Variant report

Variant	rs2309645
Chromosome Location	chr9:72830650-72830651
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr9:72830114..72831861-chr9:72833907..72836802,2	MCF-7	breast:

Extended variants
information (count: 81 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:80)

rs_ID	r²[population]
rs10114223	0.81[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10735584	0.81[AMR][1000 genomes]
rs10780924	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.93[LWK][hapmap];1.00[MKK][hapmap];0.85[YRI][hapmap];1.00[ASN][1000 genomes]
rs10868800	0.86[ASW][hapmap];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[TSI][hapmap];0.81[YRI][hapmap];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs10868810	0.87[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];0.85[YRI][hapmap];1.00[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];0.81[YRI][hapmap];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11142375	0.95[EUR][1000 genomes]
rs11142377	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]
rs11142379	1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[YRI][hapmap];1.00[ASN][1000 genomes]
rs11142380	1.00[ASN][1000 genomes]
rs11142381	1.00[ASN][1000 genomes]
rs11521805	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[YRI][hapmap];1.00[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	0.83[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1180082	1.00[CHB][hapmap]
rs1180084	1.00[CEU][hapmap];0.94[YRI][hapmap];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1180086	1.00[CHB][hapmap]
rs1180089	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];0.85[TSI][hapmap];0.95[YRI][hapmap];0.83[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1180091	1.00[CHB][hapmap]
rs1180094	1.00[CHB][hapmap]
rs1180097	1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1180099	1.00[CHB][hapmap]
rs1180100	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.92[GIH][hapmap];1.00[JPT][hapmap];0.90[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];0.86[YRI][hapmap];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1180110	1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[YRI][hapmap];1.00[ASN][1000 genomes]
rs1180113	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[YRI][hapmap];1.00[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];0.80[YRI][hapmap];1.00[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	0.83[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11999862	0.87[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];0.86[YRI][hapmap];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1888155	1.00[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];0.95[YRI][hapmap];0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1927097	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1927108	0.81[AMR][1000 genomes]
rs1927109	0.81[AMR][1000 genomes]
rs1927112	0.87[AMR][1000 genomes]
rs1927114	0.87[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs1927123	0.80[AFR][1000 genomes];0.87[AMR][1000 genomes];0.81[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1927138	0.81[AFR][1000 genomes];0.87[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1927140	0.81[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1927141	0.81[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1927145	0.83[AFR][1000 genomes];0.87[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1927146	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[YRI][hapmap];0.81[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2148854	0.81[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2148855	0.81[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2182733	0.87[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2182735	1.00[CHB][hapmap]
rs2209781	0.81[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2225128	0.87[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2309601	0.81[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs2309637	0.81[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2309641	0.86[AFR][1000 genomes];0.87[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2309643	0.81[EUR][1000 genomes]
rs2309644	1.00[CHB][hapmap]
rs2309646	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2871297	0.87[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2997683	0.84[GIH][hapmap]
rs3015215	0.84[GIH][hapmap]
rs4744587	0.87[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4744985	0.87[AMR][1000 genomes];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	1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72712300	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7341691	0.83[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7848955	0.87[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs7865289	0.81[EUR][1000 genomes]
rs9410662	1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs943532	0.93[AMR][1000 genomes];0.85[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs943533	0.93[AMR][1000 genomes];0.85[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs943535	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.86[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];0.85[TSI][hapmap];0.86[YRI][hapmap];1.00[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:1 , 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

No data

Chromatin state (count:58 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr9:72793000-72842600	Weak transcription	Rectal Smooth Muscle	rectum
2	chr9:72809600-72837800	Weak transcription	NH-A	brain
3	chr9:72820800-72835400	Weak transcription	Placenta Amnion	Placenta Amnion
4	chr9:72821200-72844800	Weak transcription	HMEC	breast
5	chr9:72821400-72832000	Weak transcription	NHEK	skin
6	chr9:72825600-72833200	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
7	chr9:72826000-72833200	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
8	chr9:72827200-72830800	Strong transcription	Muscle Satellite Cultured Cells	--
9	chr9:72827200-72832000	ZNF genes & repeats	Primary hematopoietic stem cells G-CSF-mobilized Male	--
10	chr9:72827600-72833800	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
11	chr9:72827600-72834000	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
12	chr9:72827600-72843200	Weak transcription	Skeletal Muscle Male	skeletal muscle
13	chr9:72827800-72833200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
14	chr9:72827800-72833400	Weak transcription	Osteobl	bone
15	chr9:72827800-72841600	Weak transcription	Placenta	Placenta
16	chr9:72828000-72832000	Weak transcription	Pancreatic Islets	Pancreatic Islet
17	chr9:72828000-72833200	Weak transcription	Fetal Stomach	stomach
18	chr9:72828000-72833200	Weak transcription	Left Ventricle	heart
19	chr9:72828000-72833400	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
20	chr9:72828000-72836600	Weak transcription	Right Ventricle	heart
21	chr9:72828000-72837000	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
22	chr9:72828000-72844000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
23	chr9:72828000-72858800	Weak transcription	Gastric	stomach
24	chr9:72828200-72831400	Strong transcription	HSMMtube	muscle
25	chr9:72828200-72831600	Strong transcription	Liver	Liver
26	chr9:72828200-72833200	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
27	chr9:72828200-72833400	Weak transcription	Fetal Kidney	kidney
28	chr9:72828200-72835400	Weak transcription	Adipose Nuclei	Adipose
29	chr9:72828200-72835400	Weak transcription	Small Intestine	intestine
30	chr9:72828200-72843200	Weak transcription	Fetal Lung	lung
31	chr9:72828200-72844000	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
32	chr9:72828400-72830800	Weak transcription	Brain Hippocampus Middle	brain
33	chr9:72828400-72830800	Strong transcription	Duodenum Mucosa	Duodenum
34	chr9:72828400-72831400	Weak transcription	HepG2	liver
35	chr9:72828400-72831600	Strong transcription	Rectal Mucosa Donor 31	rectum
36	chr9:72828600-72837200	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
37	chr9:72828600-72843000	Weak transcription	Cortex derived primary cultured neurospheres	brain
38	chr9:72828800-72830800	Strong transcription	Ovary	ovary
39	chr9:72828800-72831000	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
40	chr9:72828800-72831600	Strong transcription	Breast Myoepithelial Primary Cells	Breast
41	chr9:72829000-72831000	Weak transcription	Esophagus	oesophagus
42	chr9:72829000-72831600	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
43	chr9:72829000-72841800	Weak transcription	HUES64 Cell Line	embryonic stem cell
44	chr9:72829400-72831200	Weak transcription	Lung	lung
45	chr9:72829400-72833200	Weak transcription	Colon Smooth Muscle	Colon
46	chr9:72829400-72835200	Weak transcription	Psoas Muscle	Psoas
47	chr9:72829600-72831800	Weak transcription	Fetal Muscle Trunk	muscle
48	chr9:72829600-72839200	Weak transcription	Sigmoid Colon	Sigmoid Colon
49	chr9:72829600-72843400	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
50	chr9:72829800-72831800	Strong transcription	Duodenum Smooth Muscle	Duodenum

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links