Variant report

Variant	rs4882602
Chromosome Location	chr12:76026511-76026512
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr12:76019985..76022320-chr12:76024831..76027786,2	MCF-7	breast:
2	chr12:76014354..76029119-chr12:76417641..76428409,36	MCF-7	breast:

Variant related genes	Relation type
ENSG00000257453	Chromatin interaction
ENSG00000257839	Chromatin interaction
ENSG00000139289	Chromatin interaction

Extended variants
information (count: 42 )
Associated
traits (count: 8 )

rSNPs within LD-proxies of this variant (count:37)

rs_ID	r²[population]
rs10748283	0.83[ASN][1000 genomes]
rs10748284	0.89[CHB][hapmap];0.96[ASN][1000 genomes]
rs10785199	0.85[ASN][1000 genomes]
rs10785200	0.85[ASN][1000 genomes]
rs10879937	0.83[ASN][1000 genomes]
rs10879938	0.84[CHB][hapmap];0.82[CHD][hapmap];0.90[JPT][hapmap]
rs10879943	0.96[CEU][hapmap];0.81[CHB][hapmap];0.82[CHD][hapmap];0.93[GIH][hapmap];0.95[JPT][hapmap];0.88[MKK][hapmap];0.95[TSI][hapmap];0.81[AMR][1000 genomes];0.96[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs10879944	0.98[AFR][1000 genomes];0.99[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs10879945	0.90[CHB][hapmap];0.97[CHD][hapmap];1.00[JPT][hapmap];0.96[ASN][1000 genomes]
rs10879946	0.99[AFR][1000 genomes];0.99[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs10879947	0.84[ASW][hapmap];0.96[CEU][hapmap];0.81[CHB][hapmap];0.90[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.91[MEX][hapmap];0.89[MKK][hapmap];0.95[TSI][hapmap];0.97[AMR][1000 genomes];0.95[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs10879948	0.88[AFR][1000 genomes];0.99[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs11180600	0.81[AMR][1000 genomes];0.97[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs11180601	0.96[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs11180605	0.95[ASN][1000 genomes]
rs11495681	0.82[ASN][1000 genomes]
rs12310185	0.96[CEU][hapmap];0.90[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.99[AFR][1000 genomes];0.99[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs12318049	0.81[AMR][1000 genomes];0.96[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs1466464	1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[YRI][hapmap];0.94[AFR][1000 genomes];0.80[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1871548	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs34767748	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs34952545	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4882601	0.96[CEU][hapmap];0.80[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs4882637	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4882639	0.96[CEU][hapmap];0.81[CHB][hapmap];0.85[CHD][hapmap];1.00[JPT][hapmap];0.81[LWK][hapmap];0.98[TSI][hapmap];0.99[AMR][1000 genomes];0.97[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs4882640	0.92[CEU][hapmap];0.81[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.99[AFR][1000 genomes];0.99[AMR][1000 genomes];0.97[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs7137366	0.81[CHB][hapmap];1.00[JPT][hapmap];0.94[ASN][1000 genomes]
rs733880	0.90[CHB][hapmap];0.90[JPT][hapmap]
rs733881	0.90[CHB][hapmap];0.80[CHD][hapmap];0.86[JPT][hapmap]
rs7958075	1.00[CEU][hapmap];0.84[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7958490	1.00[AFR][1000 genomes];0.99[AMR][1000 genomes];0.96[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7958760	1.00[ASW][hapmap];1.00[CEU][hapmap];0.81[CHB][hapmap];1.00[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.98[MKK][hapmap];0.95[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.99[AMR][1000 genomes];0.96[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7972231	0.88[ASN][1000 genomes]
rs7973399	1.00[AFR][1000 genomes];0.99[AMR][1000 genomes];0.96[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7980645	1.00[ASW][hapmap];0.96[CEU][hapmap];0.95[CHB][hapmap];0.93[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.95[MKK][hapmap];0.95[TSI][hapmap];1.00[YRI][hapmap];0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs899658	0.97[ASN][1000 genomes]
rs899659	0.95[CHB][hapmap];0.97[CHD][hapmap];1.00[JPT][hapmap];0.95[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:5 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv492067	chr12:75415458-76077537	Flanking Active TSS Enhancers Active TSS Weak transcription Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS Genic enhancers Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	28 gene(s)	inside rSNPs	diseases
2	nsv1036987	chr12:75415532-76101559	Weak transcription Strong transcription Flanking Active TSS Enhancers Bivalent/Poised TSS Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	35 gene(s)	inside rSNPs	diseases
3	nsv899313	chr12:75715330-76057811	Weak transcription Active TSS Flanking Active TSS Enhancers Transcr. at gene 5' and 3' Strong transcription Flanking Bivalent TSS/Enh Genic enhancers ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	18 gene(s)	inside rSNPs	diseases
4	nsv1040583	chr12:75742802-76360276	Enhancers Genic enhancers Weak transcription Bivalent Enhancer Flanking Active TSS Strong transcription Transcr. at gene 5' and 3' Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	32 gene(s)	inside rSNPs	diseases
5	nsv948653	chr12:75773464-76220618	Active TSS Enhancers Flanking Active TSS Genic enhancers Weak transcription Strong transcription 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	27 gene(s)	inside rSNPs	diseases

mRNA abundance (count:8)

SNP	Gene	Cis/trans	Tissue	Source
rs4882602	GLIPR1L2	cis	cerebellum	SCAN
rs4882602	GLIPR1	Cis_1M	lymphoblastoid	RTeQTL
rs4882602	KRR1	cis	parietal	SCAN
rs4882602	GLIPR1L2	cis	Skin Sun Exposed Lower leg	GTEx
rs4882602	GLIPR1L2	cis	Artery Tibial	GTEx
rs4882602	KRR1	cis	cerebellum	SCAN
rs4882602	GLIPR1L2	cis	Thyroid	GTEx
rs4882602	GLIPR1L2	cis	parietal	SCAN

Chromatin state (count:34 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:76017800-76028800	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
2	chr12:76018000-76028600	Weak transcription	NHLF	lung
3	chr12:76018000-76028800	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
4	chr12:76018200-76029600	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
5	chr12:76018400-76027600	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
6	chr12:76018400-76029400	Weak transcription	NHEK	skin
7	chr12:76023400-76028200	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
8	chr12:76024000-76027800	Weak transcription	HepG2	liver
9	chr12:76024200-76028400	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
10	chr12:76025000-76027800	Enhancers	HUES64 Cell Line	embryonic stem cell
11	chr12:76025000-76027800	Enhancers	iPS-18 Cell Line	embryonic stem cell
12	chr12:76025000-76028400	Enhancers	HUES48 Cell Line	embryonic stem cell
13	chr12:76025200-76027000	Enhancers	Fetal Lung	lung
14	chr12:76025400-76027000	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
15	chr12:76025400-76027000	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
16	chr12:76025400-76027000	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
17	chr12:76025400-76030800	Enhancers	iPS-15b Cell Line	embryonic stem cell
18	chr12:76025600-76032400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
19	chr12:76025800-76026600	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
20	chr12:76025800-76027400	Weak transcription	H9 Cell Line	embryonic stem cell
21	chr12:76025800-76030200	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
22	chr12:76026000-76026600	Enhancers	Muscle Satellite Cultured Cells	--
23	chr12:76026000-76027000	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
24	chr12:76026200-76026600	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
25	chr12:76026200-76026600	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
26	chr12:76026200-76026600	Enhancers	Cortex derived primary cultured neurospheres	brain
27	chr12:76026200-76026600	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
28	chr12:76026200-76026600	Enhancers	NH-A	brain
29	chr12:76026200-76026600	Enhancers	NHDF-Ad	bronchial
30	chr12:76026200-76026800	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
31	chr12:76026200-76026800	Flanking Active TSS	iPS-20b Cell Line	embryonic stem cell
32	chr12:76026200-76027200	Enhancers	HUVEC	blood vessel
33	chr12:76026200-76030200	Enhancers	ES-I3 Cell Line	embryonic stem cell
34	chr12:76026400-76027600	Weak transcription	HUES6 Cell Line	embryonic stem cell

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links