Variant report

Variant	rs11563218
Chromosome Location	chr2:234835535-234835536
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	FOS	chr2:234835503-234835786	MCF10A-Er-Src	breast:	n/a	n/a
2	FOS	chr2:234835436-234835674	MCF10A-Er-Src	breast:	n/a	n/a
3	CTCF	chr2:234835520-234835670	SAEC	small airway:	n/a	n/a
4	MYC	chr2:234835474-234835874	MCF10A-Er-Src	breast:	n/a	n/a
5	CTCF	chr2:234835460-234835610	HMEC	breast:	n/a	n/a

Variant related genes	Relation type
TRPM8	TF binding region

Extended variants
information (count: 38 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:36)

rs_ID	r²[population]
rs10490009	1.00[GIH][hapmap]
rs11562956	0.85[YRI][hapmap];0.91[AMR][1000 genomes]
rs11562977	0.82[ASW][hapmap];0.93[CHB][hapmap];0.88[CHD][hapmap];1.00[GIH][hapmap];0.90[JPT][hapmap];0.87[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];0.85[YRI][hapmap];0.81[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs11563068	0.82[AMR][1000 genomes]
rs11563214	0.81[CHB][hapmap];1.00[YRI][hapmap];0.83[EUR][1000 genomes]
rs12617866	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.90[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs12620352	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.85[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs1468521	1.00[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs16849914	0.82[YRI][hapmap];0.91[AMR][1000 genomes]
rs2362291	0.92[CHB][hapmap];0.82[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs28900703	0.81[AMR][1000 genomes]
rs28900710	0.85[YRI][hapmap]
rs28900712	0.91[AMR][1000 genomes]
rs28900713	0.85[YRI][hapmap];0.91[AMR][1000 genomes]
rs28901579	0.81[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs28901582	1.00[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs28901591	0.93[CHB][hapmap];0.82[JPT][hapmap];0.85[YRI][hapmap];0.81[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs28901600	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs28901608	1.00[CHB][hapmap];1.00[JPT][hapmap];0.84[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28901610	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.90[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs28901615	1.00[EUR][1000 genomes]
rs28901618	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.90[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs28901629	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[EUR][1000 genomes]
rs28901630	1.00[YRI][hapmap]
rs28901637	1.00[YRI][hapmap];1.00[EUR][1000 genomes]
rs28901868	0.81[CHB][hapmap];1.00[YRI][hapmap];0.83[EUR][1000 genomes]
rs28902174	0.83[EUR][1000 genomes]
rs3771334	0.91[AMR][1000 genomes]
rs3806588	0.81[AMR][1000 genomes]
rs4663342	1.00[CHB][hapmap];0.85[YRI][hapmap];0.81[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs4663343	0.81[CHB][hapmap];1.00[YRI][hapmap];0.83[EUR][1000 genomes]
rs4663989	1.00[ASW][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.88[LWK][hapmap];1.00[MEX][hapmap];0.90[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.81[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs7602303	1.00[CHB][hapmap];0.90[JPT][hapmap];1.00[YRI][hapmap]
rs9789366	0.93[CHB][hapmap];0.90[JPT][hapmap];0.82[YRI][hapmap];0.81[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs9789398	0.82[ASW][hapmap];0.93[CHB][hapmap];0.88[CHD][hapmap];1.00[GIH][hapmap];0.90[JPT][hapmap];0.87[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];0.85[YRI][hapmap];0.81[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs9789675	0.82[ASW][hapmap];0.93[CHB][hapmap];1.00[GIH][hapmap];0.82[JPT][hapmap];0.87[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];0.85[YRI][hapmap];0.81[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.91[ASN][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	nsv1013712	chr2:234558457-235495825	Enhancers Weak transcription Active TSS Flanking Active TSS ZNF genes & repeats Strong transcription Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	41 gene(s)	inside rSNPs	diseases
2	nsv532476	chr2:234595695-235134381	Enhancers Active TSS Weak transcription Flanking Active TSS Bivalent Enhancer Strong transcription ZNF genes & repeats Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	37 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:10 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:234834400-234838000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
2	chr2:234834800-234837200	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
3	chr2:234835000-234836200	Enhancers	HMEC	breast
4	chr2:234835000-234836400	Enhancers	Breast Myoepithelial Primary Cells	Breast
5	chr2:234835200-234836200	Enhancers	Cortex derived primary cultured neurospheres	brain
6	chr2:234835200-234836200	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
7	chr2:234835200-234836200	Enhancers	Esophagus	oesophagus
8	chr2:234835200-234836200	Enhancers	NHEK	skin
9	chr2:234835200-234836400	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
10	chr2:234835400-234835600	Flanking Active TSS	Foreskin Keratinocyte Primary Cells skin02	Skin

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