Variant report

Variant	rs7957141
Chromosome Location	chr12:30905379-30905380
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	MAFF	chr12:30905268-30905684	K562	blood:	n/a	chr12:30905382-30905400
2	MAFK	chr12:30905295-30905514	H1-hESC	embryonic stem cell:	n/a	chr12:30905384-30905399 chr12:30905384-30905395 chr12:30905384-30905395 chr12:30905384-30905400
3	MAFK	chr12:30905219-30905569	HepG2	liver:	n/a	chr12:30905384-30905399 chr12:30905384-30905395 chr12:30905384-30905395 chr12:30905384-30905400
4	MAFK	chr12:30905238-30905569	IMR90	lung:	n/a	chr12:30905384-30905399 chr12:30905384-30905395 chr12:30905384-30905395 chr12:30905384-30905400
5	MAFF	chr12:30905231-30905553	HepG2	liver:	n/a	chr12:30905382-30905400
6	MAFK	chr12:30905233-30905868	K562	blood:	n/a	chr12:30905384-30905399 chr12:30905384-30905395 chr12:30905712-30905722 chr12:30905384-30905395 chr12:30905384-30905400
7	MAFK	chr12:30905217-30905561	HepG2	liver:	n/a	chr12:30905384-30905399 chr12:30905384-30905395 chr12:30905384-30905395 chr12:30905384-30905400
8	POLR2A	chr12:30905253-30909133	PBDE	blood:	n/a	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr12:30902650..30905580-chr12:30906095..30908998,3	MCF-7	breast:

Variant related genes	Relation type
CAPRIN2	TF binding region
ENSG00000246331	TF binding region
ENSG00000110888	Chromatin interaction
ENSG00000246331	Chromatin interaction

Extended variants
information (count: 45 )
Associated
traits (count: 2 )

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

rs_ID	r²[population]
rs10444423	0.85[CHB][hapmap];0.90[JPT][hapmap]
rs10743729	0.85[CHB][hapmap];0.90[JPT][hapmap]
rs10771765	0.98[AFR][1000 genomes];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10771766	0.98[AFR][1000 genomes];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10771767	0.98[AFR][1000 genomes];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10771768	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10843804	0.85[CHB][hapmap];0.91[JPT][hapmap]
rs10843814	0.85[CHB][hapmap];0.90[JPT][hapmap]
rs10843816	0.85[CHB][hapmap];0.90[JPT][hapmap]
rs10843817	0.85[CHB][hapmap];0.89[JPT][hapmap]
rs10843822	0.84[CHB][hapmap];0.90[JPT][hapmap]
rs10843824	0.85[CHB][hapmap];0.89[JPT][hapmap]
rs10843833	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.85[AFR][1000 genomes];0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10843835	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11051005	0.85[CHB][hapmap];0.90[JPT][hapmap]
rs11051050	0.90[JPT][hapmap]
rs11051053	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.85[AFR][1000 genomes];0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11051061	0.90[JPT][hapmap]
rs12146709	0.85[CHB][hapmap];0.90[JPT][hapmap]
rs12303852	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12305697	0.95[AFR][1000 genomes];0.94[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12370429	0.92[ASN][1000 genomes]
rs12370947	0.85[CHB][hapmap];0.91[JPT][hapmap]
rs12809335	0.85[CHB][hapmap];0.84[JPT][hapmap]
rs12830910	0.85[CHB][hapmap];0.91[JPT][hapmap]
rs1866416	0.82[ASN][1000 genomes]
rs2241828	0.85[CHB][hapmap];0.90[JPT][hapmap]
rs2289302	0.85[CHB][hapmap];0.90[JPT][hapmap]
rs2304630	0.90[CHB][hapmap];1.00[JPT][hapmap];0.92[ASN][1000 genomes]
rs35925509	0.85[AFR][1000 genomes];0.96[AMR][1000 genomes];0.89[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4082413	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs6487933	0.91[CHB][hapmap];0.86[JPT][hapmap];0.87[ASN][1000 genomes]
rs6487938	0.86[AFR][1000 genomes];0.96[AMR][1000 genomes];0.89[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6487939	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7304221	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7304976	0.92[ASN][1000 genomes]
rs7952744	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7957226	1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7966063	0.80[JPT][hapmap]
rs7971762	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7971870	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7980510	0.85[CHB][hapmap];0.91[JPT][hapmap]

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	esv3343291	chr12:30455597-30992837	Weak transcription Enhancers Strong transcription Active TSS Flanking Active TSS Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	48 gene(s)	inside rSNPs	diseases
2	nsv832361	chr12:30794030-30997241	Transcr. at gene 5' and 3' Strong transcription Flanking Active TSS Weak transcription Active TSS Enhancers Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	41 gene(s)	inside rSNPs	diseases
3	nsv949148	chr12:30800040-31131712	Strong transcription Enhancers Weak transcription Active TSS Flanking Active TSS Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	45 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs7957141	IPO8	cis	Artery Tibial	GTEx
rs7957141	IPO8	cis	multi-tissue	Pritchard

Chromatin state (count:119 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:30861400-30906200	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
2	chr12:30861400-30906600	Weak transcription	Small Intestine	intestine
3	chr12:30863400-30906400	Weak transcription	Spleen	Spleen
4	chr12:30863400-30906600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
5	chr12:30876000-30906600	Weak transcription	Fetal Intestine Small	intestine
6	chr12:30878200-30906200	Weak transcription	Skeletal Muscle Male	skeletal muscle
7	chr12:30878800-30906600	Weak transcription	Placenta Amnion	Placenta Amnion
8	chr12:30879800-30905800	Weak transcription	NHLF	lung
9	chr12:30882000-30906800	Weak transcription	Psoas Muscle	Psoas
10	chr12:30882200-30905600	Weak transcription	H9 Cell Line	embryonic stem cell
11	chr12:30882200-30905800	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
12	chr12:30882200-30906200	Weak transcription	Duodenum Smooth Muscle	Duodenum
13	chr12:30882200-30906400	Weak transcription	Lung	lung
14	chr12:30882200-30906400	Weak transcription	Rectal Smooth Muscle	rectum
15	chr12:30882200-30906600	Weak transcription	Placenta	Placenta
16	chr12:30882200-30906800	Weak transcription	Esophagus	oesophagus
17	chr12:30882400-30905400	Weak transcription	Primary T helper naive cells from peripheral blood	blood
18	chr12:30882400-30906600	Weak transcription	Rectal Mucosa Donor 29	rectum
19	chr12:30882600-30905400	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
20	chr12:30882600-30906200	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
21	chr12:30882600-30906400	Weak transcription	Right Ventricle	heart
22	chr12:30882800-30906800	Weak transcription	Gastric	stomach
23	chr12:30883200-30905800	Weak transcription	HSMMtube	muscle
24	chr12:30883200-30906400	Weak transcription	Monocytes-CD14+_RO01746	blood
25	chr12:30884800-30905800	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
26	chr12:30885000-30905600	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
27	chr12:30886600-30906400	Weak transcription	Brain Substantia Nigra	brain
28	chr12:30886800-30905800	Weak transcription	Brain Cingulate Gyrus	brain
29	chr12:30888400-30906800	Weak transcription	Fetal Intestine Large	intestine
30	chr12:30889200-30905800	Weak transcription	Fetal Stomach	stomach
31	chr12:30889200-30906200	Weak transcription	Thymus	Thymus
32	chr12:30892400-30906400	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
33	chr12:30892400-30906400	Weak transcription	Fetal Muscle Trunk	muscle
34	chr12:30892600-30906400	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
35	chr12:30894000-30905600	Weak transcription	Dnd41	blood
36	chr12:30894800-30906400	Weak transcription	Stomach Mucosa	stomach
37	chr12:30897200-30905600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
38	chr12:30897200-30906600	Weak transcription	Primary hematopoietic stem cells short term culture	blood
39	chr12:30899600-30906600	Weak transcription	Duodenum Mucosa	Duodenum
40	chr12:30900000-30905600	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
41	chr12:30900000-30906200	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
42	chr12:30900000-30906200	Weak transcription	Primary B cells from peripheral blood	blood
43	chr12:30900000-30906200	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
44	chr12:30900000-30906400	Weak transcription	Adipose Nuclei	Adipose
45	chr12:30900000-30906400	Weak transcription	Fetal Muscle Leg	muscle
46	chr12:30900000-30906600	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
47	chr12:30900000-30906600	Weak transcription	Rectal Mucosa Donor 31	rectum
48	chr12:30900000-30906800	Weak transcription	Sigmoid Colon	Sigmoid Colon
49	chr12:30900200-30905600	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
50	chr12:30900200-30905600	Weak transcription	NHDF-Ad	bronchial

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links