Variant report

Variant	rs10879942
Chromosome Location	chr12:76017475-76017476
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:0)
CpG islands
(count:0)
Chromatin interactive
region (count:11)
LncRNA
region (count:1)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

(count:11 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr12:76017394..76018226-chr12:76424820..76425629,3	MCF-7	breast:
2	chr12:76015495..76018360-chr12:76104509..76107219,2	MCF-7	breast:
3	chr12:76013741..76020372-chr12:76422912..76427305,12	MCF-7	breast:
4	chr12:76017307..76018172-chr12:76430579..76431583,4	MCF-7	breast:
5	chr12:76016288..76017848-chr12:76202923..76204830,2	MCF-7	breast:
6	chr12:76015734..76021626-chr12:76097256..76101818,9	MCF-7	breast:
7	chr12:76017332..76018157-chr12:76849234..76849752,2	MCF-7	breast:
8	chr12:76014354..76029119-chr12:76417641..76428409,36	MCF-7	breast:
9	chr12:76017322..76018337-chr12:76425217..76425917,6	MCF-7	breast:
10	chr12:76017185..76019394-chr12:76337259..76339909,2	MCF-7	breast:
11	chr12:76017340..76020194-chr12:76022357..76024091,3	MCF-7	breast:

(count:1 , 50 per page) page: 1

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-GLIPR1-6	chr12:76017303-76017952	NONHSAT029538

No data

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

Extended variants
information (count: 24 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:19)

rs_ID	r²[population]
rs10879940	0.81[AFR][1000 genomes];0.93[AMR][1000 genomes]
rs10879941	0.91[AFR][1000 genomes];0.81[AMR][1000 genomes]
rs11180599	0.91[AFR][1000 genomes];0.91[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs11180602	0.89[ASW][hapmap];1.00[CEU][hapmap];1.00[GIH][hapmap];0.94[LWK][hapmap];0.95[MKK][hapmap];0.92[TSI][hapmap];1.00[YRI][hapmap];0.99[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1147996	0.85[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs12579676	0.86[AFR][1000 genomes]
rs1275473	0.82[EUR][1000 genomes]
rs1275475	0.82[EUR][1000 genomes]
rs1295819	0.89[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs1383102	1.00[CEU][hapmap];1.00[GIH][hapmap];0.93[MEX][hapmap];0.87[MKK][hapmap];1.00[TSI][hapmap];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1679383	0.85[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs1965925	0.87[AMR][1000 genomes]
rs2013270	0.80[CEU][hapmap];0.86[MEX][hapmap];0.85[TSI][hapmap];0.87[AMR][1000 genomes];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4882633	0.80[CEU][hapmap];0.94[LWK][hapmap];0.87[MEX][hapmap];0.85[TSI][hapmap];0.91[YRI][hapmap];0.85[AFR][1000 genomes];0.93[AMR][1000 genomes];0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7136963	0.92[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7298332	0.89[ASW][hapmap];1.00[CEU][hapmap];1.00[GIH][hapmap];0.97[LWK][hapmap];0.93[MEX][hapmap];0.98[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7301086	0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7316871	0.81[AMR][1000 genomes];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7488353	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[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

No data

Chromatin state (count:40 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:76015600-76018600	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
2	chr12:76016200-76018200	Enhancers	HUES48 Cell Line	embryonic stem cell
3	chr12:76016200-76018200	Enhancers	HUES6 Cell Line	embryonic stem cell
4	chr12:76016200-76018400	Enhancers	ES-I3 Cell Line	embryonic stem cell
5	chr12:76016400-76017600	Enhancers	iPS-20b Cell Line	embryonic stem cell
6	chr12:76016400-76018000	Enhancers	HUVEC	blood vessel
7	chr12:76016400-76018400	Enhancers	NHEK	skin
8	chr12:76016400-76018600	Enhancers	Hela-S3	cervix
9	chr12:76016400-76018600	Enhancers	HepG2	liver
10	chr12:76016600-76018000	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
11	chr12:76016800-76017800	Enhancers	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
12	chr12:76016800-76017800	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
13	chr12:76016800-76018000	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
14	chr12:76016800-76018000	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
15	chr12:76016800-76020800	Weak transcription	K562	blood
16	chr12:76017000-76017800	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
17	chr12:76017000-76018000	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
18	chr12:76017000-76018000	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
19	chr12:76017000-76018000	Enhancers	Muscle Satellite Cultured Cells	--
20	chr12:76017000-76018000	Enhancers	Fetal Heart	heart
21	chr12:76017000-76018200	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
22	chr12:76017200-76017600	Weak transcription	HUES64 Cell Line	embryonic stem cell
23	chr12:76017200-76018000	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
24	chr12:76017200-76018200	Enhancers	Foreskin Fibroblast Primary Cells skin02	Skin
25	chr12:76017200-76018200	Enhancers	NHDF-Ad	bronchial
26	chr12:76017400-76017600	Enhancers	Pancreas	Pancrea
27	chr12:76017400-76017800	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
28	chr12:76017400-76017800	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
29	chr12:76017400-76017800	Enhancers	Fetal Adrenal Gland	Adrenal Gland
30	chr12:76017400-76017800	Enhancers	NH-A	brain
31	chr12:76017400-76018000	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
32	chr12:76017400-76018000	Enhancers	Breast Myoepithelial Primary Cells	Breast
33	chr12:76017400-76018000	Enhancers	Adipose Nuclei	Adipose
34	chr12:76017400-76018000	Enhancers	Skeletal Muscle Male	skeletal muscle
35	chr12:76017400-76018000	Enhancers	Skeletal Muscle Female	skeletal muscle
36	chr12:76017400-76018000	Enhancers	HSMMtube	muscle
37	chr12:76017400-76018000	Enhancers	NHLF	lung
38	chr12:76017400-76018200	Enhancers	HMEC	breast
39	chr12:76017400-76018400	Enhancers	A549	lung
40	chr12:76017400-76018800	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links