Variant report

Variant	rs11180602
Chromosome Location	chr12:76016713-76016714
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr12:76015495..76018360-chr12:76104509..76107219,2	MCF-7	breast:
2	chr12:76015220..76016961-chr12:76477481..76480006,2	MCF-7	breast:
3	chr12:76013741..76020372-chr12:76422912..76427305,12	MCF-7	breast:
4	chr12:76016288..76017848-chr12:76202923..76204830,2	MCF-7	breast:
5	chr12:76015734..76021626-chr12:76097256..76101818,9	MCF-7	breast:
6	chr12:76014354..76029119-chr12:76417641..76428409,36	MCF-7	breast:

Variant related genes	Relation type
ENSG00000187109	Chromatin interaction
ENSG00000139289	Chromatin interaction
ENSG00000257839	Chromatin interaction
ENSG00000257453	Chromatin interaction

Extended variants
information (count: 26 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:21)

rs_ID	r²[population]
rs10879940	0.82[AFR][1000 genomes];0.96[AMR][1000 genomes]
rs10879941	0.92[AFR][1000 genomes];0.84[AMR][1000 genomes]
rs10879942	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]
rs11180599	0.92[AFR][1000 genomes];0.95[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs1147996	0.89[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs12579676	0.87[AFR][1000 genomes];0.82[AMR][1000 genomes]
rs1275473	0.82[EUR][1000 genomes]
rs1275475	0.82[EUR][1000 genomes]
rs1295819	0.93[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs1383102	1.00[CEU][hapmap];1.00[GIH][hapmap];0.86[MKK][hapmap];0.92[TSI][hapmap];0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1679383	0.89[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs1965925	0.84[AMR][1000 genomes]
rs2013270	0.80[CEU][hapmap];0.91[AMR][1000 genomes];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4882633	0.80[CEU][hapmap];0.89[LWK][hapmap];0.91[YRI][hapmap];0.86[AFR][1000 genomes];0.96[AMR][1000 genomes];0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4882634	0.82[AMR][1000 genomes]
rs4882636	0.82[AMR][1000 genomes]
rs7136963	0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7298332	1.00[CEU][hapmap];1.00[GIH][hapmap];0.97[LWK][hapmap];0.96[MKK][hapmap];0.92[TSI][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]
rs7301086	0.91[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7316871	0.84[AMR][1000 genomes];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7488353	0.99[AFR][1000 genomes];0.96[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:14 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:75980000-76017000	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
2	chr12:76015600-76018600	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
3	chr12:76016000-76017000	Enhancers	Dnd41	blood
4	chr12:76016200-76018200	Enhancers	HUES48 Cell Line	embryonic stem cell
5	chr12:76016200-76018200	Enhancers	HUES6 Cell Line	embryonic stem cell
6	chr12:76016200-76018400	Enhancers	ES-I3 Cell Line	embryonic stem cell
7	chr12:76016400-76016800	Enhancers	K562	blood
8	chr12:76016400-76017600	Enhancers	iPS-20b Cell Line	embryonic stem cell
9	chr12:76016400-76018000	Enhancers	HUVEC	blood vessel
10	chr12:76016400-76018400	Enhancers	NHEK	skin
11	chr12:76016400-76018600	Enhancers	Hela-S3	cervix
12	chr12:76016400-76018600	Enhancers	HepG2	liver
13	chr12:76016600-76016800	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
14	chr12:76016600-76018000	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links