Variant report

Variant	rs12590610
Chromosome Location	chr14:70992709-70992710
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	chr14:70866335..70868798-chr14:70990397..70993089,2	MCF-7	breast:

Extended variants
information (count: 135 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:132)

rs_ID	r²[population]
rs1007402	0.85[CHB][hapmap];0.95[CHD][hapmap]
rs10129782	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[AMR][1000 genomes];0.82[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs10130071	0.84[ASN][1000 genomes]
rs10131716	1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[ASN][1000 genomes]
rs10133963	0.81[AMR][1000 genomes];0.82[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs10135356	0.83[ASN][1000 genomes]
rs10141744	0.81[ASN][1000 genomes]
rs10143254	0.85[AMR][1000 genomes];0.82[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs10144289	0.90[CHB][hapmap];0.95[CHD][hapmap];0.84[ASN][1000 genomes]
rs10144535	0.81[AMR][1000 genomes];0.82[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs10144653	0.84[ASN][1000 genomes]
rs10144696	0.81[AMR][1000 genomes];0.82[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs10147143	1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[ASN][1000 genomes]
rs10150160	0.91[ASN][1000 genomes]
rs10483830	0.90[CHB][hapmap];0.91[JPT][hapmap];0.81[ASN][1000 genomes]
rs10483832	0.93[ASW][hapmap];0.92[CEU][hapmap];1.00[CHB][hapmap];0.98[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.92[MEX][hapmap];0.85[AMR][1000 genomes];0.82[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs10873239	0.88[AMR][1000 genomes];0.90[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1112478	0.82[ASN][1000 genomes]
rs11158863	0.87[ASN][1000 genomes]
rs11158867	0.90[CHB][hapmap];0.95[CHD][hapmap]
rs1137491	0.80[ASN][1000 genomes]
rs12586441	0.87[ASN][1000 genomes]
rs12586886	0.83[ASN][1000 genomes]
rs12587666	0.81[AMR][1000 genomes];0.90[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs12587714	0.86[ASN][1000 genomes]
rs12587866	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[AMR][1000 genomes];0.82[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs12588723	0.87[ASN][1000 genomes]
rs12590117	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[AMR][1000 genomes];0.82[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs12590198	0.91[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[AMR][1000 genomes];0.82[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs12590217	1.00[CHB][hapmap];0.95[JPT][hapmap];0.81[AMR][1000 genomes];0.82[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs12590401	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[AMR][1000 genomes];0.91[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12590471	0.86[CEU][hapmap];0.90[CHB][hapmap];0.93[CHD][hapmap];0.84[MEX][hapmap];0.85[ASN][1000 genomes]
rs1538403	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.83[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.84[TSI][hapmap];0.88[AMR][1000 genomes];0.90[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs17108197	0.88[AMR][1000 genomes];0.90[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs17108201	0.86[ASN][1000 genomes]
rs17108246	0.90[CHB][hapmap];0.83[CHD][hapmap];0.87[GIH][hapmap];0.91[JPT][hapmap]
rs17108264	1.00[CHB][hapmap];0.95[JPT][hapmap];0.81[ASN][1000 genomes]
rs17108267	0.85[AMR][1000 genomes];0.82[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs17108274	0.90[CHB][hapmap];0.81[CHD][hapmap];0.87[GIH][hapmap];0.91[JPT][hapmap];0.81[ASN][1000 genomes]
rs17108276	0.81[AMR][1000 genomes];0.82[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs17108278	0.81[AMR][1000 genomes];0.82[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs17108280	0.93[ASW][hapmap];0.92[CEU][hapmap];1.00[CHB][hapmap];0.98[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.92[MEX][hapmap];0.81[AMR][1000 genomes];0.82[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs17113651	0.95[CHB][hapmap];0.95[JPT][hapmap];0.81[ASN][1000 genomes]
rs1953803	0.91[AMR][1000 genomes];0.90[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1959477	0.82[ASN][1000 genomes]
rs1962311	0.85[CHB][hapmap]
rs1962312	0.80[ASN][1000 genomes]
rs2153114	0.90[CHB][hapmap]
rs2332431	0.81[ASW][hapmap];1.00[CHB][hapmap];0.98[CHD][hapmap];1.00[JPT][hapmap];0.84[MEX][hapmap];0.93[ASN][1000 genomes]
rs28559756	0.91[AMR][1000 genomes];0.91[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs28612538	0.84[ASN][1000 genomes]
rs2877673	0.80[ASN][1000 genomes]
rs4143920	0.85[CEU][hapmap]
rs45523543	0.81[ASN][1000 genomes]
rs55965222	0.81[AMR][1000 genomes];0.82[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs56155089	0.81[AMR][1000 genomes];0.82[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs56322604	0.81[AMR][1000 genomes];0.82[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs56328037	0.82[ASN][1000 genomes]
rs56392092	0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs56687536	0.81[AMR][1000 genomes];0.82[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs56721095	0.93[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs56922268	0.81[ASN][1000 genomes]
rs57032041	0.87[ASN][1000 genomes]
rs57339942	0.81[ASN][1000 genomes]
rs57598551	0.81[ASN][1000 genomes]
rs58069917	0.82[ASN][1000 genomes]
rs58092588	0.84[ASN][1000 genomes]
rs58258245	0.83[AMR][1000 genomes];0.90[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs58777530	0.99[AFR][1000 genomes];0.85[AMR][1000 genomes];0.86[ASN][1000 genomes]
rs58919501	0.81[AMR][1000 genomes];0.82[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs58985060	0.86[ASN][1000 genomes]
rs59044667	0.82[ASN][1000 genomes]
rs59115232	0.81[AMR][1000 genomes];0.82[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs59233924	0.81[ASN][1000 genomes]
rs59475121	0.81[AMR][1000 genomes];0.82[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs59599422	0.81[AMR][1000 genomes];0.82[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs59748874	0.86[ASN][1000 genomes]
rs60120955	0.81[ASN][1000 genomes]
rs60251828	0.81[ASN][1000 genomes]
rs60370428	0.85[AMR][1000 genomes];0.82[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs60453577	0.81[AMR][1000 genomes];0.82[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs60555424	0.91[AFR][1000 genomes]
rs60848570	0.91[AMR][1000 genomes];0.91[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs60860517	0.84[ASN][1000 genomes]
rs60862805	0.87[ASN][1000 genomes]
rs60867605	0.85[AMR][1000 genomes];0.81[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs60870618	0.91[AMR][1000 genomes];0.91[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs61388426	0.82[ASN][1000 genomes]
rs6420902	0.90[CHB][hapmap];0.98[CHD][hapmap]
rs6573972	0.84[ASN][1000 genomes]
rs6573973	0.82[ASN][1000 genomes]
rs66572616	0.81[ASN][1000 genomes]
rs7141056	1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[ASN][1000 genomes]
rs7141562	0.82[ASN][1000 genomes]
rs7141713	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[AMR][1000 genomes];0.82[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7141730	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[AMR][1000 genomes];0.82[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7145530	0.97[AFR][1000 genomes]
rs7150354	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[AMR][1000 genomes];0.91[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7150545	0.82[ASN][1000 genomes]
rs7154858	0.86[CEU][hapmap];0.90[CHB][hapmap];0.86[ASN][1000 genomes]
rs7154904	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[AMR][1000 genomes];0.91[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7155088	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[AMR][1000 genomes];0.82[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7155436	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[AMR][1000 genomes];0.82[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7156661	0.92[CEU][hapmap];1.00[CHB][hapmap];0.98[CHD][hapmap];0.81[GIH][hapmap];0.95[JPT][hapmap];0.84[MEX][hapmap];0.92[ASN][1000 genomes]
rs7157073	0.85[AMR][1000 genomes];0.82[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7157455	0.81[AMR][1000 genomes];0.82[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7157618	0.87[ASN][1000 genomes]
rs7157685	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[ASN][1000 genomes]
rs7158201	0.86[ASN][1000 genomes]
rs7158848	0.85[CEU][hapmap];0.90[CHB][hapmap];0.95[CHD][hapmap];0.84[MEX][hapmap];0.80[ASN][1000 genomes]
rs73282126	0.87[ASN][1000 genomes]
rs73282127	0.87[ASN][1000 genomes]
rs73282153	0.99[AFR][1000 genomes];0.85[AMR][1000 genomes];0.86[ASN][1000 genomes]
rs73283917	0.99[AFR][1000 genomes];0.83[ASN][1000 genomes]
rs7359112	0.85[AMR][1000 genomes];0.82[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs74062726	0.87[ASN][1000 genomes]
rs74062730	0.87[ASN][1000 genomes]
rs74062733	0.87[ASN][1000 genomes]
rs74062743	0.84[ASN][1000 genomes]
rs74062746	0.84[ASN][1000 genomes]
rs74062750	0.84[ASN][1000 genomes]
rs74062769	0.81[ASN][1000 genomes]
rs8004054	0.86[ASN][1000 genomes]
rs8005893	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.85[AMR][1000 genomes];0.82[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs8006487	0.87[ASN][1000 genomes]
rs8010044	0.85[CEU][hapmap];0.90[CHB][hapmap];0.95[CHD][hapmap];0.80[ASN][1000 genomes]
rs8011847	0.84[ASN][1000 genomes]
rs8012025	0.99[AFR][1000 genomes];0.85[AMR][1000 genomes];0.87[ASN][1000 genomes]
rs8016953	0.91[AMR][1000 genomes];0.91[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs8018765	0.82[ASN][1000 genomes]
rs8021911	0.92[CEU][hapmap];1.00[CHB][hapmap];0.98[CHD][hapmap];0.81[GIH][hapmap];1.00[JPT][hapmap];0.92[MEX][hapmap];0.92[ASN][1000 genomes]
rs9323542	0.85[CEU][hapmap];0.90[CHB][hapmap];0.81[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	nsv565042	chr14:70951234-71011734	Weak transcription ZNF genes & repeats Strong transcription Enhancers Genic enhancers Active TSS Flanking Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region	3 gene(s)	inside rSNPs	diseases
2	nsv1050615	chr14:70954149-71013235	Weak transcription ZNF genes & repeats Strong transcription Enhancers Transcr. at gene 5' and 3' Active TSS Genic enhancers Flanking Active TSS	TF binding region CpG island Chromatin interactive region	3 gene(s)	inside rSNPs	diseases
3	esv2763072	chr14:70954149-71013247	Strong transcription ZNF genes & repeats Weak transcription Enhancers Transcr. at gene 5' and 3' Active TSS Genic enhancers Flanking Active TSS	TF binding region CpG island Chromatin interactive region	3 gene(s)	inside rSNPs	diseases

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs12590610	MAP3K9	cis	cerebellum	SCAN
rs12590610	MED6	cis	parietal	SCAN
rs12590610	ADAM20	cis	cerebellum	SCAN
rs12590610	MED6	cis	cerebellum	SCAN

Chromatin state (count:60 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr14:70958800-70993800	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
2	chr14:70981200-70994400	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
3	chr14:70982000-71003600	Weak transcription	HSMM	muscle
4	chr14:70982400-71003200	Weak transcription	Psoas Muscle	Psoas
5	chr14:70985800-71003800	Weak transcription	HSMMtube	muscle
6	chr14:70987600-70993200	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
7	chr14:70987800-70995800	Weak transcription	Colon Smooth Muscle	Colon
8	chr14:70987800-71005800	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
9	chr14:70988000-71028200	Weak transcription	Esophagus	oesophagus
10	chr14:70988000-71029800	Weak transcription	Rectal Mucosa Donor 29	rectum
11	chr14:70988400-70994600	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
12	chr14:70988400-71003800	Weak transcription	Primary B cells from cord blood	blood
13	chr14:70988600-70993000	Weak transcription	Brain Germinal Matrix	brain
14	chr14:70988600-70993200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
15	chr14:70988600-70997000	Weak transcription	Placenta	Placenta
16	chr14:70988800-71028800	Weak transcription	Primary T helper cells fromperipheralblood	blood
17	chr14:70990000-70993000	Weak transcription	Fetal Heart	heart
18	chr14:70990400-70992800	Weak transcription	Pancreatic Islets	Pancreatic Islet
19	chr14:70990400-70994800	Weak transcription	Primary hematopoietic stem cells	blood
20	chr14:70990400-71029600	Weak transcription	Primary T helper naive cells from peripheral blood	blood
21	chr14:70991200-71006400	Weak transcription	Primary B cells from peripheral blood	blood
22	chr14:70991400-70993200	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
23	chr14:70991400-70993200	Weak transcription	Brain Hippocampus Middle	brain
24	chr14:70991400-70999400	Weak transcription	Primary T cells from cord blood	blood
25	chr14:70991400-71003800	Weak transcription	Brain Substantia Nigra	brain
26	chr14:70991400-71028200	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
27	chr14:70991600-70993400	Weak transcription	Fetal Stomach	stomach
28	chr14:70991600-70993400	Weak transcription	Gastric	stomach
29	chr14:70991600-70993800	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
30	chr14:70991600-70994400	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
31	chr14:70991600-70995200	Weak transcription	Lung	lung
32	chr14:70991600-70996800	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
33	chr14:70991600-70998800	Weak transcription	Brain Anterior Caudate	brain
34	chr14:70991600-70999000	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
35	chr14:70991600-70999200	Weak transcription	Brain Angular Gyrus	brain
36	chr14:70991600-71001200	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
37	chr14:70991600-71003800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
38	chr14:70991600-71003800	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
39	chr14:70991600-71003800	Weak transcription	Aorta	Aorta
40	chr14:70991600-71003800	Weak transcription	Brain Inferior Temporal Lobe	brain
41	chr14:70991600-71003800	Weak transcription	Ovary	ovary
42	chr14:70991600-71003800	Weak transcription	Rectal Smooth Muscle	rectum
43	chr14:70991600-71003800	Weak transcription	Stomach Smooth Muscle	stomach
44	chr14:70991600-71003800	Weak transcription	Spleen	Spleen
45	chr14:70991600-71004000	Weak transcription	Right Ventricle	heart
46	chr14:70991600-71004000	Weak transcription	Sigmoid Colon	Sigmoid Colon
47	chr14:70991600-71004200	Weak transcription	Pancreas	Pancrea
48	chr14:70991600-71014600	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
49	chr14:70991600-71022400	Weak transcription	Skeletal Muscle Female	skeletal muscle
50	chr14:70991600-71028200	Weak transcription	Brain Cingulate Gyrus	brain

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links