Variant report

Variant	rs757608
Chromosome Location	chr17:59497277-59497278
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:0)
CpG islands
(count:0)
Chromatin interactive
region (count:8)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

(count:8 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr17:59496790..59499054-chr20:49345945..49348014,2	MCF-7	breast:
2	chr17:59496898..59499415-chr20:52415404..52417279,2	MCF-7	breast:
3	chr17:59496517..59498736-chr17:59916457..59918359,2	MCF-7	breast:
4	chr17:59496823..59497470-chr17:59651228..59652165,2	MCF-7	breast:
5	chr17:59496687..59497666-chr17:59627914..59628881,2	MCF-7	breast:
6	chr12:120728848..120730983-chr17:59496123..59498287,2	MCF-7	breast:
7	chr17:59496140..59498788-chr17:60003815..60006322,2	MCF-7	breast:
8	chr17:59447417..59500105-chr20:49391742..49424382,639	MCF-7	breast:

No data

Variant related genes	Relation type
ENSG00000202538	Chromatin interaction
ENSG00000108506	Chromatin interaction
ENSG00000124243	Chromatin interaction

Extended variants
information (count: 20 )
Associated
traits (count: 5 )

rSNPs within LD-proxies of this variant (count:14)

rs_ID	r²[population]
rs1076392	1.00[CEU][hapmap];0.83[CHD][hapmap];0.91[GIH][hapmap];0.82[JPT][hapmap];0.80[MEX][hapmap];0.97[TSI][hapmap];0.99[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs1476781	0.86[ASN][1000 genomes]
rs2079795	1.00[CEU][hapmap];0.88[CHD][hapmap];0.93[GIH][hapmap];0.82[JPT][hapmap];0.80[MEX][hapmap];1.00[TSI][hapmap];0.99[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs2109019	0.89[CHB][hapmap];0.88[CHD][hapmap];0.86[GIH][hapmap];0.95[JPT][hapmap];0.84[MEX][hapmap];0.82[MKK][hapmap];0.84[ASN][1000 genomes]
rs7214743	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.99[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs740755	0.82[CEU][hapmap];0.82[JPT][hapmap]
rs758598	1.00[CEU][hapmap];0.83[CHD][hapmap];0.91[GIH][hapmap];0.82[JPT][hapmap];0.80[MEX][hapmap];0.97[TSI][hapmap];0.98[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs758599	1.00[CEU][hapmap];0.99[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs8064243	0.99[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs882367	1.00[CEU][hapmap];0.85[CHD][hapmap];0.93[GIH][hapmap];0.80[MEX][hapmap];0.97[TSI][hapmap];0.99[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs887258	1.00[CHB][hapmap];0.95[JPT][hapmap];0.87[ASN][1000 genomes]
rs9892365	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.85[YRI][hapmap];0.93[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs9905385	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];0.96[MEX][hapmap];0.98[MKK][hapmap];1.00[YRI][hapmap];0.94[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9907379	1.00[CHB][hapmap];0.93[CHD][hapmap];0.86[GIH][hapmap];0.95[JPT][hapmap];0.83[LWK][hapmap];0.83[MEX][hapmap];0.93[MKK][hapmap]

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	nsv1065939	chr17:59283350-59517730	Enhancers Active TSS Flanking Active TSS Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Weak transcription Genic enhancers Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	331 gene(s)	inside rSNPs	diseases
2	nsv833505	chr17:59323466-59518007	Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Enhancers Weak transcription Flanking Active TSS Active TSS Strong transcription Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	326 gene(s)	inside rSNPs	diseases
3	nsv833506	chr17:59362377-59562984	Bivalent Enhancer Enhancers Active TSS Weak transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS Flanking Active TSS Transcr. at gene 5' and 3' Strong transcription Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	334 gene(s)	inside rSNPs	diseases
4	nsv908663	chr17:59464069-59521310	Bivalent Enhancer Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3' Weak transcription Flanking Bivalent TSS/Enh Enhancers Flanking Active TSS Genic enhancers Strong transcription ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	278 gene(s)	inside rSNPs	diseases
5	nsv519931	chr17:59491281-59514461	Enhancers Bivalent Enhancer Weak transcription Active TSS Genic enhancers Flanking Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region	59 gene(s)	inside rSNPs	diseases
6	nsv523855	chr17:59496238-59516834	Enhancers Bivalent Enhancer Flanking Active TSS Weak transcription Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats Active TSS	Chromatin interactive region	18 gene(s)	inside rSNPs	diseases

Variant related diseases (count:2)

Disease	PMID	Source
Height	18391951	GWAS catalog
Height	25429064	GWAS catalog

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs757608	TBX4	cis	cerebellum	SCAN
rs757608	NACA2	cis	cerebellum	SCAN
rs757608	MRC2	cis	cerebellum	SCAN

Chromatin state (count:11 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr17:59491000-59504200	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
2	chr17:59494600-59503000	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
3	chr17:59495600-59503400	Weak transcription	NHLF	lung
4	chr17:59497000-59497600	Enhancers	HepG2	liver
5	chr17:59497200-59497400	Enhancers	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
6	chr17:59497200-59497400	Bivalent Enhancer	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
7	chr17:59497200-59497400	Bivalent Enhancer	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
8	chr17:59497200-59497600	Enhancers	Placenta	Placenta
9	chr17:59497200-59498000	Enhancers	Dnd41	blood
10	chr17:59497200-59498200	Bivalent Enhancer	Fetal Muscle Leg	muscle
11	chr17:59497200-59498600	Enhancers	Fetal Lung	lung

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