Variant report

Variant	rs2805774
Chromosome Location	chr9:100386186-100386187
allele	A/T
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	chr9:100264233..100266882-chr9:100385504..100387245,2	MCF-7	breast:
3	chr9:100379176..100382054-chr9:100384930..100386612,2	K562	blood:

Variant related genes	Relation type
ENSG00000136925	Chromatin interaction

Extended variants
information (count: 36 )
Associated
traits (count: 5 )

rSNPs within LD-proxies of this variant (count:33)

rs_ID	r²[population]
rs10123528	1.00[JPT][hapmap]
rs10982745	0.85[CHD][hapmap]
rs16922598	1.00[JPT][hapmap]
rs1962592	0.89[AFR][1000 genomes];0.92[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs2149984	0.87[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2245694	1.00[CEU][hapmap];0.94[TSI][hapmap];0.90[EUR][1000 genomes]
rs2254733	0.89[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2773343	1.00[CEU][hapmap];0.85[CHD][hapmap];0.86[GIH][hapmap];0.82[MEX][hapmap];0.94[TSI][hapmap];0.88[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2773344	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.93[AFR][1000 genomes];0.96[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2773349	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2773350	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.94[LWK][hapmap];1.00[MEX][hapmap];0.94[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2773354	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.89[AFR][1000 genomes];0.92[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs2773358	0.94[EUR][1000 genomes]
rs2805768	1.00[JPT][hapmap]
rs2805771	1.00[JPT][hapmap]
rs2805773	1.00[JPT][hapmap]
rs2805778	1.00[JPT][hapmap]
rs2805783	0.86[CEU][hapmap]
rs2805785	1.00[CEU][hapmap];0.90[EUR][1000 genomes]
rs2805786	0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2805787	0.89[EUR][1000 genomes]
rs2805788	0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2805792	0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2805793	0.88[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2805802	0.82[EUR][1000 genomes]
rs2805831	0.92[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.91[GIH][hapmap];1.00[JPT][hapmap];0.84[MEX][hapmap];0.90[MKK][hapmap];0.97[TSI][hapmap];0.89[YRI][hapmap];0.88[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs2805834	0.86[AFR][1000 genomes];0.92[AMR][1000 genomes]
rs2805835	1.00[JPT][hapmap]
rs2808669	0.86[AFR][1000 genomes];0.92[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs2808676	0.89[AFR][1000 genomes];0.87[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs2808682	1.00[JPT][hapmap]
rs7863516	0.88[ASN][1000 genomes]
rs932916	0.87[EUR][1000 genomes];0.88[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	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:5)

SNP	Gene	Cis/trans	Tissue	Source
rs2805774	C9orf89	cis	cerebellum	SCAN
rs2805774	TMOD1	cis	multi-tissue	Pritchard
rs2805774	ZNF367	cis	parietal	SCAN
rs2805774	TBC1D2	cis	parietal	SCAN
rs2805774	TMOD1	cis	cerebellum	SCAN

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr9:100361800-100389000	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
2	chr9:100361800-100394000	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
3	chr9:100363000-100394600	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
4	chr9:100365800-100389400	Weak transcription	Stomach Mucosa	stomach
5	chr9:100367400-100386200	Weak transcription	Primary T killer memory cells from peripheral blood	blood
6	chr9:100367400-100387000	Weak transcription	HMEC	breast
7	chr9:100367600-100390400	Weak transcription	Small Intestine	intestine
8	chr9:100368200-100386200	Weak transcription	Esophagus	oesophagus
9	chr9:100368200-100394000	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
10	chr9:100368200-100394200	Weak transcription	Primary neutrophils fromperipheralblood	blood
11	chr9:100368400-100387800	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
12	chr9:100368400-100394000	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
13	chr9:100369000-100386400	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
14	chr9:100369000-100388200	Strong transcription	Fetal Muscle Leg	muscle
15	chr9:100372200-100388200	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
16	chr9:100372800-100387600	Weak transcription	Psoas Muscle	Psoas
17	chr9:100372800-100394000	Weak transcription	Colonic Mucosa	Colon
18	chr9:100373000-100389400	Weak transcription	Pancreatic Islets	Pancreatic Islet
19	chr9:100373200-100386600	Weak transcription	HUVEC	blood vessel
20	chr9:100373400-100389400	Weak transcription	NHDF-Ad	bronchial
21	chr9:100374000-100386200	Weak transcription	Osteobl	bone
22	chr9:100374000-100394000	Weak transcription	Muscle Satellite Cultured Cells	--
23	chr9:100374400-100386200	Weak transcription	Primary T helper naive cells from peripheral blood	blood
24	chr9:100374600-100393800	Weak transcription	Fetal Kidney	kidney
25	chr9:100375600-100387600	Weak transcription	NH-A	brain
26	chr9:100376000-100387400	Weak transcription	Brain Substantia Nigra	brain
27	chr9:100377400-100394000	Weak transcription	NHEK	skin
28	chr9:100377800-100386200	Weak transcription	Brain Cingulate Gyrus	brain
29	chr9:100377800-100386200	Weak transcription	Fetal Brain Male	brain
30	chr9:100378000-100386200	Weak transcription	Brain Anterior Caudate	brain
31	chr9:100378000-100386200	Weak transcription	K562	blood
32	chr9:100378000-100387600	Weak transcription	Rectal Smooth Muscle	rectum
33	chr9:100378400-100388200	Strong transcription	Fetal Lung	lung
34	chr9:100378400-100388400	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
35	chr9:100378600-100387800	Strong transcription	Skeletal Muscle Female	skeletal muscle
36	chr9:100378600-100388200	Strong transcription	Stomach Smooth Muscle	stomach
37	chr9:100378600-100388400	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
38	chr9:100379000-100386200	Weak transcription	Thymus	Thymus
39	chr9:100379000-100387600	Weak transcription	Rectal Mucosa Donor 31	rectum
40	chr9:100379200-100386400	Weak transcription	Colon Smooth Muscle	Colon
41	chr9:100379200-100388000	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
42	chr9:100379400-100388200	Strong transcription	Primary T cells from cord blood	blood
43	chr9:100380200-100386400	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
44	chr9:100380200-100387600	Weak transcription	Brain Hippocampus Middle	brain
45	chr9:100380400-100386200	Weak transcription	Gastric	stomach
46	chr9:100380400-100386200	Weak transcription	NHLF	lung
47	chr9:100380400-100386800	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
48	chr9:100380400-100394400	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
49	chr9:100381200-100388200	Strong transcription	Fetal Brain Female	brain
50	chr9:100381400-100387000	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links