Variant report

Variant	rs12512646
Chromosome Location	chr4:120585733-120585734
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr4:120583446..120585876-chr4:120986631..120988328,2	K562	blood:

Variant related genes	Relation type
ENSG00000250938	Chromatin interaction
ENSG00000164109	Chromatin interaction

Extended variants
information (count: 55 )
Associated
traits (count: 7 )

rSNPs within LD-proxies of this variant (count:49)

rs_ID	r²[population]
rs10009566	0.87[EUR][1000 genomes]
rs10012252	0.87[EUR][1000 genomes]
rs10022185	0.86[EUR][1000 genomes]
rs10034450	0.81[CEU][hapmap]
rs10050092	0.82[EUR][1000 genomes]
rs11098531	0.83[CEU][hapmap]
rs11098534	0.87[EUR][1000 genomes]
rs11737395	0.83[CEU][hapmap]
rs12499377	0.81[AFR][1000 genomes];0.93[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs12504773	0.84[EUR][1000 genomes]
rs12642411	0.89[EUR][1000 genomes]
rs13104219	0.80[JPT][hapmap]
rs13122709	0.83[EUR][1000 genomes]
rs13136462	0.83[EUR][1000 genomes]
rs17050695	0.85[CEU][hapmap];0.85[TSI][hapmap]
rs17051352	0.89[EUR][1000 genomes]
rs17051356	0.93[CEU][hapmap];1.00[CHB][hapmap];0.91[JPT][hapmap];0.90[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2127821	0.80[CEU][hapmap]
rs2170276	0.81[CEU][hapmap]
rs2389880	0.87[EUR][1000 genomes]
rs2389882	0.86[EUR][1000 genomes]
rs2389885	0.80[EUR][1000 genomes]
rs2389886	0.86[EUR][1000 genomes]
rs2389887	0.86[EUR][1000 genomes]
rs28535956	0.82[TSI][hapmap];0.81[EUR][1000 genomes]
rs28578366	0.82[TSI][hapmap];0.82[EUR][1000 genomes]
rs28787668	0.87[EUR][1000 genomes]
rs28850368	0.83[EUR][1000 genomes]
rs34278750	0.84[EUR][1000 genomes]
rs34835603	0.85[EUR][1000 genomes]
rs3733519	0.84[CEU][hapmap]
rs3756156	0.82[CEU][hapmap]
rs3775841	0.88[CEU][hapmap]
rs3806808	0.80[CEU][hapmap];0.88[TSI][hapmap];0.85[EUR][1000 genomes]
rs41464847	0.83[JPT][hapmap]
rs4504231	0.92[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs4833624	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.98[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.98[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];0.92[YRI][hapmap];0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6832740	0.88[TSI][hapmap];0.84[EUR][1000 genomes]
rs6844263	0.82[JPT][hapmap]
rs6855918	0.85[EUR][1000 genomes]
rs7664440	0.87[EUR][1000 genomes]
rs7671096	0.87[EUR][1000 genomes]
rs7676296	0.87[EUR][1000 genomes]
rs7680914	0.85[EUR][1000 genomes]
rs7693919	0.85[EUR][1000 genomes]
rs7695292	0.84[EUR][1000 genomes]
rs9994488	0.86[AMR][1000 genomes];0.81[ASN][1000 genomes]
rs9994651	0.96[AFR][1000 genomes];0.87[AMR][1000 genomes];0.81[ASN][1000 genomes]
rs9997631	0.87[CEU][hapmap]

Variant overlapped rSNPs/rCNVs (count:6 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv916641	chr4:119780023-120777320	Strong transcription Weak transcription Enhancers Active TSS Flanking Active TSS Bivalent/Poised TSS Genic enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	72 gene(s)	inside rSNPs	diseases
2	nsv532739	chr4:120392824-121098103	Enhancers Flanking Active TSS Strong transcription Weak transcription Bivalent/Poised TSS Active TSS ZNF genes & repeats Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	33 gene(s)	inside rSNPs	diseases
3	nsv1010753	chr4:120429028-120684310	Bivalent/Poised TSS Strong transcription Weak transcription Enhancers Transcr. at gene 5' and 3' Active TSS Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Flanking Active TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
4	nsv537233	chr4:120429028-120684310	ZNF genes & repeats Enhancers Weak transcription Strong transcription Active TSS Flanking Active TSS Genic enhancers Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
5	nsv1006572	chr4:120432494-120694243	Enhancers Weak transcription Flanking Active TSS Genic enhancers ZNF genes & repeats Strong transcription Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
6	esv1802546	chr4:120558608-120675026	Enhancers Weak transcription Flanking Active TSS Active TSS ZNF genes & repeats Bivalent Enhancer Genic enhancers	Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases

mRNA abundance (count:7)

SNP	Gene	Cis/trans	Tissue	Source
rs12512646	RP11-33B1.1	cis	Whole Blood	GTEx
rs12512646	C4orf3	cis	cerebellum	SCAN
rs12512646	FLJ14186///LOC284701///LOC441124///LOC728624	Cis_chr	lymphoblastoid	RTeQTL
rs12512646	RP11-33B1.1	cis	Esophagus Mucosa	GTEx
rs12512646	LOC645513	Cis_1M	lymphoblastoid	RTeQTL
rs12512646	RP11-33B1.1	cis	lung	GTEx
rs12512646	RP11-33B1.1	cis	Heart Left Ventricle	GTEx

Chromatin state (count:29 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:120577600-120605000	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
2	chr4:120578800-120588000	Weak transcription	HUES6 Cell Line	embryonic stem cell
3	chr4:120578800-120592800	Weak transcription	ES-I3 Cell Line	embryonic stem cell
4	chr4:120583600-120587800	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
5	chr4:120584400-120585800	Enhancers	Liver	Liver
6	chr4:120584400-120585800	Active TSS	Stomach Smooth Muscle	stomach
7	chr4:120584400-120586000	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
8	chr4:120584400-120586000	Active TSS	Aorta	Aorta
9	chr4:120584600-120585800	Flanking Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
10	chr4:120584600-120585800	Active TSS	Duodenum Smooth Muscle	Duodenum
11	chr4:120584600-120585800	Active TSS	Rectal Mucosa Donor 29	rectum
12	chr4:120584600-120586000	Flanking Active TSS	Rectal Smooth Muscle	rectum
13	chr4:120584800-120585800	Active TSS	Pancreatic Islets	Pancreatic Islet
14	chr4:120585000-120585800	Enhancers	Fetal Lung	lung
15	chr4:120585000-120586000	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
16	chr4:120585200-120585800	Flanking Active TSS	GM12878-XiMat	blood
17	chr4:120585200-120587200	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
18	chr4:120585200-120587400	Weak transcription	Fetal Stomach	stomach
19	chr4:120585200-120587600	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
20	chr4:120585200-120587800	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
21	chr4:120585400-120585800	Flanking Active TSS	Breast Myoepithelial Primary Cells	Breast
22	chr4:120585400-120586000	Active TSS	NHDF-Ad	bronchial
23	chr4:120585400-120586000	Enhancers	NHEK	skin
24	chr4:120585400-120588000	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
25	chr4:120585600-120585800	Enhancers	HMEC	breast
26	chr4:120585600-120585800	Enhancers	NHLF	lung
27	chr4:120585600-120586200	Enhancers	Osteobl	bone
28	chr4:120585600-120589000	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
29	chr4:120585600-120589600	Enhancers	Colon Smooth Muscle	Colon

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links