Variant report

Variant	rs56901035
Chromosome Location	chr8:96043188-96043189
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	EBF1	chr8:96043161-96043321	GM12878	blood:	n/a	chr8:96043235-96043246
2	EBF1	chr8:96043072-96043349	GM12878	blood:	n/a	chr8:96043235-96043246
3	USF2	chr8:96043051-96043188	GM12878	blood:	n/a	n/a
4	EBF1	chr8:96043051-96043336	GM12878	blood:	n/a	chr8:96043235-96043246

No.	Distal block	Cell Line	Cell type
1	chr8:96042773..96045129-chr8:96053091..96055278,3	K562	blood:
2	chr8:96041290..96045030-chr8:96046427..96048931,4	MCF-7	breast:
3	chr8:96041538..96045239-chr8:96047596..96052623,5	K562	blood:
4	chr8:96035744..96039512-chr8:96039788..96046844,8	K562	blood:
5	chr8:96040889..96043562-chr8:96144686..96147417,3	MCF-7	breast:
6	chr8:95905480..95909063-chr8:96040642..96043498,3	MCF-7	breast:

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

Extended variants
information (count: 79 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:76)

rs_ID	r²[population]
rs10086541	0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10092003	0.88[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10093594	0.88[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10096455	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10097930	0.97[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs10098197	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10098453	0.97[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs10100089	0.97[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs10103841	0.86[EUR][1000 genomes]
rs10105437	0.88[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10106491	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10110635	0.97[EUR][1000 genomes]
rs10111154	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10111300	0.97[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs10112230	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10113545	0.97[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs1031388	1.00[ASN][1000 genomes]
rs11774085	0.90[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs11776189	0.88[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11779506	0.93[ASN][1000 genomes]
rs11780931	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11781001	0.88[AMR][1000 genomes];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11781040	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11781619	0.87[EUR][1000 genomes]
rs11784178	0.88[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs11786380	0.96[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs11786878	0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13279040	0.87[ASN][1000 genomes]
rs1545480	0.93[ASN][1000 genomes]
rs16917224	0.88[AMR][1000 genomes];0.97[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs16917233	0.88[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2340536	0.87[EUR][1000 genomes]
rs2599711	0.93[ASN][1000 genomes]
rs2599713	1.00[ASN][1000 genomes]
rs2599714	1.00[ASN][1000 genomes]
rs2599715	1.00[ASN][1000 genomes]
rs2678823	1.00[ASN][1000 genomes]
rs2678829	0.93[ASN][1000 genomes]
rs28363725	0.97[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs28378156	0.97[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs28406132	0.88[AMR][1000 genomes];0.97[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs28419772	0.88[AMR][1000 genomes];0.94[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs28440026	0.97[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs28477467	0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28496357	0.96[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs28616734	0.88[AMR][1000 genomes];0.94[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs28651964	0.88[AMR][1000 genomes];0.97[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs28712702	0.97[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs34700722	0.93[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs35518242	0.87[ASN][1000 genomes]
rs4323442	0.93[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs57925408	0.80[AMR][1000 genomes];0.99[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs61596977	0.86[EUR][1000 genomes]
rs6471505	0.97[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs6471506	0.96[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs6651271	0.90[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6651272	0.90[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6985880	0.97[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs6989862	0.97[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7002940	0.96[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7008542	0.97[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs71532343	0.87[ASN][1000 genomes]
rs73276406	0.88[AMR][1000 genomes];0.87[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs73276417	0.97[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs73276437	0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73276439	0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73276444	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7812312	0.88[AMR][1000 genomes];0.94[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7818688	0.88[AMR][1000 genomes];0.97[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7826046	0.83[ASN][1000 genomes]
rs7826196	0.97[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7832570	0.88[AMR][1000 genomes];0.97[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7842703	0.83[ASN][1000 genomes]
rs7842715	0.94[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs9297950	0.88[AMR][1000 genomes];0.96[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs9297951	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[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:2)

SNP	Gene	Cis/trans	Tissue	Source
rs56901035	INTS8	Cis_1M	lymphoblastoid	RTeQTL
rs56901035	C8orf38	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:119 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr8:96037800-96070200	Weak transcription	Aorta	Aorta
2	chr8:96038000-96063800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
3	chr8:96038200-96043200	Weak transcription	Fetal Lung	lung
4	chr8:96038200-96045000	Weak transcription	Rectal Mucosa Donor 31	rectum
5	chr8:96038200-96045400	Weak transcription	Ovary	ovary
6	chr8:96038200-96046000	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
7	chr8:96038200-96050200	Weak transcription	Spleen	Spleen
8	chr8:96038200-96054400	Weak transcription	Fetal Kidney	kidney
9	chr8:96038200-96058800	Weak transcription	Placenta Amnion	Placenta Amnion
10	chr8:96038200-96059200	Weak transcription	Right Ventricle	heart
11	chr8:96038200-96061000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
12	chr8:96038200-96061200	Weak transcription	H9 Cell Line	embryonic stem cell
13	chr8:96038200-96061200	Weak transcription	Psoas Muscle	Psoas
14	chr8:96038200-96072400	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
15	chr8:96038200-96080000	Weak transcription	Colonic Mucosa	Colon
16	chr8:96038400-96043200	Weak transcription	Skeletal Muscle Male	skeletal muscle
17	chr8:96038400-96044200	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
18	chr8:96038400-96044400	Weak transcription	HUES48 Cell Line	embryonic stem cell
19	chr8:96038400-96044400	Weak transcription	HUES64 Cell Line	embryonic stem cell
20	chr8:96038400-96044400	Weak transcription	Stomach Smooth Muscle	stomach
21	chr8:96038400-96044400	Weak transcription	HSMM	muscle
22	chr8:96038400-96044600	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
23	chr8:96038400-96044600	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
24	chr8:96038400-96044600	Weak transcription	Adipose Nuclei	Adipose
25	chr8:96038400-96044600	Weak transcription	Duodenum Mucosa	Duodenum
26	chr8:96038400-96044800	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
27	chr8:96038400-96044800	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
28	chr8:96038400-96044800	Weak transcription	Brain Anterior Caudate	brain
29	chr8:96038400-96044800	Weak transcription	Brain Inferior Temporal Lobe	brain
30	chr8:96038400-96044800	Weak transcription	Placenta	Placenta
31	chr8:96038400-96044800	Weak transcription	Rectal Mucosa Donor 29	rectum
32	chr8:96038400-96045400	Weak transcription	Brain Germinal Matrix	brain
33	chr8:96038400-96045600	Weak transcription	Duodenum Smooth Muscle	Duodenum
34	chr8:96038400-96045600	Weak transcription	NHEK	skin
35	chr8:96038400-96045800	Weak transcription	iPS-18 Cell Line	embryonic stem cell
36	chr8:96038400-96046000	Weak transcription	Rectal Smooth Muscle	rectum
37	chr8:96038400-96048600	Weak transcription	Osteobl	bone
38	chr8:96038400-96054000	Weak transcription	Muscle Satellite Cultured Cells	--
39	chr8:96038400-96054000	Weak transcription	HUVEC	blood vessel
40	chr8:96038400-96054200	Weak transcription	Fetal Heart	heart
41	chr8:96038400-96054200	Weak transcription	NH-A	brain
42	chr8:96038400-96054200	Weak transcription	NHDF-Ad	bronchial
43	chr8:96038400-96054400	Weak transcription	Colon Smooth Muscle	Colon
44	chr8:96038400-96055000	Weak transcription	HSMMtube	muscle
45	chr8:96038400-96060600	Weak transcription	NHLF	lung
46	chr8:96038400-96061000	Weak transcription	iPS-15b Cell Line	embryonic stem cell
47	chr8:96038400-96063600	Weak transcription	ES-I3 Cell Line	embryonic stem cell
48	chr8:96038400-96066800	Weak transcription	Stomach Mucosa	stomach
49	chr8:96038400-96085200	Weak transcription	Pancreatic Islets	Pancreatic Islet
50	chr8:96038600-96044200	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived

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