Variant report

Variant	rs3860883
Chromosome Location	chr8:118934480-118934481
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 44 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:35)

rs_ID	r²[population]
rs10098363	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1125103	0.84[CEU][hapmap]
rs11777220	0.94[EUR][1000 genomes]
rs11780699	0.84[CEU][hapmap]
rs11781245	0.84[CEU][hapmap]
rs13251463	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs13252084	0.82[CHB][hapmap];0.88[ASN][1000 genomes]
rs1542519	0.92[GIH][hapmap]
rs2447535	0.80[CEU][hapmap]
rs2447536	0.83[CEU][hapmap]
rs2447537	0.84[CEU][hapmap]
rs2447538	0.83[CEU][hapmap]
rs2447539	0.83[CEU][hapmap]
rs2447540	0.88[CEU][hapmap];0.85[GIH][hapmap]
rs2447541	0.88[CEU][hapmap];0.92[GIH][hapmap];0.80[EUR][1000 genomes]
rs2514719	0.80[CEU][hapmap]
rs2514720	0.84[CEU][hapmap]
rs3101574	0.84[CEU][hapmap]
rs4298514	0.84[CEU][hapmap];0.95[CHB][hapmap];1.00[CHD][hapmap];0.95[GIH][hapmap];0.95[JPT][hapmap];0.87[MEX][hapmap];0.99[ASN][1000 genomes]
rs4467961	0.91[ASW][hapmap];0.96[CEU][hapmap];0.81[CHD][hapmap];1.00[GIH][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.85[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs4475517	0.88[ASN][1000 genomes]
rs4480148	0.82[CHB][hapmap];0.89[CHD][hapmap];0.82[JPT][hapmap];0.88[ASN][1000 genomes]
rs4541958	0.84[CEU][hapmap];0.85[GIH][hapmap]
rs4621831	0.82[CHB][hapmap];0.89[CHD][hapmap];0.88[ASN][1000 genomes]
rs4644291	0.95[CHB][hapmap];0.90[JPT][hapmap];0.99[ASN][1000 genomes]
rs4876771	1.00[CEU][hapmap];0.95[CHB][hapmap];0.85[JPT][hapmap];0.95[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4876775	0.81[CHB][hapmap];0.85[ASN][1000 genomes]
rs4876777	0.80[CEU][hapmap]
rs4876783	0.87[GIH][hapmap]
rs4876784	0.85[GIH][hapmap]
rs6469718	0.84[CEU][hapmap];0.95[CHB][hapmap];0.95[JPT][hapmap];0.99[ASN][1000 genomes]
rs6981592	0.82[JPT][hapmap]
rs7812722	0.83[CEU][hapmap];0.91[CHB][hapmap];0.98[CHD][hapmap];0.97[GIH][hapmap];0.95[JPT][hapmap];0.86[MEX][hapmap];0.95[ASN][1000 genomes]
rs7841914	0.82[JPT][hapmap]
rs958381	0.84[CEU][hapmap];0.82[GIH][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	nsv1019636	chr8:118598433-118946091	Enhancers Weak transcription Genic enhancers Strong transcription Flanking Active TSS ZNF genes & repeats Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
2	nsv539734	chr8:118598433-118946091	Weak transcription Enhancers Strong transcription Flanking Active TSS Genic enhancers ZNF genes & repeats Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
3	nsv933516	chr8:118764605-119009093	Weak transcription Enhancers Genic enhancers Bivalent Enhancer Strong transcription Flanking Active TSS ZNF genes & repeats Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
4	nsv1030459	chr8:118840179-119155835	Weak transcription Flanking Active TSS Enhancers Active TSS Genic enhancers Strong transcription Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	14 gene(s)	inside rSNPs	diseases
5	nsv831440	chr8:118871930-119052269	Weak transcription Enhancers Flanking Active TSS Genic enhancers ZNF genes & repeats Bivalent Enhancer Active TSS Strong transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
6	nsv891411	chr8:118891896-118942698	Weak transcription Genic enhancers Enhancers Flanking Active TSS Strong transcription Bivalent Enhancer Active TSS ZNF genes & repeats	Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
7	nsv1032355	chr8:118896733-119003223	Weak transcription Enhancers Flanking Active TSS Active TSS Genic enhancers Strong transcription Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS	Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
8	nsv465785	chr8:118901928-118970300	Enhancers Weak transcription Flanking Active TSS Strong transcription Active TSS Genic enhancers Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS	Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
9	nsv612046	chr8:118901928-118970300	Weak transcription Enhancers Genic enhancers ZNF genes & repeats Bivalent Enhancer Active TSS Flanking Active TSS Strong transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS	Chromatin interactive region	1 gene(s)	inside rSNPs	diseases

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs3860883	NOV	cis	cerebellum	SCAN
rs3860883	MED30	cis	parietal	SCAN
rs3860883	SNTB1	cis	parietal	SCAN
rs3860883	MAL2	cis	cerebellum	SCAN

Chromatin state (count:68 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr8:118922800-118934800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
2	chr8:118927000-118935000	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
3	chr8:118931000-118935000	Weak transcription	Pancreas	Pancrea
4	chr8:118932000-118935200	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
5	chr8:118932400-118935200	Enhancers	iPS-20b Cell Line	embryonic stem cell
6	chr8:118932400-118935400	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
7	chr8:118932400-118935400	Enhancers	NHDF-Ad	bronchial
8	chr8:118932600-118934600	Enhancers	Fetal Lung	lung
9	chr8:118932600-118934600	Enhancers	NHLF	lung
10	chr8:118932600-118935000	Enhancers	HUES48 Cell Line	embryonic stem cell
11	chr8:118932600-118935000	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
12	chr8:118932600-118935000	Enhancers	Fetal Heart	heart
13	chr8:118932600-118935200	Enhancers	ES-I3 Cell Line	embryonic stem cell
14	chr8:118932600-118935200	Enhancers	HUES6 Cell Line	embryonic stem cell
15	chr8:118932600-118935200	Enhancers	HUES64 Cell Line	embryonic stem cell
16	chr8:118932600-118935400	Enhancers	Muscle Satellite Cultured Cells	--
17	chr8:118932600-118937000	Enhancers	HSMM	muscle
18	chr8:118932800-118934600	Enhancers	H1 Cell Line	embryonic stem cell
19	chr8:118932800-118934600	Enhancers	GM12878-XiMat	blood
20	chr8:118932800-118935000	Enhancers	Fetal Adrenal Gland	Adrenal Gland
21	chr8:118932800-118935000	Enhancers	HUVEC	blood vessel
22	chr8:118932800-118935200	Enhancers	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
23	chr8:118932800-118935200	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
24	chr8:118932800-118935200	Enhancers	Liver	Liver
25	chr8:118932800-118935200	Enhancers	A549	lung
26	chr8:118933000-118934800	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
27	chr8:118933000-118934800	Enhancers	iPS-18 Cell Line	embryonic stem cell
28	chr8:118933000-118935000	Enhancers	Cortex derived primary cultured neurospheres	brain
29	chr8:118933000-118935000	Enhancers	Colon Smooth Muscle	Colon
30	chr8:118933000-118935200	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
31	chr8:118933000-118935200	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
32	chr8:118933200-118934800	Weak transcription	Esophagus	oesophagus
33	chr8:118933200-118934800	Weak transcription	Skeletal Muscle Female	skeletal muscle
34	chr8:118933200-118935200	Enhancers	ES-WA7 Cell Line	embryonic stem cell
35	chr8:118933200-118935400	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
36	chr8:118933200-118935400	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
37	chr8:118933200-118935400	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
38	chr8:118933200-118936000	Weak transcription	Breast Myoepithelial Primary Cells	Breast
39	chr8:118933200-118943800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
40	chr8:118933200-118946600	Weak transcription	Gastric	stomach
41	chr8:118933400-118940800	Enhancers	Osteobl	bone
42	chr8:118933600-118935200	Enhancers	NHEK	skin
43	chr8:118933600-118935400	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
44	chr8:118933600-118937000	Enhancers	Foreskin Fibroblast Primary Cells skin02	Skin
45	chr8:118933600-118938600	Weak transcription	Small Intestine	intestine
46	chr8:118933600-118938800	Weak transcription	Fetal Muscle Leg	muscle
47	chr8:118933600-118938800	Weak transcription	HSMMtube	muscle
48	chr8:118933600-118940000	Weak transcription	Sigmoid Colon	Sigmoid Colon
49	chr8:118933600-118941400	Weak transcription	H9 Cell Line	embryonic stem cell
50	chr8:118933600-118945600	Weak transcription	Stomach Smooth Muscle	stomach

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