap];0.86[TSI][hapmap]
rs7013189	0.82[CHB][hapmap];0.80[JPT][hapmap];0.82[MEX][hapmap];0.86[TSI][hapmap]
rs72657089	0.80[AMR][1000 genomes];0.81[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs7462486	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.87[YRI][hapmap]
rs7819628	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7823286	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7825172	0.82[CHB][hapmap];0.84[CHD][hapmap];0.84[JPT][hapmap];0.88[MEX][hapmap];0.81[ASN][1000 genomes]
rs7839203	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs903027	0.87[CHB][hapmap];0.81[MEX][hapmap]

Variant overlapped rSNPs/rCNVs (count:10 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv948922	chr8:61818964-62475097	Enhancers Weak transcription Flanking Bivalent TSS/Enh Active TSS Bivalent Enhancer Strong transcription Flanking Active TSS ZNF genes & repeats Bivalent/Poised TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	17 gene(s)	inside rSNPs	diseases
2	nsv1024432	chr8:62086247-62898782	Flanking Active TSS Enhancers Weak transcription Strong transcription Active TSS ZNF genes & repeats Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	31 gene(s)	inside rSNPs	diseases
3	nsv1027742	chr8:62206883-62613533	Weak transcription Strong transcription Enhancers Flanking Active TSS ZNF genes & repeats Active TSS Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	10 gene(s)	inside rSNPs	diseases
4	nsv539633	chr8:62206883-62613533	Weak transcription Strong transcription Enhancers Genic enhancers ZNF genes & repeats Active TSS Flanking Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	10 gene(s)	inside rSNPs	diseases
5	nsv1021377	chr8:62214279-62596721	Strong transcription Enhancers Weak transcription Genic enhancers Flanking Active TSS ZNF genes & repeats Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	8 gene(s)	inside rSNPs	diseases
6	nsv539634	chr8:62214279-62596721	ZNF genes & repeats Genic enhancers Enhancers Weak transcription Strong transcription Flanking Bivalent TSS/Enh Flanking Active TSS Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	8 gene(s)	inside rSNPs	diseases
7	nsv1029046	chr8:62224341-62535277	Strong transcription Enhancers ZNF genes & repeats Weak transcription Genic enhancers Flanking Active TSS Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	5 gene(s)	inside rSNPs	diseases
8	nsv932198	chr8:62336705-62914562	Enhancers Weak transcription Flanking Active TSS Strong transcription Active TSS Genic enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	25 gene(s)	inside rSNPs	diseases
9	nsv1032489	chr8:62450784-62555994	Weak transcription Strong transcription Enhancers ZNF genes & repeats Genic enhancers Flanking Active TSS Active TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	5 gene(s)	inside rSNPs	diseases
10	nsv539635	chr8:62450784-62555994	Strong transcription Weak transcription Genic enhancers Enhancers ZNF genes & repeats Flanking Active TSS Active TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	5 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs7839363	GGH	cis	cerebellum	SCAN
rs7839363	ARMC1	cis	parietal	SCAN

Chromatin state (count:82 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr8:62411000-62505800	Weak transcription	Brain Angular Gyrus	brain
2	chr8:62411200-62493800	Weak transcription	Brain Inferior Temporal Lobe	brain
3	chr8:62414800-62503400	Weak transcription	Fetal Heart	heart
4	chr8:62430400-62487400	Weak transcription	Colonic Mucosa	Colon
5	chr8:62430600-62479600	Weak transcription	Brain Substantia Nigra	brain
6	chr8:62442600-62493200	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
7	chr8:62449800-62503600	Weak transcription	Rectal Smooth Muscle	rectum
8	chr8:62453400-62480200	Weak transcription	Primary T cells from cord blood	blood
9	chr8:62453400-62480800	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
10	chr8:62456000-62482800	Strong transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
11	chr8:62456000-62482800	Strong transcription	Adipose Nuclei	Adipose
12	chr8:62456000-62491600	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
13	chr8:62456600-62492800	Weak transcription	Small Intestine	intestine
14	chr8:62456600-62503800	Weak transcription	Stomach Mucosa	stomach
15	chr8:62456800-62479400	Weak transcription	Psoas Muscle	Psoas
16	chr8:62456800-62482200	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
17	chr8:62457000-62475400	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
18	chr8:62457000-62479600	Weak transcription	NHEK	skin
19	chr8:62457000-62496600	Weak transcription	Brain Hippocampus Middle	brain
20	chr8:62457000-62503000	Weak transcription	HSMMtube	muscle
21	chr8:62457800-62488400	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
22	chr8:62458000-62497000	Weak transcription	Skeletal Muscle Male	skeletal muscle
23	chr8:62458200-62482000	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
24	chr8:62458800-62491000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
25	chr8:62459000-62479400	Weak transcription	Aorta	Aorta
26	chr8:62459200-62476200	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
27	chr8:62460200-62495800	Weak transcription	Placenta Amnion	Placenta Amnion
28	chr8:62463000-62475200	Strong transcription	A549	lung
29	chr8:62463400-62476200	Weak transcription	iPS-20b Cell Line	embryonic stem cell
30	chr8:62463800-62479200	Weak transcription	Sigmoid Colon	Sigmoid Colon
31	chr8:62463800-62481200	Weak transcription	Pancreatic Islets	Pancreatic Islet
32	chr8:62464000-62480400	Weak transcription	Lung	lung
33	chr8:62464000-62492400	Weak transcription	Fetal Muscle Leg	muscle
34	chr8:62464000-62492600	Weak transcription	Fetal Muscle Trunk	muscle
35	chr8:62464000-62494000	Weak transcription	HUVEC	blood vessel
36	chr8:62464200-62479000	Weak transcription	Brain Cingulate Gyrus	brain
37	chr8:62464400-62492600	Weak transcription	Primary hematopoietic stem cells short term culture	blood
38	chr8:62464600-62478200	Weak transcription	Skeletal Muscle Female	skeletal muscle
39	chr8:62465000-62479600	Weak transcription	Primary monocytes fromperipheralblood	blood
40	chr8:62465000-62488400	Weak transcription	Colon Smooth Muscle	Colon
41	chr8:62465000-62488600	Weak transcription	Brain Anterior Caudate	brain
42	chr8:62466600-62490200	Weak transcription	K562	blood
43	chr8:62466800-62479000	Weak transcription	Primary hematopoietic stem cells	blood
44	chr8:62466800-62508600	Weak transcription	Pancreas	Pancrea
45	chr8:62467200-62487400	Weak transcription	Rectal Mucosa Donor 29	rectum
46	chr8:62467600-62492600	Weak transcription	Spleen	Spleen
47	chr8:62468600-62479000	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
48	chr8:62468600-62479200	Weak transcription	Ovary	ovary
49	chr8:62468600-62479400	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
50	chr8:62468600-62549000	Weak transcription	Right Ventricle	heart

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