Variant report

Variant	rs7970459
Chromosome Location	chr12:72703898-72703899
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	chr12:72682098..72683659-chr12:72703353..72706268,2	MCF-7	breast:

Extended variants
information (count: 33 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:25)

rs_ID	r²[population]
rs11612036	0.95[CHB][hapmap];0.86[JPT][hapmap];0.83[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs12302831	0.95[CHB][hapmap];0.86[JPT][hapmap];0.83[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs12309288	0.95[CHB][hapmap];0.90[JPT][hapmap];0.84[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs12319066	0.80[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs12321111	0.95[CHB][hapmap];0.80[ASN][1000 genomes]
rs12321257	0.95[CHB][hapmap];0.87[CHD][hapmap];0.81[GIH][hapmap];0.86[JPT][hapmap];0.85[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs12321315	0.95[CHB][hapmap];0.92[CHD][hapmap];0.87[GIH][hapmap];0.86[JPT][hapmap];0.83[MEX][hapmap];0.84[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs12321379	0.95[CHB][hapmap];0.92[CHD][hapmap];0.87[GIH][hapmap];0.86[JPT][hapmap];0.84[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs12322759	0.95[CHB][hapmap];0.85[JPT][hapmap];0.83[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs12426376	0.83[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs17111049	0.90[CHB][hapmap];0.86[JPT][hapmap];0.83[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs3935113	0.85[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs3935114	0.84[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs4309196	0.95[CHB][hapmap];0.90[CHD][hapmap];0.86[JPT][hapmap];0.83[MEX][hapmap]
rs4316545	0.83[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs4390383	0.95[CHB][hapmap];0.86[JPT][hapmap];0.85[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs4394876	0.85[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs4533084	0.95[CHB][hapmap];0.86[JPT][hapmap];0.85[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs4760760	0.90[CHB][hapmap];1.00[CHD][hapmap];0.84[ASN][1000 genomes]
rs56297022	0.84[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs7304027	0.85[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs7488259	0.88[ASW][hapmap];0.90[CHB][hapmap];1.00[CHD][hapmap];0.82[GIH][hapmap];0.82[JPT][hapmap];0.95[MEX][hapmap];0.83[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs7962187	0.95[CHB][hapmap];0.86[JPT][hapmap];0.85[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs7970630	0.86[AFR][1000 genomes];0.90[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs7970646	0.92[CEU][hapmap];0.95[CHB][hapmap];0.85[JPT][hapmap];0.86[YRI][hapmap];0.86[AFR][1000 genomes];0.90[EUR][1000 genomes];0.90[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:8 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv2422452	chr12:72485933-73175581	Flanking Bivalent TSS/Enh Active TSS Weak transcription Enhancers Bivalent/Poised TSS Bivalent Enhancer Flanking Active TSS Strong transcription ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	19 gene(s)	inside rSNPs	diseases
2	nsv899257	chr12:72569746-73145896	ZNF genes & repeats Weak transcription Enhancers Flanking Bivalent TSS/Enh Flanking Active TSS Active TSS Bivalent/Poised TSS Bivalent Enhancer Genic enhancers Strong transcription Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	19 gene(s)	inside rSNPs	diseases
3	nsv832452	chr12:72584971-72764495	Enhancers Bivalent/Poised TSS Genic enhancers Weak transcription Flanking Active TSS Flanking Bivalent TSS/Enh Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' Strong transcription ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	14 gene(s)	inside rSNPs	diseases
4	nsv899258	chr12:72624088-72957899	Bivalent Enhancer Weak transcription Bivalent/Poised TSS Flanking Active TSS Enhancers Genic enhancers Active TSS Flanking Bivalent TSS/Enh Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	16 gene(s)	inside rSNPs	diseases
5	nsv1044083	chr12:72647640-73275526	Enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Weak transcription Genic enhancers Strong transcription Bivalent Enhancer Active TSS Flanking Active TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	20 gene(s)	inside rSNPs	diseases
6	nsv469465	chr12:72655925-73259114	Weak transcription Active TSS Enhancers Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh Flanking Active TSS Genic enhancers Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	15 gene(s)	inside rSNPs	diseases
7	nsv559363	chr12:72655925-73259114	Weak transcription Flanking Bivalent TSS/Enh Enhancers Bivalent/Poised TSS Active TSS Flanking Active TSS Bivalent Enhancer Strong transcription ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	15 gene(s)	inside rSNPs	diseases
8	nsv868884	chr12:72664763-73241518	Enhancers Bivalent/Poised TSS Weak transcription Active TSS Flanking Bivalent TSS/Enh Flanking Active TSS ZNF genes & repeats Bivalent Enhancer Strong transcription Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	14 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs7970459	TBC1D15	cis	parietal	SCAN

Chromatin state (count:6 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:72692000-72705800	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
2	chr12:72696600-72704400	Enhancers	Fetal Intestine Large	intestine
3	chr12:72701400-72705200	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
4	chr12:72702000-72707200	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
5	chr12:72703000-72707200	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
6	chr12:72703200-72707600	Weak transcription	Fetal Intestine Small	intestine

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