Variant report

Variant	rs4712075
Chromosome Location	chr6:54709692-54709693
allele	G/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	POLR2A	chr6:54709547-54709894	MCF-7	breast:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr6:54483454..54486448-chr6:54709404..54710933,2	MCF-7	breast:
2	chr6:54709139..54711220-chr6:54750997..54752618,2	MCF-7	breast:
3	chr20:52738859..52741782-chr6:54708785..54710307,2	MCF-7	breast:
4	chr6:54556132..54558033-chr6:54708676..54711461,2	MCF-7	breast:
5	chr6:54709202..54711186-chr6:54779955..54782595,2	MCF-7	breast:

Variant related genes	Relation type
FAM83B	TF binding region
ENSG00000224984	TF binding region

Extended variants
information (count: 44 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:41)

rs_ID	r²[population]
rs10807484	0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10807485	0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10948862	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];0.95[MEX][hapmap];0.94[MKK][hapmap];0.93[TSI][hapmap];1.00[YRI][hapmap];0.94[AFR][1000 genomes];0.96[AMR][1000 genomes];0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10948864	0.81[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12191299	0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12191386	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.87[GIH][hapmap];1.00[JPT][hapmap];0.91[TSI][hapmap];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12194667	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12195438	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.95[MEX][hapmap];1.00[TSI][hapmap];0.89[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12196314	0.92[CHB][hapmap];0.86[ASN][1000 genomes]
rs12199827	0.89[CEU][hapmap];0.86[GIH][hapmap];0.86[MEX][hapmap];0.81[TSI][hapmap]
rs12201892	0.85[ASN][1000 genomes]
rs12202062	0.85[ASN][1000 genomes]
rs12203709	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12205222	0.84[AMR][1000 genomes];0.92[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs12205372	0.92[CEU][hapmap];0.94[CHB][hapmap];0.89[CHD][hapmap];0.89[GIH][hapmap];0.86[JPT][hapmap];0.91[MEX][hapmap];0.85[TSI][hapmap];0.81[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs12207559	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.96[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.98[LWK][hapmap];0.95[MEX][hapmap];0.94[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12216039	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12216049	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1393778	0.84[AMR][1000 genomes]
rs1393779	0.89[CEU][hapmap];0.88[AMR][1000 genomes]
rs1910357	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2270989	0.94[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs34713378	0.85[ASN][1000 genomes]
rs62412605	0.81[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs6908745	0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6911198	0.84[CHB][hapmap];0.96[CHD][hapmap]
rs6938005	0.80[LWK][hapmap]
rs72957572	0.81[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs7747352	0.81[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7760490	0.86[ASN][1000 genomes]
rs9296769	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9464148	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs9464149	0.89[ASW][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.82[GIH][hapmap];1.00[JPT][hapmap];0.80[TSI][hapmap];0.83[YRI][hapmap];0.99[ASN][1000 genomes]
rs9475005	0.92[CEU][hapmap]
rs9475029	0.83[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs9475038	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs9475039	0.87[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9475040	0.98[AFR][1000 genomes];0.93[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9475041	0.99[ASN][1000 genomes]
rs9475045	0.89[ASN][1000 genomes]
rs9475046	0.85[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.82[GIH][hapmap];1.00[JPT][hapmap];0.84[TSI][hapmap];0.80[EUR][1000 genomes];0.99[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv885900	chr6:54517968-54852462	Active TSS Bivalent Enhancer Enhancers Weak transcription Strong transcription Bivalent/Poised TSS Genic enhancers Flanking Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	13 gene(s)	inside rSNPs	diseases
2	esv2763553	chr6:54687979-54820487	Weak transcription Active TSS Transcr. at gene 5' and 3' Flanking Active TSS Enhancers Flanking Bivalent TSS/Enh Strong transcription Bivalent/Poised TSS Genic enhancers ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases
3	nsv823700	chr6:54709648-54710116	Active TSS Enhancers Weak transcription Bivalent/Poised TSS	TF binding region Chromatin interactive region	2 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs4712075	ICK	cis	cerebellum	SCAN

Chromatin state (count:13 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:54707200-54710800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
2	chr6:54707400-54710200	Weak transcription	NHEK	skin
3	chr6:54707400-54710800	Weak transcription	Placenta	Placenta
4	chr6:54709000-54710000	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
5	chr6:54709000-54710400	Weak transcription	Breast Myoepithelial Primary Cells	Breast
6	chr6:54709000-54713400	Active TSS	Rectal Mucosa Donor 29	rectum
7	chr6:54709000-54714200	Active TSS	Duodenum Mucosa	Duodenum
8	chr6:54709200-54709800	Enhancers	Rectal Mucosa Donor 31	rectum
9	chr6:54709200-54710200	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
10	chr6:54709200-54710200	Enhancers	HMEC	breast
11	chr6:54709400-54709800	Enhancers	Pancreatic Islets	Pancreatic Islet
12	chr6:54709400-54710800	Weak transcription	Fetal Intestine Small	intestine
13	chr6:54709600-54709800	Enhancers	Sigmoid Colon	Sigmoid Colon

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