Variant report

Variant	rs10086541
Chromosome Location	chr8:96033950-96033951
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:3)
CpG islands
(count:0)
Chromatin interactive
region (count:8)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:3 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	RAD21	chr8:96033889-96034261	HepG2	liver:	n/a	n/a
2	MAZ	chr8:96033735-96034080	HepG2	liver:	n/a	n/a
3	FOXA1	chr8:96033908-96034294	HepG2	liver:	n/a	n/a

No data

(count:8 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr8:96029908..96032695-chr8:96032996..96034738,2	K562	blood:
2	chr8:96033821..96037970-chr8:96145284..96149341,6	MCF-7	breast:
3	chr8:96029908..96032764-chr8:96033238..96034870,2	K562	blood:
4	chr8:96032678..96034884-chr8:96035365..96037674,4	K562	blood:
5	chr8:95905055..95911257-chr8:96032486..96039313,18	MCF-7	breast:
6	chr8:96033508..96040236-chr8:96084539..96089897,8	MCF-7	breast:
7	chr8:95962646..95965102-chr8:96032516..96035099,2	MCF-7	breast:
8	chr8:95959565..95963058-chr8:96031680..96034201,4	MCF-7	breast:

No data

Variant related genes	Relation type
NDUFAF6	TF binding region
ENSG00000175895	Chromatin interaction
ENSG00000164938	Chromatin interaction
ENSG00000175305	Chromatin interaction
ENSG00000253878	Chromatin interaction
ENSG00000156170	Chromatin interaction
ENSG00000245080	Chromatin interaction

Extended variants
information (count: 91 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:88)

rs_ID	r²[population]
rs10087402	0.87[GIH][hapmap]
rs10089123	0.87[GIH][hapmap]
rs10092003	1.00[CEU][hapmap];0.89[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.83[MKK][hapmap];1.00[TSI][hapmap];0.88[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10093594	1.00[CEU][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.86[LWK][hapmap];1.00[MEX][hapmap];0.83[MKK][hapmap];1.00[TSI][hapmap];0.88[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10096455	1.00[CEU][hapmap];1.00[JPT][hapmap];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10097930	1.00[CEU][hapmap];0.89[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.92[LWK][hapmap];0.92[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.84[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs10098197	1.00[CEU][hapmap];1.00[JPT][hapmap];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10098453	1.00[CEU][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.93[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.84[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs10100089	0.84[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs10103841	0.95[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs10105437	0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10106491	0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10110635	0.84[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs10111154	1.00[CEU][hapmap];0.89[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.91[MEX][hapmap];0.96[TSI][hapmap];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10111300	1.00[CEU][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.84[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs10112230	0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10113545	0.90[CEU][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.84[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs1031388	1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs10504939	0.81[CEU][hapmap]
rs11774085	0.92[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs11776189	1.00[CEU][hapmap];0.89[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.83[MKK][hapmap];1.00[TSI][hapmap];0.88[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11778553	0.81[CEU][hapmap];0.82[TSI][hapmap]
rs11779506	0.81[CHD][hapmap];0.96[GIH][hapmap];1.00[JPT][hapmap];0.84[MEX][hapmap];0.93[ASN][1000 genomes]
rs11779698	0.81[CEU][hapmap]
rs11780931	1.00[CEU][hapmap];0.89[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.92[MEX][hapmap];0.96[TSI][hapmap];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11781001	0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11781040	1.00[CEU][hapmap];1.00[JPT][hapmap];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11781619	0.90[EUR][1000 genomes]
rs11781757	0.81[CEU][hapmap]
rs11782818	0.81[CEU][hapmap];0.85[TSI][hapmap]
rs11783878	0.81[CEU][hapmap];0.85[TSI][hapmap]
rs11784178	0.89[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs11786380	0.84[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs11786878	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13279040	0.96[GIH][hapmap];1.00[JPT][hapmap];0.92[MEX][hapmap];0.87[ASN][1000 genomes]
rs1545480	0.89[CHD][hapmap];0.92[GIH][hapmap];1.00[JPT][hapmap];0.93[ASN][1000 genomes]
rs16917117	0.87[CEU][hapmap]
rs16917224	1.00[CEU][hapmap];1.00[JPT][hapmap];0.88[AMR][1000 genomes];0.99[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs16917233	1.00[CEU][hapmap];0.89[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.92[MEX][hapmap];1.00[TSI][hapmap];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17665737	0.86[CEU][hapmap]
rs2340536	0.90[EUR][1000 genomes]
rs2599711	1.00[JPT][hapmap];0.93[ASN][1000 genomes]
rs2599713	1.00[ASN][1000 genomes]
rs2599714	1.00[ASN][1000 genomes]
rs2599715	1.00[ASN][1000 genomes]
rs2678823	0.89[CHD][hapmap];0.96[GIH][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs2678829	1.00[CHD][hapmap];0.96[GIH][hapmap];1.00[JPT][hapmap];0.93[ASN][1000 genomes]
rs28363725	0.84[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs28378156	0.84[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs28399553	0.81[CEU][hapmap]
rs28406132	0.88[AMR][1000 genomes];0.99[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs28419772	0.88[AMR][1000 genomes];0.96[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs28440026	0.84[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs28477467	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28496357	1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs28616734	0.88[AMR][1000 genomes];0.96[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs28651964	0.88[AMR][1000 genomes];0.99[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs28712702	0.84[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs34700722	1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs35518242	0.87[ASN][1000 genomes]
rs3802191	0.81[CEU][hapmap];0.85[TSI][hapmap]
rs4323442	1.00[CEU][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs56901035	0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs57925408	0.80[AMR][1000 genomes];0.97[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs61596977	0.89[EUR][1000 genomes]
rs6471505	1.00[CEU][hapmap];1.00[YRI][hapmap];0.84[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs6471506	0.82[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs6651271	1.00[CEU][hapmap];1.00[JPT][hapmap];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6651272	1.00[CEU][hapmap];0.89[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.84[MEX][hapmap];1.00[TSI][hapmap];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6985880	0.84[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs6989862	0.84[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7002940	1.00[CEU][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.84[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7008542	1.00[JPT][hapmap];1.00[YRI][hapmap];0.84[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs71532343	0.87[ASN][1000 genomes]
rs73276406	0.88[AMR][1000 genomes];0.89[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs73276417	0.84[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs73276437	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73276439	0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73276444	0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7812312	1.00[CEU][hapmap];0.89[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.85[MKK][hapmap];0.96[TSI][hapmap];0.88[AMR][1000 genomes];0.96[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7818688	0.88[AMR][1000 genomes];0.99[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7826046	0.95[AMR][1000 genomes];0.83[ASN][1000 genomes]
rs7826196	1.00[CEU][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.93[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.84[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7832570	0.88[AMR][1000 genomes];0.99[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7842703	1.00[AMR][1000 genomes];0.82[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs7842715	1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs9297950	1.00[CEU][hapmap];1.00[JPT][hapmap];0.88[AMR][1000 genomes];0.98[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs9297951	0.93[CEU][hapmap];0.81[CHD][hapmap];1.00[GIH][hapmap];0.83[MEX][hapmap];1.00[TSI][hapmap];0.98[EUR][1000 genomes];1.00[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	nsv1017301	chr8:95273503-96248352	Weak transcription Enhancers Active TSS Flanking Active TSS Flanking Bivalent TSS/Enh Strong transcription Bivalent Enhancer Bivalent/Poised TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	87 gene(s)	inside rSNPs	diseases
2	nsv539680	chr8:95273503-96248352	Enhancers Weak transcription Strong transcription Flanking Active TSS Genic enhancers Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	87 gene(s)	inside rSNPs	diseases
3	nsv508520	chr8:95939373-96140068	Enhancers Weak transcription Strong transcription Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	35 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs10086541	C8orf38	cis	cerebellum	SCAN

Chromatin state (count:44 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr8:96009000-96036400	Weak transcription	Spleen	Spleen
2	chr8:96023400-96036600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
3	chr8:96024800-96036400	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
4	chr8:96026800-96036400	Weak transcription	HMEC	breast
5	chr8:96029600-96036400	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
6	chr8:96029800-96036600	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
7	chr8:96032600-96034200	Enhancers	Left Ventricle	heart
8	chr8:96032600-96034200	Enhancers	Pancreas	Pancrea
9	chr8:96032600-96034400	Enhancers	Liver	Liver
10	chr8:96032600-96034600	Enhancers	HepG2	liver
11	chr8:96032600-96036600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
12	chr8:96032800-96034200	Enhancers	Cortex derived primary cultured neurospheres	brain
13	chr8:96032800-96036400	Weak transcription	Skeletal Muscle Female	skeletal muscle
14	chr8:96032800-96036400	Weak transcription	GM12878-XiMat	blood
15	chr8:96032800-96036600	Weak transcription	Right Ventricle	heart
16	chr8:96033000-96035600	Weak transcription	Breast Myoepithelial Primary Cells	Breast
17	chr8:96033000-96036200	Weak transcription	Primary B cells from cord blood	blood
18	chr8:96033000-96036200	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
19	chr8:96033000-96036200	Weak transcription	Rectal Mucosa Donor 31	rectum
20	chr8:96033000-96036400	Weak transcription	Primary monocytes fromperipheralblood	blood
21	chr8:96033000-96036400	Weak transcription	Primary B cells from peripheral blood	blood
22	chr8:96033000-96036400	Weak transcription	Primary hematopoietic stem cells short term culture	blood
23	chr8:96033000-96036400	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
24	chr8:96033000-96036400	Weak transcription	Fetal Thymus	thymus
25	chr8:96033000-96036400	Weak transcription	Lung	lung
26	chr8:96033000-96036600	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
27	chr8:96033000-96036600	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
28	chr8:96033000-96036600	Weak transcription	Esophagus	oesophagus
29	chr8:96033000-96036600	Weak transcription	Gastric	stomach
30	chr8:96033200-96036200	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
31	chr8:96033200-96036200	Weak transcription	Rectal Mucosa Donor 29	rectum
32	chr8:96033200-96036400	Weak transcription	Primary hematopoietic stem cells	blood
33	chr8:96033200-96036400	Weak transcription	Colon Smooth Muscle	Colon
34	chr8:96033200-96036400	Weak transcription	Monocytes-CD14+_RO01746	blood
35	chr8:96033200-96036600	Weak transcription	Right Atrium	heart
36	chr8:96033400-96036400	Weak transcription	Primary neutrophils fromperipheralblood	blood
37	chr8:96033400-96036400	Weak transcription	Duodenum Mucosa	Duodenum
38	chr8:96033400-96036400	Weak transcription	Stomach Mucosa	stomach
39	chr8:96033600-96034000	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
40	chr8:96033600-96034000	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
41	chr8:96033600-96036600	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
42	chr8:96033600-96036600	Weak transcription	Psoas Muscle	Psoas
43	chr8:96033800-96034200	Enhancers	A549	lung
44	chr8:96033800-96036400	Weak transcription	Adipose Nuclei	Adipose

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