Variant report

Variant	rs11142377
Chromosome Location	chr9:72958237-72958238
allele	A/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	POLR2A	chr9:72957353-72958482	K562	blood:	n/a	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr9:72957661..72959834-chr9:72968408..72970281,2	MCF-7	breast:

Variant related genes	Relation type
SMC5	TF binding region

Extended variants
information (count: 78 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:75)

rs_ID	r²[population]
rs10114223	0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10780924	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.83[LWK][hapmap];0.83[MKK][hapmap];0.94[YRI][hapmap];0.81[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs10868800	0.84[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.93[LWK][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.90[AFR][1000 genomes];0.87[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs10868810	0.87[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1112937	1.00[CHB][hapmap]
rs11142348	0.86[CEU][hapmap];0.91[EUR][1000 genomes]
rs11142364	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.90[AFR][1000 genomes];0.87[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11142365	1.00[ASN][1000 genomes]
rs11142372	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.88[AFR][1000 genomes];0.87[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11142375	0.95[EUR][1000 genomes]
rs11142379	1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[YRI][hapmap];0.83[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs11142380	0.82[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs11142381	0.82[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs11521805	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];0.87[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11795149	0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1180080	0.87[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1180082	1.00[CHB][hapmap]
rs1180084	1.00[CEU][hapmap];0.86[YRI][hapmap];0.87[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1180086	1.00[CHB][hapmap]
rs1180089	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.84[MKK][hapmap];1.00[TSI][hapmap];0.85[YRI][hapmap];0.87[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1180091	1.00[CHB][hapmap]
rs1180094	1.00[CHB][hapmap]
rs1180097	0.84[AFR][1000 genomes];0.87[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1180099	1.00[CHB][hapmap]
rs1180100	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.92[GIH][hapmap];1.00[JPT][hapmap];0.83[LWK][hapmap];1.00[MEX][hapmap];0.84[MKK][hapmap];0.87[TSI][hapmap];0.94[YRI][hapmap];0.87[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1180110	1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[YRI][hapmap];1.00[ASN][1000 genomes]
rs1180113	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.84[AFR][1000 genomes];0.87[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1180119	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.87[AFR][1000 genomes];0.87[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1180127	1.00[CHB][hapmap]
rs1180134	1.00[CEU][hapmap];0.95[EUR][1000 genomes]
rs1183311	0.87[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11999862	0.87[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17052678	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[YRI][hapmap];0.87[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1888155	0.80[AFR][1000 genomes];0.87[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1927094	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.85[YRI][hapmap];0.87[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1927097	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1927114	0.81[EUR][1000 genomes]
rs1927123	0.81[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1927138	0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1927140	0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1927141	0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1927145	0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1927146	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1927148	0.85[YRI][hapmap]
rs2148854	0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2148855	0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2182733	0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2182735	1.00[CHB][hapmap]
rs2209781	0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2225128	0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2309601	0.81[EUR][1000 genomes]
rs2309637	0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2309641	0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2309643	0.81[EUR][1000 genomes]
rs2309644	1.00[CHB][hapmap]
rs2309645	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.85[MKK][hapmap];0.85[TSI][hapmap];0.81[YRI][hapmap];0.87[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2309646	0.87[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2871297	0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4744587	0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4744985	0.81[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs66524845	0.95[EUR][1000 genomes]
rs66756859	0.91[EUR][1000 genomes]
rs7020575	0.81[EUR][1000 genomes]
rs7042675	0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7043171	1.00[CHB][hapmap];0.85[CHD][hapmap]
rs7047789	1.00[CHB][hapmap]
rs72712293	0.90[AFR][1000 genomes];0.87[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72712300	0.91[AFR][1000 genomes];0.87[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7341691	0.87[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7848955	0.81[EUR][1000 genomes]
rs7865289	0.81[EUR][1000 genomes]
rs9410662	0.87[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs943532	0.84[AFR][1000 genomes];0.85[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs943533	0.81[AFR][1000 genomes];0.85[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs943535	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.84[LWK][hapmap];1.00[MEX][hapmap];0.83[MKK][hapmap];1.00[TSI][hapmap];0.94[YRI][hapmap];0.87[AMR][1000 genomes];0.93[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	nsv1047862	chr9:72746875-73138287	Enhancers Strong transcription Genic enhancers Flanking Active TSS Weak transcription 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 miRNA target site	66 gene(s)	inside rSNPs	diseases
2	nsv831615	chr9:72852705-73019692	Strong transcription Weak transcription Flanking Active TSS Enhancers Active TSS ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	19 gene(s)	inside rSNPs	diseases
3	nsv1049132	chr9:72895382-73005897	Strong transcription Weak transcription Genic enhancers ZNF genes & repeats Enhancers Flanking Active TSS Active TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	4 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:118 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr9:72926400-72965000	Weak transcription	Fetal Brain Male	brain
2	chr9:72926400-72967000	Weak transcription	Fetal Heart	heart
3	chr9:72936000-72970800	Weak transcription	Psoas Muscle	Psoas
4	chr9:72939600-72974000	Weak transcription	Colon Smooth Muscle	Colon
5	chr9:72941200-72965000	Weak transcription	Hela-S3	cervix
6	chr9:72941400-72965200	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
7	chr9:72942800-72961400	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
8	chr9:72943000-72966400	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
9	chr9:72943000-72966600	Weak transcription	Primary T helper naive cells from peripheral blood	blood
10	chr9:72943200-72968600	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
11	chr9:72943400-72963400	Weak transcription	HepG2	liver
12	chr9:72943400-72967200	Weak transcription	Primary T killer memory cells from peripheral blood	blood
13	chr9:72943600-72970800	Weak transcription	Gastric	stomach
14	chr9:72944000-72962000	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
15	chr9:72944000-72963200	Weak transcription	Pancreas	Pancrea
16	chr9:72944000-72963400	Weak transcription	Small Intestine	intestine
17	chr9:72944000-72963600	Weak transcription	Fetal Brain Female	brain
18	chr9:72944000-72965200	Weak transcription	Brain Cingulate Gyrus	brain
19	chr9:72944000-72965200	Weak transcription	Colonic Mucosa	Colon
20	chr9:72944000-72970800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
21	chr9:72944000-72974600	Weak transcription	Aorta	Aorta
22	chr9:72944000-72978800	Weak transcription	Brain Inferior Temporal Lobe	brain
23	chr9:72944000-73002600	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
24	chr9:72944200-72961400	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
25	chr9:72944200-72961600	Weak transcription	Brain Germinal Matrix	brain
26	chr9:72944200-72961800	Weak transcription	Brain Angular Gyrus	brain
27	chr9:72944200-72963200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
28	chr9:72944200-72963400	Weak transcription	Esophagus	oesophagus
29	chr9:72944200-72964600	Weak transcription	H1 Cell Line	embryonic stem cell
30	chr9:72944200-72968600	Weak transcription	H9 Cell Line	embryonic stem cell
31	chr9:72944200-72974000	Weak transcription	Spleen	Spleen
32	chr9:72944200-72974800	Weak transcription	Lung	lung
33	chr9:72944400-72959600	Weak transcription	NHLF	lung
34	chr9:72944400-72963200	Weak transcription	Rectal Smooth Muscle	rectum
35	chr9:72944400-72963800	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
36	chr9:72944400-72964000	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
37	chr9:72944400-72965200	Weak transcription	Brain Hippocampus Middle	brain
38	chr9:72944400-72965200	Weak transcription	Skeletal Muscle Male	skeletal muscle
39	chr9:72944400-72966000	Weak transcription	Right Ventricle	heart
40	chr9:72944600-72964000	Weak transcription	Sigmoid Colon	Sigmoid Colon
41	chr9:72944800-72960800	Weak transcription	Rectal Mucosa Donor 31	rectum
42	chr9:72945000-72960200	Weak transcription	Primary hematopoietic stem cells	blood
43	chr9:72945000-72965000	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
44	chr9:72945200-72963600	Weak transcription	Thymus	Thymus
45	chr9:72946800-72961600	Weak transcription	HUES48 Cell Line	embryonic stem cell
46	chr9:72947200-72961400	Weak transcription	Adipose Nuclei	Adipose
47	chr9:72947400-72960800	Weak transcription	Primary T cells fromperipheralblood	blood
48	chr9:72947400-72965400	Weak transcription	Placenta Amnion	Placenta Amnion
49	chr9:72948000-72960200	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
50	chr9:72948000-72961200	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links