Variant report

Variant	rs12634587
Chromosome Location	chr3:195988743-195988744
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr3:195986241..195988788-chr3:196013204..196014924,2	MCF-7	breast:
2	chr3:195986524..195988790-chr3:196013840..196016157,2	MCF-7	breast:
3	chr3:195987889..195991350-chr3:195994108..195996834,3	K562	blood:

Variant related genes	Relation type
ENSG00000161217	Chromatin interaction

Extended variants
information (count: 62 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:42)

rs_ID	r²[population]
rs11185519	0.87[JPT][hapmap];0.82[ASN][1000 genomes]
rs12632779	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AFR][1000 genomes];0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12633454	0.92[ASN][1000 genomes]
rs12633827	0.88[ASN][1000 genomes]
rs12634350	0.87[ASN][1000 genomes]
rs12635925	0.90[AFR][1000 genomes];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12637288	0.81[JPT][hapmap]
rs1357290	0.90[CEU][hapmap];0.90[CHB][hapmap];0.94[JPT][hapmap];0.86[AMR][1000 genomes];0.92[ASN][1000 genomes]
rs17852687	0.80[JPT][hapmap]
rs1875088	0.87[JPT][hapmap]
rs2047551	0.81[JPT][hapmap]
rs2088666	0.81[JPT][hapmap]
rs2342309	0.87[JPT][hapmap]
rs3772107	1.00[AFR][1000 genomes];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3772108	1.00[AFR][1000 genomes];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs3772109	0.81[JPT][hapmap]
rs4396926	0.94[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs4916421	0.81[JPT][hapmap]
rs4916484	0.82[CEU][hapmap];0.86[CHB][hapmap];0.80[JPT][hapmap]
rs56701784	1.00[AFR][1000 genomes];0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs56875789	0.81[ASN][1000 genomes]
rs57987393	0.85[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs58297632	0.90[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs58568267	0.85[AMR][1000 genomes];0.85[ASN][1000 genomes]
rs58845625	1.00[AFR][1000 genomes];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs59289255	0.92[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs59708858	0.84[AMR][1000 genomes];0.87[ASN][1000 genomes]
rs60167422	0.88[AMR][1000 genomes];0.90[ASN][1000 genomes]
rs61254593	0.91[ASN][1000 genomes]
rs61588443	0.81[AFR][1000 genomes];0.88[AMR][1000 genomes];0.91[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs66935510	0.92[ASN][1000 genomes]
rs67199839	0.88[AMR][1000 genomes];0.93[ASN][1000 genomes]
rs72611187	1.00[AFR][1000 genomes];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72611188	0.98[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs72611189	0.89[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs72611190	1.00[AFR][1000 genomes];0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73212156	0.85[ASN][1000 genomes]
rs7617236	1.00[AFR][1000 genomes];0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7635355	0.90[AFR][1000 genomes];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7636149	0.81[JPT][hapmap]
rs7638797	0.87[JPT][hapmap]
rs939885	0.84[CHB][hapmap];0.93[JPT][hapmap];0.81[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:20 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv2759213	chr3:195102787-196071593	Active TSS Weak transcription Flanking Active TSS Strong transcription Enhancers Bivalent Enhancer Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	144 gene(s)	inside rSNPs	diseases
2	esv2757913	chr3:195379484-196071593	Weak transcription Genic enhancers Enhancers Active TSS Strong transcription ZNF genes & repeats Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	108 gene(s)	inside rSNPs	diseases
3	nsv532213	chr3:195643944-196063636	Enhancers Weak transcription Flanking Active TSS Strong transcription Active TSS Genic enhancers Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	87 gene(s)	inside rSNPs	diseases
4	nsv997797	chr3:195658360-196212958	Weak transcription Flanking Active TSS Genic enhancers Strong transcription Enhancers Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	98 gene(s)	inside rSNPs	diseases
5	nsv432543	chr3:195746690-196015690	Enhancers Active TSS Flanking Active TSS ZNF genes & repeats Weak transcription Strong transcription Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	69 gene(s)	inside rSNPs	diseases
6	nsv1009811	chr3:195851796-196138071	Weak transcription Strong transcription Flanking Bivalent TSS/Enh Enhancers Flanking Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Active TSS Genic enhancers Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	53 gene(s)	inside rSNPs	diseases
7	nsv461131	chr3:195858887-196072442	Enhancers Flanking Active TSS Weak transcription Active TSS Genic enhancers Strong transcription ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	49 gene(s)	inside rSNPs	diseases
8	nsv593071	chr3:195858887-196072442	Enhancers Weak transcription Strong transcription Flanking Active TSS Active TSS Genic enhancers Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	49 gene(s)	inside rSNPs	diseases
9	nsv1009178	chr3:195864466-196081670	Weak transcription Enhancers Bivalent Enhancer Strong transcription Flanking Active TSS Active TSS Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	51 gene(s)	inside rSNPs	diseases
10	nsv536892	chr3:195864466-196081670	Enhancers Flanking Active TSS Strong transcription Bivalent Enhancer Weak transcription Active TSS ZNF genes & repeats Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	51 gene(s)	inside rSNPs	diseases
11	nsv1003550	chr3:195885340-196159824	Flanking Active TSS Weak transcription Enhancers Strong transcription Genic enhancers ZNF genes & repeats Active TSS Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	49 gene(s)	inside rSNPs	diseases
12	nsv536893	chr3:195885340-196159824	Strong transcription Weak transcription Enhancers Active TSS Flanking Active TSS Bivalent/Poised TSS Genic enhancers Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	49 gene(s)	inside rSNPs	diseases
13	nsv878178	chr3:195929268-195998451	Weak transcription Strong transcription Flanking Active TSS Enhancers Bivalent Enhancer Active TSS Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	14 gene(s)	inside rSNPs	diseases
14	nsv878179	chr3:195929268-196019680	Active TSS Weak transcription Enhancers Genic enhancers Strong transcription Flanking Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	29 gene(s)	inside rSNPs	diseases
15	nsv1014563	chr3:195934010-196085951	Genic enhancers ZNF genes & repeats Flanking Active TSS Enhancers Active TSS Weak transcription Strong transcription Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	41 gene(s)	inside rSNPs	diseases
16	nsv878180	chr3:195946535-196066569	Enhancers Weak transcription Strong transcription Flanking Active TSS Genic enhancers Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	33 gene(s)	inside rSNPs	diseases
17	nsv878181	chr3:195946535-196072442	Enhancers Bivalent Enhancer Weak transcription Strong transcription Active TSS Flanking Active TSS Flanking Bivalent TSS/Enh Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	36 gene(s)	inside rSNPs	diseases
18	nsv1003194	chr3:195960270-196342423	Strong transcription Weak transcription Enhancers Flanking Active TSS Active TSS ZNF genes & repeats Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	64 gene(s)	inside rSNPs	diseases
19	nsv536894	chr3:195960270-196342423	Flanking Active TSS Weak transcription Enhancers Strong transcription Active TSS Bivalent/Poised TSS ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	64 gene(s)	inside rSNPs	diseases
20	nsv878182	chr3:195974181-196228360	Strong transcription Weak transcription Flanking Active TSS Active TSS Enhancers Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	45 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs12634587	TCTEX1D2	cis	Adipose Subcutaneous	GTEx

Chromatin state (count:122 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:195965200-195994200	Weak transcription	A549	lung
2	chr3:195965800-196012400	Weak transcription	Pancreatic Islets	Pancreatic Islet
3	chr3:195968800-195993400	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
4	chr3:195969600-196012400	Weak transcription	Fetal Brain Male	brain
5	chr3:195973400-195997200	Weak transcription	Small Intestine	intestine
6	chr3:195974400-195988800	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
7	chr3:195974400-195999800	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
8	chr3:195974600-195999800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
9	chr3:195974800-195999600	Weak transcription	H9 Cell Line	embryonic stem cell
10	chr3:195974800-195999600	Weak transcription	Pancreas	Pancrea
11	chr3:195974800-196005000	Weak transcription	Stomach Mucosa	stomach
12	chr3:195975000-195988800	Weak transcription	ES-I3 Cell Line	embryonic stem cell
13	chr3:195975000-195988800	Weak transcription	iPS-15b Cell Line	embryonic stem cell
14	chr3:195975000-195988800	Weak transcription	iPS-20b Cell Line	embryonic stem cell
15	chr3:195975000-195990800	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
16	chr3:195975000-195994000	Weak transcription	Right Ventricle	heart
17	chr3:195975000-195995000	Weak transcription	Primary T killer memory cells from peripheral blood	blood
18	chr3:195975000-195997200	Weak transcription	Esophagus	oesophagus
19	chr3:195975000-195999600	Weak transcription	H1 Cell Line	embryonic stem cell
20	chr3:195975200-195990200	Weak transcription	Rectal Smooth Muscle	rectum
21	chr3:195975200-195990800	Weak transcription	NHLF	lung
22	chr3:195975200-195991200	Weak transcription	Thymus	Thymus
23	chr3:195975200-195992800	Weak transcription	Brain Anterior Caudate	brain
24	chr3:195975200-195993400	Weak transcription	Aorta	Aorta
25	chr3:195975200-195994200	Weak transcription	Fetal Kidney	kidney
26	chr3:195975200-195994200	Weak transcription	Gastric	stomach
27	chr3:195975400-195992400	Weak transcription	Lung	lung
28	chr3:195975400-195993400	Weak transcription	Colonic Mucosa	Colon
29	chr3:195976400-195994200	Weak transcription	Spleen	Spleen
30	chr3:195977600-195989000	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
31	chr3:195978200-195994800	Weak transcription	Brain Angular Gyrus	brain
32	chr3:195978400-195994200	Weak transcription	Brain Substantia Nigra	brain
33	chr3:195978800-195994200	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
34	chr3:195979000-195993400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
35	chr3:195979000-195995000	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
36	chr3:195981200-195995200	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
37	chr3:195981400-195994600	Strong transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
38	chr3:195981400-195997800	Strong transcription	Monocytes-CD14+_RO01746	blood
39	chr3:195982200-195994200	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
40	chr3:195982400-195997600	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
41	chr3:195982600-195989600	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
42	chr3:195982800-195995000	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
43	chr3:195983000-195995800	Weak transcription	HMEC	breast
44	chr3:195983200-195999800	Weak transcription	Psoas Muscle	Psoas
45	chr3:195983600-195993400	Weak transcription	Ovary	ovary
46	chr3:195983800-195991400	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
47	chr3:195984000-195990200	Weak transcription	Brain Hippocampus Middle	brain
48	chr3:195984000-195997400	Weak transcription	Brain Cingulate Gyrus	brain
49	chr3:195984200-195991200	Weak transcription	Brain Germinal Matrix	brain
50	chr3:195984200-195994000	Weak transcription	Hela-S3	cervix

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links