Variant report

Variant	rs2280779
Chromosome Location	chr8:90961615-90961616
allele	C/T
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	IRF1	chr8:90961609-90962000	K562	blood:	n/a	chr8:90961764-90961777 chr8:90961765-90961777 chr8:90961763-90961780 chr8:90961765-90961782 chr8:90961762-90961776 chr8:90961764-90961777 chr8:90961766-90961780 chr8:90961758-90961778 chr8:90961764-90961778 chr8:90961766-90961776 chr8:90961767-90961778 chr8:90961766-90961777 chr8:90961764-90961777 chr8:90961763-90961777

No.	Distal block	Cell Line	Cell type
1	chr8:90961129..90964552-chr8:90965641..90969617,4	K562	blood:
2	chr8:90801163..90803261-chr8:90961126..90962760,2	MCF-7	breast:
3	chr8:90961019..90964644-chr8:90995252..90998339,3	MCF-7	breast:
4	chr8:90960549..90963013-chr8:91657884..91660323,2	K562	blood:
5	chr8:90961168..90963768-chr8:90966157..90968949,2	MCF-7	breast:
6	chr8:90913045..90914972-chr8:90961075..90963494,3	MCF-7	breast:

Variant related genes	Relation type
NBN	TF binding region
ENSG00000180694	Chromatin interaction
ENSG00000104320	Chromatin interaction
ENSG00000164823	Chromatin interaction
ENSG00000246792	Chromatin interaction
ENSG00000207359	Chromatin interaction

Extended variants
information (count: 61 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:59)

rs_ID	r²[population]
rs10435550	1.00[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs10435551	0.81[AMR][1000 genomes];1.00[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs10504888	1.00[CEU][hapmap];0.92[CHB][hapmap];0.92[JPT][hapmap];0.86[AMR][1000 genomes];1.00[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs12675530	0.92[JPT][hapmap];0.93[MEX][hapmap]
rs13312921	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs13312954	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1468078	0.83[JPT][hapmap]
rs16893166	0.92[CHB][hapmap];0.83[JPT][hapmap];1.00[LWK][hapmap];0.84[MEX][hapmap]
rs16901941	1.00[CEU][hapmap];1.00[CHB][hapmap];0.94[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs16902273	1.00[CEU][hapmap];0.92[CHB][hapmap];0.82[CHD][hapmap];1.00[GIH][hapmap];0.92[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];1.00[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs16902355	1.00[CEU][hapmap];0.92[CHB][hapmap];0.92[JPT][hapmap];0.86[AMR][1000 genomes];1.00[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs16902558	1.00[CEU][hapmap];0.92[CHB][hapmap];0.92[JPT][hapmap];0.81[AMR][1000 genomes];1.00[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs16903927	1.00[AFR][1000 genomes]
rs16904011	1.00[AFR][1000 genomes]
rs16904016	1.00[AFR][1000 genomes]
rs1805811	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1805815	0.89[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1805824	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1805826	1.00[CEU][hapmap];1.00[CHB][hapmap];0.94[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1805837	1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1805839	1.00[CEU][hapmap];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1805850	1.00[AFR][1000 genomes];0.90[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs1805855	1.00[CEU][hapmap];0.92[CHB][hapmap];0.82[CHD][hapmap];1.00[GIH][hapmap];0.92[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.86[AMR][1000 genomes];1.00[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs1805862	1.00[CEU][hapmap];0.92[CHB][hapmap];0.92[JPT][hapmap];0.86[AMR][1000 genomes];1.00[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs1805880	1.00[CEU][hapmap];0.92[CHB][hapmap];0.92[JPT][hapmap];0.86[AMR][1000 genomes];1.00[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs1805882	1.00[CEU][hapmap];0.92[CHB][hapmap];0.92[JPT][hapmap];0.86[AMR][1000 genomes];1.00[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs1805885	1.00[CEU][hapmap];0.92[CHB][hapmap];1.00[GIH][hapmap];0.92[JPT][hapmap];1.00[LWK][hapmap];0.92[MEX][hapmap];1.00[TSI][hapmap];0.86[AMR][1000 genomes];1.00[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs1805888	1.00[CEU][hapmap];0.92[CHB][hapmap];0.82[CHD][hapmap];1.00[GIH][hapmap];0.92[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.86[AMR][1000 genomes];1.00[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs1805892	0.81[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs1805894	0.86[CHB][hapmap];0.92[JPT][hapmap];0.81[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs1805901	0.86[CHB][hapmap];0.92[JPT][hapmap];0.81[EUR][1000 genomes]
rs1805902	0.86[CHB][hapmap];0.84[JPT][hapmap];0.81[EUR][1000 genomes]
rs1805907	0.86[CHB][hapmap];0.85[JPT][hapmap];0.81[EUR][1000 genomes]
rs1805911	0.86[CHB][hapmap];0.92[JPT][hapmap];0.81[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs1805912	0.92[JPT][hapmap];0.81[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs1805914	0.86[CHB][hapmap];0.92[JPT][hapmap];0.81[EUR][1000 genomes]
rs1805915	0.86[CHB][hapmap];0.92[JPT][hapmap];0.81[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs2074594	1.00[CEU][hapmap];0.92[CHB][hapmap];0.92[JPT][hapmap];0.86[AMR][1000 genomes];1.00[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs2074595	1.00[CEU][hapmap];0.92[CHB][hapmap];0.92[JPT][hapmap];0.86[AMR][1000 genomes];1.00[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2267542	0.86[AMR][1000 genomes];1.00[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs3026287	0.86[CHB][hapmap];0.92[JPT][hapmap];0.81[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs3358	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs3758145	0.92[JPT][hapmap]
rs4477076	0.81[EUR][1000 genomes]
rs6982611	1.00[AFR][1000 genomes]
rs6989727	0.82[AMR][1000 genomes];1.00[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs6997558	1.00[AFR][1000 genomes]
rs73306482	1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs769418	1.00[CEU][hapmap];1.00[CHB][hapmap];0.94[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7813378	1.00[CEU][hapmap];0.92[CHB][hapmap];0.92[JPT][hapmap];0.86[AMR][1000 genomes];1.00[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs7818138	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7822786	1.00[CEU][hapmap];0.92[CHB][hapmap];0.92[JPT][hapmap];0.86[AMR][1000 genomes];1.00[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs7826471	1.00[CEU][hapmap];0.92[CHB][hapmap];0.92[JPT][hapmap];0.81[AMR][1000 genomes];1.00[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs7830738	0.84[CHB][hapmap];0.83[ASN][1000 genomes]
rs7834282	0.81[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs7844005	1.00[CEU][hapmap];0.92[CHB][hapmap];0.82[CHD][hapmap];1.00[GIH][hapmap];0.92[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.86[AMR][1000 genomes];1.00[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs7845155	1.00[CEU][hapmap];0.92[CHB][hapmap];0.92[JPT][hapmap];0.86[AMR][1000 genomes];1.00[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs7845572	0.86[AMR][1000 genomes];0.96[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs7845669	1.00[CEU][hapmap];0.92[CHB][hapmap];0.92[JPT][hapmap];0.86[AMR][1000 genomes];1.00[EUR][1000 genomes];0.88[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:2 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv933502	chr8:90702392-91049100	Weak transcription Enhancers Active TSS Strong transcription Genic enhancers Flanking Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	62 gene(s)	inside rSNPs	diseases
2	nsv934114	chr8:90720182-90999106	Active TSS Weak transcription Enhancers Flanking Active TSS Strong transcription Transcr. at gene 5' and 3' ZNF genes & repeats Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	58 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:124 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr8:90915400-90966800	Weak transcription	Placenta Amnion	Placenta Amnion
2	chr8:90915800-90995000	Weak transcription	Fetal Brain Male	brain
3	chr8:90916600-90969600	Weak transcription	Brain Substantia Nigra	brain
4	chr8:90917600-90975400	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
5	chr8:90924800-90986600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
6	chr8:90925400-90970200	Weak transcription	Pancreas	Pancrea
7	chr8:90925400-90979200	Weak transcription	Gastric	stomach
8	chr8:90925600-90967200	Weak transcription	Colonic Mucosa	Colon
9	chr8:90925600-90975200	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
10	chr8:90927000-90978000	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
11	chr8:90927200-90964200	Weak transcription	Cortex derived primary cultured neurospheres	brain
12	chr8:90927600-90988400	Weak transcription	ES-I3 Cell Line	embryonic stem cell
13	chr8:90927800-90963800	Weak transcription	NHEK	skin
14	chr8:90927800-90969800	Weak transcription	Esophagus	oesophagus
15	chr8:90927800-90970200	Weak transcription	Spleen	Spleen
16	chr8:90927800-90970400	Weak transcription	Right Ventricle	heart
17	chr8:90927800-90996000	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
18	chr8:90928000-90965200	Weak transcription	Fetal Kidney	kidney
19	chr8:90928000-90970400	Weak transcription	Small Intestine	intestine
20	chr8:90929400-90966000	Weak transcription	Skeletal Muscle Male	skeletal muscle
21	chr8:90931600-90965200	Weak transcription	HepG2	liver
22	chr8:90934000-90965400	Weak transcription	Fetal Brain Female	brain
23	chr8:90937200-90969800	Weak transcription	Brain Cingulate Gyrus	brain
24	chr8:90937200-90970400	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
25	chr8:90937200-90970400	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
26	chr8:90937600-90969400	Weak transcription	H1 Cell Line	embryonic stem cell
27	chr8:90937600-90970000	Weak transcription	Lung	lung
28	chr8:90938200-90974600	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
29	chr8:90938400-90970000	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
30	chr8:90938800-90963000	Weak transcription	iPS-18 Cell Line	embryonic stem cell
31	chr8:90939000-90964800	Weak transcription	HUES6 Cell Line	embryonic stem cell
32	chr8:90941400-90970000	Weak transcription	Brain Germinal Matrix	brain
33	chr8:90942600-90977400	Weak transcription	iPS-15b Cell Line	embryonic stem cell
34	chr8:90942600-90982600	Strong transcription	Primary monocytes fromperipheralblood	blood
35	chr8:90942800-90970000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
36	chr8:90944400-90977000	Strong transcription	Dnd41	blood
37	chr8:90944400-90982800	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
38	chr8:90944600-90982000	Strong transcription	Monocytes-CD14+_RO01746	blood
39	chr8:90944800-90984400	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
40	chr8:90947200-90964400	Weak transcription	HMEC	breast
41	chr8:90947200-90964600	Weak transcription	Brain Hippocampus Middle	brain
42	chr8:90947200-90969800	Weak transcription	Brain Angular Gyrus	brain
43	chr8:90947400-90965400	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
44	chr8:90948200-90974000	Weak transcription	Primary T helper naive cells from peripheral blood	blood
45	chr8:90952200-90970400	Weak transcription	Brain Inferior Temporal Lobe	brain
46	chr8:90952600-90964200	Weak transcription	Left Ventricle	heart
47	chr8:90952600-90966400	Weak transcription	Sigmoid Colon	Sigmoid Colon
48	chr8:90952600-90966800	Weak transcription	Thymus	Thymus
49	chr8:90952800-90961800	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
50	chr8:90952800-90967000	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung

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