Variant report

Variant	rs2805777
Chromosome Location	chr9:100381034-100381035
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr9:100380827..100383668-chr9:100385010..100387087,2	K562	blood:
2	chr9:100371893..100374516-chr9:100380257..100382614,2	MCF-7	breast:
3	chr9:100379940..100382784-chr9:100394672..100397527,3	MCF-7	breast:

Variant related genes	Relation type
ENSG00000136937	Chromatin interaction
ENSG00000136925	Chromatin interaction

Extended variants
information (count: 39 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:36)

rs_ID	r²[population]
rs10983030	1.00[CEU][hapmap];0.99[EUR][1000 genomes]
rs10983035	0.83[CHD][hapmap];0.95[JPT][hapmap];0.80[ASN][1000 genomes]
rs10983447	0.84[EUR][1000 genomes]
rs12375457	0.84[ASN][1000 genomes]
rs1800975	1.00[CEU][hapmap];0.83[GIH][hapmap];1.00[TSI][hapmap];0.87[EUR][1000 genomes]
rs2026132	1.00[CEU][hapmap];0.83[GIH][hapmap];0.97[TSI][hapmap];0.97[EUR][1000 genomes]
rs2036959	0.84[CEU][hapmap];0.81[EUR][1000 genomes]
rs2480721	0.80[ASN][1000 genomes]
rs2668792	0.92[CEU][hapmap]
rs2668793	0.81[EUR][1000 genomes]
rs2668798	0.84[EUR][1000 genomes]
rs2773347	1.00[CEU][hapmap];0.83[GIH][hapmap];1.00[TSI][hapmap];0.96[EUR][1000 genomes]
rs2773351	1.00[CEU][hapmap];0.98[EUR][1000 genomes]
rs2773357	0.88[ASN][1000 genomes]
rs2805767	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];0.95[TSI][hapmap];1.00[YRI][hapmap];0.93[AFR][1000 genomes];0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2805775	1.00[AFR][1000 genomes];0.99[EUR][1000 genomes]
rs2805779	0.96[CEU][hapmap];0.83[GIH][hapmap];1.00[TSI][hapmap];0.99[EUR][1000 genomes]
rs2805824	0.92[CEU][hapmap]
rs2805826	0.81[EUR][1000 genomes]
rs2805828	1.00[CEU][hapmap];0.82[GIH][hapmap];1.00[TSI][hapmap];0.87[EUR][1000 genomes]
rs2805829	0.87[EUR][1000 genomes]
rs2805832	0.86[EUR][1000 genomes]
rs2805837	1.00[CEU][hapmap];0.83[GIH][hapmap];0.97[TSI][hapmap];0.87[EUR][1000 genomes]
rs2805839	1.00[CEU][hapmap];0.83[GIH][hapmap];0.97[TSI][hapmap];0.84[EUR][1000 genomes]
rs2808668	1.00[CEU][hapmap];0.87[EUR][1000 genomes]
rs2808673	1.00[CEU][hapmap];0.82[GIH][hapmap];1.00[TSI][hapmap];0.87[EUR][1000 genomes]
rs2808675	1.00[CEU][hapmap];0.82[GIH][hapmap];1.00[TSI][hapmap];0.87[EUR][1000 genomes]
rs2808677	1.00[CEU][hapmap];0.86[EUR][1000 genomes]
rs2808685	0.81[EUR][1000 genomes]
rs2808686	0.92[CEU][hapmap];0.82[GIH][hapmap];0.87[TSI][hapmap];0.81[EUR][1000 genomes]
rs2808703	0.87[EUR][1000 genomes]
rs3176689	0.82[CHB][hapmap];0.95[JPT][hapmap]
rs3994138	0.87[JPT][hapmap]
rs6478325	0.83[AFR][1000 genomes];0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7853179	0.83[JPT][hapmap]
rs958346	0.96[CEU][hapmap];0.83[GIH][hapmap];0.95[TSI][hapmap];0.91[EUR][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	nsv1039240	chr9:100292680-100415269	Weak transcription Strong transcription Genic enhancers Flanking Active TSS Enhancers Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	27 gene(s)	inside rSNPs	diseases
2	nsv540179	chr9:100292680-100415269	Genic enhancers Strong transcription Weak transcription Active TSS Enhancers Flanking Active TSS Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	27 gene(s)	inside rSNPs	diseases
3	nsv893610	chr9:100324086-100496160	Active TSS Strong transcription Enhancers ZNF genes & repeats Weak transcription Genic enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	32 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs2805777	XPA	cis	parietal	SCAN

Chromatin state (count:126 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr9:100348800-100384000	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
2	chr9:100361000-100381200	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
3	chr9:100361800-100383400	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
4	chr9:100361800-100389000	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
5	chr9:100361800-100394000	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
6	chr9:100363000-100394600	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
7	chr9:100365200-100382200	Weak transcription	ES-I3 Cell Line	embryonic stem cell
8	chr9:100365800-100389400	Weak transcription	Stomach Mucosa	stomach
9	chr9:100367400-100386200	Weak transcription	Primary T killer memory cells from peripheral blood	blood
10	chr9:100367400-100387000	Weak transcription	HMEC	breast
11	chr9:100367600-100384000	Weak transcription	iPS-15b Cell Line	embryonic stem cell
12	chr9:100367600-100390400	Weak transcription	Small Intestine	intestine
13	chr9:100367800-100383800	Weak transcription	A549	lung
14	chr9:100367800-100384000	Weak transcription	Aorta	Aorta
15	chr9:100367800-100384400	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
16	chr9:100368200-100386200	Weak transcription	Esophagus	oesophagus
17	chr9:100368200-100394000	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
18	chr9:100368200-100394200	Weak transcription	Primary neutrophils fromperipheralblood	blood
19	chr9:100368400-100384000	Weak transcription	Pancreas	Pancrea
20	chr9:100368400-100387800	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
21	chr9:100368400-100394000	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
22	chr9:100369000-100386400	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
23	chr9:100369000-100388200	Strong transcription	Fetal Muscle Leg	muscle
24	chr9:100369600-100382600	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
25	chr9:100371000-100382400	Weak transcription	Fetal Intestine Small	intestine
26	chr9:100371200-100382800	Strong transcription	HUES64 Cell Line	embryonic stem cell
27	chr9:100372200-100388200	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
28	chr9:100372800-100383200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
29	chr9:100372800-100387600	Weak transcription	Psoas Muscle	Psoas
30	chr9:100372800-100394000	Weak transcription	Colonic Mucosa	Colon
31	chr9:100373000-100383800	Weak transcription	Placenta Amnion	Placenta Amnion
32	chr9:100373000-100389400	Weak transcription	Pancreatic Islets	Pancreatic Islet
33	chr9:100373200-100386600	Weak transcription	HUVEC	blood vessel
34	chr9:100373400-100389400	Weak transcription	NHDF-Ad	bronchial
35	chr9:100373800-100382400	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
36	chr9:100373800-100383800	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
37	chr9:100374000-100383200	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
38	chr9:100374000-100383800	Weak transcription	H9 Cell Line	embryonic stem cell
39	chr9:100374000-100386200	Weak transcription	Osteobl	bone
40	chr9:100374000-100394000	Weak transcription	Muscle Satellite Cultured Cells	--
41	chr9:100374200-100383200	Weak transcription	Ovary	ovary
42	chr9:100374200-100384400	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
43	chr9:100374400-100382800	Weak transcription	Lung	lung
44	chr9:100374400-100386200	Weak transcription	Primary T helper naive cells from peripheral blood	blood
45	chr9:100374600-100393800	Weak transcription	Fetal Kidney	kidney
46	chr9:100375600-100387600	Weak transcription	NH-A	brain
47	chr9:100376000-100382400	Weak transcription	Duodenum Mucosa	Duodenum
48	chr9:100376000-100382600	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
49	chr9:100376000-100387400	Weak transcription	Brain Substantia Nigra	brain
50	chr9:100376400-100383600	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived

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