Variant report

Variant	rs3088008
Chromosome Location	chr12:49724955-49724956
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr12:49724830..49727128-chr12:49748718..49750720,2	MCF-7	breast:
2	chr12:49659208..49661762-chr12:49723498..49725947,3	K562	blood:
3	chr12:49722840..49725192-chr12:49730603..49732392,2	MCF-7	breast:
4	chr12:49721808..49725568-chr12:49752625..49757232,4	MCF-7	breast:
5	chr12:49724052..49726858-chr12:49947435..49949990,2	K562	blood:
6	chr12:49724272..49727239-chr12:49903612..49905113,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000186897	Chromatin interaction
ENSG00000135519	Chromatin interaction

Extended variants
information (count: 47 )
Associated
traits (count: 5 )

rSNPs within LD-proxies of this variant (count:39)

rs_ID	r²[population]
rs10400435	0.91[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.88[GIH][hapmap];0.82[MEX][hapmap];1.00[TSI][hapmap];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs10400567	0.89[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs10875948	1.00[CEU][hapmap];1.00[JPT][hapmap]
rs11168967	1.00[JPT][hapmap]
rs11168973	0.93[ASN][1000 genomes]
rs11168974	0.82[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs11168975	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.96[ASN][1000 genomes]
rs11168981	0.82[CHB][hapmap]
rs11503617	0.93[ASN][1000 genomes]
rs11835037	1.00[JPT][hapmap]
rs11835303	0.85[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.96[GIH][hapmap];1.00[JPT][hapmap];0.95[LWK][hapmap];0.91[MEX][hapmap];0.94[MKK][hapmap];1.00[TSI][hapmap];0.90[YRI][hapmap];0.86[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11837234	1.00[JPT][hapmap]
rs12306866	0.82[CHB][hapmap]
rs12313488	0.93[ASN][1000 genomes]
rs12318618	1.00[CEU][hapmap];0.87[GIH][hapmap];1.00[JPT][hapmap];0.80[MEX][hapmap]
rs12322335	1.00[JPT][hapmap]
rs12580931	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.89[ASN][1000 genomes]
rs12581428	1.00[JPT][hapmap]
rs12822293	0.85[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.95[LWK][hapmap];1.00[MEX][hapmap];0.92[MKK][hapmap];1.00[TSI][hapmap];0.90[YRI][hapmap];0.82[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2070760	0.89[ASN][1000 genomes]
rs2236746	1.00[JPT][hapmap]
rs2270741	0.82[CHB][hapmap]
rs28493849	0.89[ASN][1000 genomes]
rs4243545	0.91[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.85[GIH][hapmap];1.00[JPT][hapmap];0.93[TSI][hapmap];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4382953	0.83[CEU][hapmap]
rs4898502	1.00[CEU][hapmap];0.80[MEX][hapmap]
rs4898504	0.90[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs4898519	0.91[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.85[GIH][hapmap];1.00[JPT][hapmap];0.86[TSI][hapmap];0.85[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs57241318	0.96[ASN][1000 genomes]
rs59575791	0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs67236923	0.89[ASN][1000 genomes]
rs67309388	0.89[ASN][1000 genomes]
rs7295247	1.00[JPT][hapmap]
rs7299812	0.82[CHB][hapmap]
rs73112143	0.89[ASN][1000 genomes]
rs73309977	0.85[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7342318	1.00[JPT][hapmap]
rs7342384	1.00[JPT][hapmap]
rs7488343	0.89[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:8 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1051161	chr12:49314550-49828473	Flanking Bivalent TSS/Enh Weak transcription Transcr. at gene 5' and 3' Genic enhancers Bivalent Enhancer Active TSS Strong transcription Enhancers Bivalent/Poised TSS Flanking Active TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	322 gene(s)	inside rSNPs	diseases
2	nsv541489	chr12:49314550-49828473	Flanking Active TSS Transcr. at gene 5' and 3' Enhancers Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh Genic enhancers Weak transcription Strong transcription Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	322 gene(s)	inside rSNPs	diseases
3	nsv1036452	chr12:49376285-49867760	Weak transcription Flanking Active TSS Enhancers Genic enhancers Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Strong transcription Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	315 gene(s)	inside rSNPs	diseases
4	nsv428801	chr12:49536659-49744884	Flanking Bivalent TSS/Enh Bivalent Enhancer Enhancers Flanking Active TSS Transcr. at gene 5' and 3' Strong transcription Weak transcription Active TSS Genic enhancers Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	145 gene(s)	inside rSNPs	diseases
5	nsv1042122	chr12:49678529-49823168	Bivalent Enhancer Bivalent/Poised TSS Flanking Active TSS Flanking Bivalent TSS/Enh Strong transcription Enhancers Active TSS Weak transcription ZNF genes & repeats Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	54 gene(s)	inside rSNPs	diseases
6	nsv1039176	chr12:49678529-49832618	Weak transcription Flanking Bivalent TSS/Enh Bivalent Enhancer Enhancers Bivalent/Poised TSS Strong transcription Transcr. at gene 5' and 3' Flanking Active TSS Active TSS Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	55 gene(s)	inside rSNPs	diseases
7	nsv899068	chr12:49714103-49924637	Flanking Bivalent TSS/Enh Weak transcription Genic enhancers Enhancers Strong transcription Flanking Active TSS Bivalent Enhancer Active TSS Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	52 gene(s)	inside rSNPs	diseases
8	nsv832405	chr12:49720279-49910862	Weak transcription Flanking Active TSS Bivalent Enhancer Enhancers Flanking Bivalent TSS/Enh Strong transcription Genic enhancers Bivalent/Poised TSS Active TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	49 gene(s)	inside rSNPs	diseases

mRNA abundance (count:5)

SNP	Gene	Cis/trans	Tissue	Source
rs3088008	DDN	cis	parietal	SCAN
rs3088008	GSTM1	trans	lymphoblastoid	seeQTL
rs3088008	PRPH	cis	cerebellum	SCAN
rs3088008	C1QL4	cis	Thyroid	GTEx
rs3088008	TMEM117	cis	cerebellum	SCAN

Chromatin state (count:77 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:49717400-49726800	Weak transcription	Right Atrium	heart
2	chr12:49717600-49725000	Weak transcription	Pancreas	Pancrea
3	chr12:49717800-49727000	Weak transcription	Esophagus	oesophagus
4	chr12:49718000-49725000	Weak transcription	Colonic Mucosa	Colon
5	chr12:49718000-49725000	Weak transcription	Fetal Heart	heart
6	chr12:49718000-49725000	Weak transcription	Placenta Amnion	Placenta Amnion
7	chr12:49718000-49725200	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
8	chr12:49718000-49725200	Weak transcription	Duodenum Mucosa	Duodenum
9	chr12:49718000-49725200	Weak transcription	Rectal Mucosa Donor 29	rectum
10	chr12:49718000-49725400	Weak transcription	Placenta	Placenta
11	chr12:49718000-49726200	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
12	chr12:49718000-49726400	Weak transcription	Primary B cells from cord blood	blood
13	chr12:49718000-49730200	Weak transcription	Gastric	stomach
14	chr12:49718200-49725200	Weak transcription	Fetal Brain Female	brain
15	chr12:49718200-49725400	Strong transcription	HUES6 Cell Line	embryonic stem cell
16	chr12:49718200-49725600	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
17	chr12:49718200-49725600	Weak transcription	Fetal Kidney	kidney
18	chr12:49718600-49725000	Strong transcription	Cortex derived primary cultured neurospheres	brain
19	chr12:49718600-49725400	Strong transcription	NHEK	skin
20	chr12:49718600-49725600	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
21	chr12:49719200-49725000	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
22	chr12:49719200-49725000	Strong transcription	Fetal Intestine Small	intestine
23	chr12:49719200-49725200	Strong transcription	H1 Cell Line	embryonic stem cell
24	chr12:49719200-49725200	Strong transcription	HUES48 Cell Line	embryonic stem cell
25	chr12:49719200-49725200	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
26	chr12:49719200-49725400	Strong transcription	Primary hematopoietic stem cells short term culture	blood
27	chr12:49719200-49725400	Strong transcription	NHLF	lung
28	chr12:49719200-49725600	Strong transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
29	chr12:49719200-49725600	Strong transcription	Monocytes-CD14+_RO01746	blood
30	chr12:49719400-49725400	Strong transcription	Fetal Thymus	thymus
31	chr12:49719400-49725400	Strong transcription	Thymus	Thymus
32	chr12:49719600-49725000	Strong transcription	H9 Cell Line	embryonic stem cell
33	chr12:49719800-49725200	Strong transcription	Primary neutrophils fromperipheralblood	blood
34	chr12:49720000-49725000	Strong transcription	Ganglion Eminence derived primary cultured neurospheres	brain
35	chr12:49720000-49725400	Strong transcription	Dnd41	blood
36	chr12:49720400-49725200	Strong transcription	Primary monocytes fromperipheralblood	blood
37	chr12:49720400-49725800	Weak transcription	ES-I3 Cell Line	embryonic stem cell
38	chr12:49721400-49727000	Weak transcription	NHDF-Ad	bronchial
39	chr12:49721600-49729600	Weak transcription	HSMM	muscle
40	chr12:49721800-49725200	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
41	chr12:49721800-49726400	Weak transcription	HUVEC	blood vessel
42	chr12:49722600-49725000	Strong transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
43	chr12:49722800-49725000	Strong transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
44	chr12:49722800-49725000	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
45	chr12:49723000-49725000	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
46	chr12:49723200-49725000	Strong transcription	iPS DF 6.9 Cell Line	embryonic stem cell
47	chr12:49723800-49725000	Weak transcription	Muscle Satellite Cultured Cells	--
48	chr12:49723800-49725200	Weak transcription	iPS-20b Cell Line	embryonic stem cell
49	chr12:49723800-49725400	Enhancers	HSMMtube	muscle
50	chr12:49724200-49725000	Transcr. at gene 5' and 3'	Foreskin Fibroblast Primary Cells skin02	Skin

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links