Variant report

Variant	rs10060662
Chromosome Location	chr5:150950870-150950871
allele	C/G
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	chr5:150949609-150951629	ECC-1	luminal epithelium:	n/a	n/a
2	NFIC	chr5:150950712-150951521	ECC-1	luminal epithelium:	n/a	n/a
3	MAX	chr5:150949934-150951424	ECC-1	luminal epithelium:	n/a	chr5:150950813-150950822
4	NFIC	chr5:150948291-150951634	ECC-1	luminal epithelium:	n/a	n/a
5	POLR2A	chr5:150950847-150951355	ECC-1	luminal epithelium:	n/a	n/a
6	E2F6	chr5:150950502-150950892	H1-hESC	embryonic stem cell:	n/a	chr5:150950687-150950694 chr5:150950687-150950694 chr5:150950686-150950695 chr5:150950687-150950694 chr5:150950686-150950698
7	MAX	chr5:150949571-150951459	ECC-1	luminal epithelium:	n/a	chr5:150950813-150950822 chr5:150949823-150949832
8	TCF12	chr5:150950744-150951547	ECC-1	luminal epithelium:	n/a	chr5:150951194-150951201
9	TCF12	chr5:150948287-150951635	ECC-1	luminal epithelium:	n/a	chr5:150950155-150950165 chr5:150951194-150951201
10	EP300	chr5:150948268-150951579	ECC-1	luminal epithelium:	n/a	n/a
11	E2F6	chr5:150950195-150950982	H1-hESC	embryonic stem cell:	n/a	chr5:150950687-150950694 chr5:150950687-150950694 chr5:150950686-150950695 chr5:150950687-150950694 chr5:150950686-150950698

No.	Distal block	Cell Line	Cell type
1	chr5:150949470..150952211-chr5:150958873..150961683,3	MCF-7	breast:
2	chr5:150948647..150952629-chr5:150970748..150974404,4	MCF-7	breast:
3	chr5:150950232..150951828-chr5:150992759..150995006,2	MCF-7	breast:
4	chr5:150949333..150952291-chr5:151000084..151002404,2	MCF-7	breast:
5	chr5:150949275..150951752-chr5:151137668..151139701,2	K562	blood:

Variant related genes	Relation type
FAT2	TF binding region
ENSG00000177556	Chromatin interaction

Extended variants
information (count: 47 )
Associated
traits (count: 0)

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

rs_ID	r²[population]
rs10044120	0.94[CHB][hapmap]
rs10052817	0.84[AFR][1000 genomes];0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs10054406	0.86[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs10060613	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10069540	1.00[CEU][hapmap];1.00[CHB][hapmap];0.85[JPT][hapmap];0.86[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs10069901	0.86[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs10072841	0.94[CHB][hapmap];0.93[JPT][hapmap]
rs10085060	1.00[CEU][hapmap];0.93[CHB][hapmap];0.85[JPT][hapmap];0.85[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs12055366	1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[ASN][1000 genomes]
rs13158643	0.86[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs13159039	0.89[CEU][hapmap]
rs1432862	1.00[CEU][hapmap];1.00[CHB][hapmap];0.85[JPT][hapmap];0.85[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs1541910	0.83[AFR][1000 genomes];0.88[ASN][1000 genomes]
rs2163769	0.85[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs2288778	0.86[CHB][hapmap]
rs2304053	1.00[CEU][hapmap];1.00[CHB][hapmap];0.92[JPT][hapmap];0.84[YRI][hapmap];0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2304054	1.00[CEU][hapmap];1.00[CHB][hapmap];0.85[JPT][hapmap];0.86[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs28449749	0.86[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs34335300	0.86[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs34346367	0.86[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs35908499	0.86[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs35957412	0.86[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs3734055	1.00[CEU][hapmap];1.00[CHB][hapmap];0.85[JPT][hapmap];0.86[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs3734057	1.00[CEU][hapmap];1.00[CHB][hapmap];0.85[JPT][hapmap];0.85[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs3734058	1.00[CEU][hapmap];1.00[CHB][hapmap];0.85[JPT][hapmap];0.82[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs3734059	1.00[CEU][hapmap];1.00[CHB][hapmap];0.85[JPT][hapmap];0.85[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs3734060	1.00[CEU][hapmap];1.00[CHB][hapmap];0.85[JPT][hapmap];0.85[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs4320248	1.00[CHB][hapmap];0.92[JPT][hapmap];0.85[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs6859217	0.85[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs6878528	0.85[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs6878532	0.85[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs6878556	0.85[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs6878627	0.85[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs6879740	0.85[ASN][1000 genomes]
rs6883153	0.85[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs6883216	0.85[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs6890712	0.86[CHB][hapmap];0.84[YRI][hapmap]
rs7724472	0.89[ASN][1000 genomes]
rs7726769	0.86[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs7727173	0.85[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs7737011	1.00[CHB][hapmap]
rs7737419	1.00[CHB][hapmap];0.85[JPT][hapmap]
rs9324698	0.85[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs9324699	0.88[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs9324700	1.00[CEU][hapmap];1.00[CHB][hapmap];0.85[AMR][1000 genomes];0.98[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:2 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv20633	chr5:150941705-150955343	Strong transcription Enhancers Genic enhancers Bivalent Enhancer Weak transcription Flanking Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Active TSS	TF binding region CpG island Chromatin interactive region	3 gene(s)	inside rSNPs	diseases
2	nsv600038	chr5:150950853-150955127	Enhancers Weak transcription Flanking Active TSS Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region Chromatin interactive region	3 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:24 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:150948400-150951200	Enhancers	Esophagus	oesophagus
2	chr5:150948400-150953600	Enhancers	Breast Myoepithelial Primary Cells	Breast
3	chr5:150948400-150953600	Enhancers	Fetal Thymus	thymus
4	chr5:150948600-150951000	Enhancers	Placenta Amnion	Placenta Amnion
5	chr5:150948600-150951400	Enhancers	Placenta	Placenta
6	chr5:150948600-150952600	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
7	chr5:150949000-150951400	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
8	chr5:150949600-150951600	Flanking Active TSS	NHEK	skin
9	chr5:150949800-150951000	Enhancers	iPS-18 Cell Line	embryonic stem cell
10	chr5:150949800-150951200	Bivalent Enhancer	H1 Cell Line	embryonic stem cell
11	chr5:150949800-150951200	Transcr. at gene 5' and 3'	Foreskin Keratinocyte Primary Cells skin02	Skin
12	chr5:150949800-150951400	Bivalent Enhancer	H9 Cell Line	embryonic stem cell
13	chr5:150950000-150951200	Enhancers	iPS DF 19.11 Cell Line	embryonic stem cell
14	chr5:150950000-150951200	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
15	chr5:150950200-150951200	Flanking Active TSS	Foreskin Keratinocyte Primary Cells skin03	Skin
16	chr5:150950200-150951200	Enhancers	Spleen	Spleen
17	chr5:150950200-150951200	Flanking Active TSS	HMEC	breast
18	chr5:150950600-150951000	Bivalent Enhancer	ES-I3 Cell Line	embryonic stem cell
19	chr5:150950600-150951200	Bivalent Enhancer	HUES6 Cell Line	embryonic stem cell
20	chr5:150950600-150951200	Enhancers	Right Ventricle	heart
21	chr5:150950800-150951000	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
22	chr5:150950800-150951200	Bivalent Enhancer	iPS DF 6.9 Cell Line	embryonic stem cell
23	chr5:150950800-150951600	Enhancers	Primary B cells from cord blood	blood
24	chr5:150950800-150951600	Enhancers	Primary B cells from peripheral blood	blood

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