Variant report

Variant	rs6581931
Chromosome Location	chr12:41134912-41134913
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	GATA3	chr12:41134872-41135035	SH-SY5Y	brain:	n/a	n/a

Variant related genes	Relation type
CNTN1	TF binding region

Extended variants
information (count: 51 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:45)

rs_ID	r²[population]
rs10506173	0.91[EUR][1000 genomes]
rs10784813	0.90[EUR][1000 genomes]
rs11836043	0.86[ASN][1000 genomes]
rs1348509	0.90[EUR][1000 genomes]
rs1373424	0.90[EUR][1000 genomes]
rs1444203	0.92[CEU][hapmap];0.90[EUR][1000 genomes]
rs1444204	0.92[CEU][hapmap];0.88[TSI][hapmap];0.90[EUR][1000 genomes]
rs1584093	0.82[LWK][hapmap];0.88[TSI][hapmap];0.90[EUR][1000 genomes]
rs1596509	1.00[CEU][hapmap];1.00[JPT][hapmap];1.00[AFR][1000 genomes];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1596539	0.85[CHD][hapmap];1.00[JPT][hapmap];0.86[ASN][1000 genomes]
rs17120936	0.85[CHD][hapmap];1.00[JPT][hapmap]
rs17128689	0.90[EUR][1000 genomes]
rs1816856	0.90[EUR][1000 genomes]
rs1867430	0.93[EUR][1000 genomes]
rs2053629	0.92[AFR][1000 genomes];0.97[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs2120599	0.91[EUR][1000 genomes]
rs4275691	0.92[CEU][hapmap];0.90[EUR][1000 genomes]
rs55635729	0.94[EUR][1000 genomes]
rs55736346	0.89[EUR][1000 genomes]
rs55786396	0.94[EUR][1000 genomes]
rs56032335	0.91[EUR][1000 genomes]
rs56334222	0.90[EUR][1000 genomes]
rs56383533	0.90[EUR][1000 genomes]
rs57772297	0.91[EUR][1000 genomes]
rs57816451	0.91[EUR][1000 genomes]
rs59066229	0.91[EUR][1000 genomes]
rs6581906	0.90[EUR][1000 genomes]
rs6581932	0.86[ASN][1000 genomes]
rs6581934	0.93[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7137967	0.94[EUR][1000 genomes]
rs7138084	0.94[EUR][1000 genomes]
rs7296616	0.90[AFR][1000 genomes];0.97[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs7301307	0.85[CHD][hapmap];1.00[JPT][hapmap]
rs73110852	0.90[EUR][1000 genomes]
rs73110883	0.81[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs74076704	0.91[EUR][1000 genomes]
rs74076712	0.93[EUR][1000 genomes]
rs74078532	0.91[EUR][1000 genomes]
rs74078558	0.90[EUR][1000 genomes]
rs74078563	0.90[EUR][1000 genomes]
rs74078569	0.90[EUR][1000 genomes]
rs74078570	0.90[EUR][1000 genomes]
rs7959703	0.90[EUR][1000 genomes]
rs7977934	0.93[EUR][1000 genomes]
rs935230	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[YRI][hapmap];0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]

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	nsv427909	chr12:41054306-41322257	Flanking Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Active TSS Enhancers Weak transcription Bivalent Enhancer Strong transcription ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
2	nsv832379	chr12:41054440-41232749	Weak transcription Enhancers Bivalent/Poised TSS Flanking Active TSS Flanking Bivalent TSS/Enh Active TSS Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3' Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
3	esv2751098	chr12:41082399-41180235	Enhancers Bivalent/Poised TSS Bivalent Enhancer Weak transcription Active TSS Flanking Bivalent TSS/Enh Flanking Active TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
4	nsv1044513	chr12:41091822-41175151	Weak transcription Flanking Active TSS Enhancers Active TSS ZNF genes & repeats	TF binding region Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
5	nsv558696	chr12:41092666-41172010	Weak transcription Enhancers Flanking Active TSS Active TSS ZNF genes & repeats	TF binding region Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
6	nsv832380	chr12:41132306-41323961	Weak transcription Strong transcription Enhancers Flanking Active TSS Active TSS ZNF genes & repeats Bivalent/Poised TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases

No data

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:41128400-41141400	Weak transcription	Pancreatic Islets	Pancreatic Islet
2	chr12:41129800-41140600	Weak transcription	Ovary	ovary
3	chr12:41130000-41139200	Weak transcription	iPS-18 Cell Line	embryonic stem cell
4	chr12:41131600-41135200	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
5	chr12:41133600-41145200	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
6	chr12:41133800-41162400	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin

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