Variant report

Variant	rs12451343
Chromosome Location	chr17:17002380-17002381
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr17:17001973..17004582-chr17:17006426..17009352,2	MCF-7	breast:
2	chr17:16992481..16994529-chr17:17001211..17003120,2	MCF-7	breast:
3	chr17:17000263..17003828-chr17:17006059..17008926,3	MCF-7	breast:
4	chr17:16989031..16991528-chr17:17000273..17002775,2	MCF-7	breast:

Extended variants
information (count: 87 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:86)

rs_ID	r²[population]
rs1047799	0.94[CHB][hapmap]
rs10852844	0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs10852846	0.87[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs11078368	0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11078371	0.91[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11078372	0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs11078373	0.91[CEU][hapmap];1.00[CHB][hapmap];0.87[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs1110505	0.83[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs11551189	0.83[ASN][1000 genomes]
rs11651938	0.91[CEU][hapmap];1.00[CHB][hapmap];0.87[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs11652678	0.91[CEU][hapmap];1.00[CHB][hapmap];0.87[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs11654887	1.00[CEU][hapmap];1.00[CHB][hapmap];0.90[AMR][1000 genomes];0.87[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs11657189	1.00[CEU][hapmap];1.00[CHB][hapmap];0.90[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs11870035	0.85[ASN][1000 genomes]
rs11870483	0.94[ASN][1000 genomes]
rs12452303	0.96[AMR][1000 genomes]
rs12601422	0.94[CHB][hapmap];0.95[JPT][hapmap];0.81[ASN][1000 genomes]
rs12602124	0.96[AMR][1000 genomes]
rs12602583	0.84[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs12602592	1.00[CEU][hapmap];1.00[CHB][hapmap];0.90[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs12602839	0.83[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12603417	0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1567815	1.00[CEU][hapmap];1.00[CHB][hapmap];0.90[AMR][1000 genomes];0.87[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs17794784	0.95[CHB][hapmap];0.80[ASN][1000 genomes]
rs2292526	0.91[CEU][hapmap];1.00[CHB][hapmap];0.87[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2292530	0.94[CHB][hapmap];0.80[ASN][1000 genomes]
rs2349645	0.85[ASN][1000 genomes]
rs2349648	0.94[ASN][1000 genomes]
rs28452405	0.96[ASN][1000 genomes]
rs34001712	0.96[ASN][1000 genomes]
rs35650871	0.92[ASN][1000 genomes]
rs3744125	0.91[CEU][hapmap];1.00[CHB][hapmap];0.80[EUR][1000 genomes]
rs3744127	0.80[EUR][1000 genomes]
rs3744131	0.95[CHB][hapmap];0.83[ASN][1000 genomes]
rs3744132	0.91[CEU][hapmap];1.00[CHB][hapmap];0.87[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs3744134	0.94[CHB][hapmap];0.80[ASN][1000 genomes]
rs3744136	0.91[CEU][hapmap];1.00[CHB][hapmap];0.87[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs3744137	0.94[CHB][hapmap];0.85[ASN][1000 genomes]
rs3744138	0.89[CHB][hapmap];0.85[ASN][1000 genomes]
rs3744139	0.94[CHB][hapmap];0.85[ASN][1000 genomes]
rs4073688	1.00[CEU][hapmap];0.89[CHB][hapmap];0.95[JPT][hapmap];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs4073940	0.84[YRI][hapmap];0.96[AMR][1000 genomes]
rs4074612	0.91[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4074819	0.87[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs4283273	0.80[EUR][1000 genomes]
rs4321246	0.87[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs4468683	0.87[ASN][1000 genomes]
rs4629023	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[YRI][hapmap];0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4641803	0.83[ASN][1000 genomes]
rs4985703	0.91[CEU][hapmap];1.00[CHB][hapmap];0.85[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs4985704	1.00[CEU][hapmap];0.89[CHB][hapmap];0.90[AMR][1000 genomes];0.91[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs4985715	0.82[YRI][hapmap];0.96[AMR][1000 genomes]
rs4985716	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs4985721	0.96[ASN][1000 genomes]
rs4985723	0.96[AMR][1000 genomes]
rs4985728	0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4985730	0.94[ASN][1000 genomes]
rs4985737	0.83[CEU][hapmap];1.00[CHB][hapmap];0.90[AMR][1000 genomes];0.81[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs4985741	0.94[CHB][hapmap]
rs4985742	1.00[CEU][hapmap];1.00[CHB][hapmap];0.90[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs4985743	0.90[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs56133536	0.85[ASN][1000 genomes]
rs57729820	0.81[AMR][1000 genomes];0.94[ASN][1000 genomes]
rs58326998	0.83[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs59394251	0.87[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs60128647	0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs61242604	0.89[ASN][1000 genomes]
rs7212275	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7214429	0.94[CHB][hapmap];0.83[ASN][1000 genomes]
rs7216677	0.90[AMR][1000 genomes];0.91[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs7218781	0.91[CEU][hapmap];1.00[CHB][hapmap]
rs7223924	0.96[AMR][1000 genomes]
rs73979060	0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs73979078	0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs8066111	0.87[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs8066234	0.94[CHB][hapmap]
rs8069259	0.90[AMR][1000 genomes];0.91[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs8071254	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs8076273	0.84[CHB][hapmap];1.00[JPT][hapmap];0.83[ASN][1000 genomes]
rs8077360	0.90[AMR][1000 genomes];0.91[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs9892695	0.83[ASN][1000 genomes]
rs9893676	0.83[ASN][1000 genomes]
rs9897510	0.83[ASN][1000 genomes]
rs9906028	0.92[ASN][1000 genomes]
rs9907109	0.94[ASN][1000 genomes]
rs9910857	0.85[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	nsv1059280	chr17:16975059-17017957	Enhancers Strong transcription Weak transcription Genic enhancers Transcr. at gene 5' and 3' Flanking Active TSS ZNF genes & repeats Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs12451343	M-RIP	Cis_1M	lymphoblastoid	RTeQTL
rs12451343	LOC201164	Cis_1M	lymphoblastoid	RTeQTL

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr17:16986800-17013600	Weak transcription	HUVEC	blood vessel
2	chr17:16992400-17010000	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
3	chr17:16993200-17003800	Genic enhancers	Fetal Intestine Small	intestine
4	chr17:16993400-17011400	Weak transcription	Primary T killer memory cells from peripheral blood	blood
5	chr17:16994600-17003400	Enhancers	Ovary	ovary
6	chr17:16994600-17011600	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
7	chr17:16995400-17002400	Enhancers	iPS-18 Cell Line	embryonic stem cell
8	chr17:16996400-17006200	Weak transcription	Liver	Liver
9	chr17:16997000-17016600	Enhancers	Left Ventricle	heart
10	chr17:16997200-17005000	Weak transcription	K562	blood
11	chr17:16997400-17006200	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
12	chr17:16997400-17010000	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
13	chr17:16998000-17003600	Genic enhancers	Fetal Stomach	stomach
14	chr17:16998200-17002800	Enhancers	NHDF-Ad	bronchial
15	chr17:16998200-17016200	Enhancers	Fetal Heart	heart
16	chr17:16998400-17002600	Genic enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
17	chr17:16998400-17002600	Enhancers	Stomach Mucosa	stomach
18	chr17:16998600-17002600	Enhancers	Brain Substantia Nigra	brain
19	chr17:16998600-17002800	Enhancers	Foreskin Melanocyte Primary Cells skin01	Skin
20	chr17:16998600-17003800	Enhancers	Right Atrium	heart
21	chr17:16998600-17004000	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
22	chr17:16998600-17006800	Enhancers	Psoas Muscle	Psoas
23	chr17:16998600-17015400	Genic enhancers	Fetal Muscle Leg	muscle
24	chr17:16998600-17016600	Enhancers	Skeletal Muscle Female	skeletal muscle
25	chr17:16998800-17003000	Enhancers	Brain Cingulate Gyrus	brain
26	chr17:16999000-17002400	Genic enhancers	Muscle Satellite Cultured Cells	--
27	chr17:16999000-17002800	Genic enhancers	Duodenum Mucosa	Duodenum
28	chr17:16999000-17012800	Strong transcription	Primary hematopoietic stem cells short term culture	blood
29	chr17:16999200-17002600	Enhancers	Cortex derived primary cultured neurospheres	brain
30	chr17:16999200-17002600	Enhancers	Brain Angular Gyrus	brain
31	chr17:16999200-17002800	Genic enhancers	Brain Hippocampus Middle	brain
32	chr17:16999200-17003000	Enhancers	Duodenum Smooth Muscle	Duodenum
33	chr17:16999200-17006400	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
34	chr17:16999400-17002600	Enhancers	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
35	chr17:16999400-17002800	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
36	chr17:16999400-17002800	Enhancers	Brain Anterior Caudate	brain
37	chr17:16999400-17002800	Enhancers	NHLF	lung
38	chr17:16999400-17003000	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
39	chr17:16999600-17002400	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
40	chr17:16999600-17002600	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
41	chr17:16999600-17003600	Genic enhancers	Fetal Adrenal Gland	Adrenal Gland
42	chr17:16999600-17005000	Weak transcription	Gastric	stomach
43	chr17:16999600-17008200	Strong transcription	Primary B cells from peripheral blood	blood
44	chr17:16999800-17002600	Genic enhancers	Osteobl	bone
45	chr17:16999800-17003000	Genic enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
46	chr17:17000200-17002600	Genic enhancers	Breast Myoepithelial Primary Cells	Breast
47	chr17:17000200-17002600	Genic enhancers	Foreskin Fibroblast Primary Cells skin02	Skin
48	chr17:17000200-17002600	Enhancers	HSMMtube	muscle
49	chr17:17000200-17005600	Weak transcription	Rectal Mucosa Donor 29	rectum
50	chr17:17000200-17012600	Weak transcription	Monocytes-CD14+_RO01746	blood

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links