Variant report

Variant	rs11980882
Chromosome Location	chr7:38931930-38931931
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr7:38929214..38932230-chr7:38932411..38935645,3	K562	blood:

Extended variants
information (count: 52 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:50)

rs_ID	r²[population]
rs10247503	0.85[CHB][hapmap];0.85[JPT][hapmap]
rs10486677	0.91[CHB][hapmap];0.90[JPT][hapmap]
rs10486678	0.91[CHB][hapmap];0.91[CHD][hapmap];0.84[GIH][hapmap];0.90[JPT][hapmap];0.82[TSI][hapmap]
rs12670221	0.92[EUR][1000 genomes]
rs12672793	0.82[CHB][hapmap];0.85[JPT][hapmap]
rs12672885	0.90[CHB][hapmap];0.90[JPT][hapmap]
rs12674115	0.95[CHB][hapmap];0.93[CHD][hapmap];0.95[GIH][hapmap];0.95[JPT][hapmap];0.96[TSI][hapmap];0.90[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs1468348	0.80[JPT][hapmap]
rs17700142	0.82[CHB][hapmap];0.81[CHD][hapmap];0.85[JPT][hapmap]
rs17700172	0.80[JPT][hapmap]
rs17700262	0.91[CHB][hapmap];0.90[JPT][hapmap]
rs17700752	0.82[CHB][hapmap];0.85[CHD][hapmap];0.82[GIH][hapmap];0.85[TSI][hapmap]
rs17767818	0.82[CHB][hapmap];0.81[CHD][hapmap];0.85[JPT][hapmap]
rs17768153	0.91[CHB][hapmap];0.88[CHD][hapmap];0.87[GIH][hapmap];0.90[JPT][hapmap];0.85[TSI][hapmap]
rs17768711	1.00[CHB][hapmap];0.94[JPT][hapmap];0.93[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs17768753	1.00[CEU][hapmap];0.83[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.81[AMR][1000 genomes];0.94[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs2074655	0.91[CHB][hapmap];0.88[CHD][hapmap];0.87[GIH][hapmap];0.90[JPT][hapmap];0.85[TSI][hapmap]
rs2074657	0.91[CHB][hapmap];0.86[CHD][hapmap];0.87[GIH][hapmap];0.85[JPT][hapmap];0.82[TSI][hapmap]
rs2108507	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.93[MEX][hapmap];0.96[TSI][hapmap];0.99[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2189855	0.89[CHB][hapmap];0.90[JPT][hapmap]
rs2240351	0.86[CHB][hapmap];0.85[JPT][hapmap]
rs2240352	0.86[CHB][hapmap];0.84[CHD][hapmap];0.80[JPT][hapmap]
rs2240353	0.91[CHB][hapmap];0.88[CHD][hapmap];0.87[GIH][hapmap];0.90[JPT][hapmap];0.85[TSI][hapmap]
rs2286086	0.85[CHB][hapmap];0.83[JPT][hapmap]
rs2286088	0.91[CHB][hapmap];0.90[JPT][hapmap]
rs2286098	0.91[CHB][hapmap];0.90[JPT][hapmap]
rs2286105	0.91[CHB][hapmap];0.88[CHD][hapmap];0.87[GIH][hapmap];0.90[JPT][hapmap];0.85[TSI][hapmap]
rs2286106	0.86[CHB][hapmap];0.86[CHD][hapmap];0.85[JPT][hapmap]
rs2286109	0.82[CHB][hapmap];0.81[CHD][hapmap];0.85[JPT][hapmap]
rs2392598	0.81[CHB][hapmap];0.83[JPT][hapmap]
rs34724372	0.92[CEU][hapmap];1.00[CHB][hapmap];0.93[CHD][hapmap];1.00[GIH][hapmap];0.95[JPT][hapmap];0.93[TSI][hapmap];0.93[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs3801139	0.86[CHB][hapmap];0.84[CHD][hapmap];0.80[JPT][hapmap]
rs3801140	0.86[CHB][hapmap];0.84[CHD][hapmap];0.80[JPT][hapmap]
rs3801143	0.86[CHB][hapmap];0.86[CHD][hapmap];0.85[JPT][hapmap]
rs3801145	0.86[CHB][hapmap];0.84[CHD][hapmap];0.85[JPT][hapmap]
rs4723785	0.86[CHB][hapmap];0.80[JPT][hapmap]
rs61363591	0.84[ASN][1000 genomes]
rs6462872	0.93[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs6956146	0.91[EUR][1000 genomes]
rs6975048	0.95[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs733150	0.86[CHB][hapmap];0.85[JPT][hapmap]
rs73357792	0.84[EUR][1000 genomes]
rs7780490	0.92[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs7780625	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.93[MEX][hapmap];1.00[TSI][hapmap];1.00[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs7785911	0.86[CHB][hapmap];0.86[CHD][hapmap];0.85[JPT][hapmap]
rs7795874	0.86[CHB][hapmap];0.86[CHD][hapmap];0.85[JPT][hapmap]
rs7800167	0.93[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs7803397	0.82[JPT][hapmap]
rs886646	0.84[CHB][hapmap];0.88[JPT][hapmap]
rs9638944	0.81[JPT][hapmap]

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	nsv887966	chr7:38835035-38933942	Enhancers Weak transcription Strong transcription ZNF genes & repeats Genic enhancers Active TSS Flanking Active TSS Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region	2 gene(s)	inside rSNPs	diseases
2	nsv830967	chr7:38913837-39069253	Flanking Bivalent TSS/Enh Enhancers Weak transcription Active TSS Bivalent Enhancer Flanking Active TSS Bivalent/Poised TSS Strong transcription ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs11980882	SEPT7	cis	cerebellum	SCAN
rs11980882	C7orf36	cis	parietal	SCAN

Chromatin state (count:95 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr7:38879800-38938000	Weak transcription	Right Ventricle	heart
2	chr7:38886200-38947800	Weak transcription	Stomach Smooth Muscle	stomach
3	chr7:38889400-38948200	Weak transcription	Gastric	stomach
4	chr7:38889600-38932600	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
5	chr7:38903800-38939600	Weak transcription	A549	lung
6	chr7:38903800-38947000	Weak transcription	Small Intestine	intestine
7	chr7:38905600-38937800	Weak transcription	Colonic Mucosa	Colon
8	chr7:38906000-38947800	Weak transcription	H1 Cell Line	embryonic stem cell
9	chr7:38908000-38941000	Weak transcription	Colon Smooth Muscle	Colon
10	chr7:38908200-38932800	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
11	chr7:38908200-38933800	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
12	chr7:38908200-38935000	Weak transcription	Rectal Mucosa Donor 31	rectum
13	chr7:38908200-38935400	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
14	chr7:38908200-38935400	Weak transcription	Duodenum Smooth Muscle	Duodenum
15	chr7:38908200-38938600	Weak transcription	Rectal Smooth Muscle	rectum
16	chr7:38908600-38935200	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
17	chr7:38908800-38932600	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
18	chr7:38908800-38934200	Weak transcription	Primary T helper cells fromperipheralblood	blood
19	chr7:38908800-38935400	Weak transcription	Muscle Satellite Cultured Cells	--
20	chr7:38908800-38943000	Weak transcription	Esophagus	oesophagus
21	chr7:38908800-38947800	Weak transcription	HUES48 Cell Line	embryonic stem cell
22	chr7:38908800-38948000	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
23	chr7:38909000-38933800	Weak transcription	Rectal Mucosa Donor 29	rectum
24	chr7:38909000-38934200	Weak transcription	Duodenum Mucosa	Duodenum
25	chr7:38909000-38947800	Weak transcription	iPS-18 Cell Line	embryonic stem cell
26	chr7:38911800-38948200	Weak transcription	Aorta	Aorta
27	chr7:38912000-38932800	Weak transcription	Spleen	Spleen
28	chr7:38914000-38934200	Weak transcription	Liver	Liver
29	chr7:38914200-38935000	Weak transcription	Dnd41	blood
30	chr7:38916600-38941600	Weak transcription	Placenta Amnion	Placenta Amnion
31	chr7:38916800-38948200	Weak transcription	Sigmoid Colon	Sigmoid Colon
32	chr7:38917600-38934000	Weak transcription	Ovary	ovary
33	chr7:38918800-38934200	Weak transcription	Primary neutrophils fromperipheralblood	blood
34	chr7:38918800-38948000	Weak transcription	Skeletal Muscle Male	skeletal muscle
35	chr7:38919000-38932800	Weak transcription	Left Ventricle	heart
36	chr7:38919400-38942200	Weak transcription	Pancreas	Pancrea
37	chr7:38920200-38934200	Weak transcription	Primary B cells from peripheral blood	blood
38	chr7:38920400-38940800	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
39	chr7:38920600-38935000	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
40	chr7:38920600-38935000	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
41	chr7:38920600-38935400	Weak transcription	Brain Hippocampus Middle	brain
42	chr7:38920600-38936200	Weak transcription	Primary T helper cells PMA-I stimulated	--
43	chr7:38920800-38934600	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
44	chr7:38920800-38942400	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
45	chr7:38921000-38938000	Weak transcription	Brain Anterior Caudate	brain
46	chr7:38921000-38946800	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
47	chr7:38921200-38935600	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
48	chr7:38921800-38947800	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
49	chr7:38923600-38932400	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
50	chr7:38925200-38947800	Weak transcription	HUVEC	blood vessel

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links