Variant report

Variant	rs497836
Chromosome Location	chr13:94807508-94807509
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr13:94806835..94809679-chr13:94815918..94817523,2	MCF-7	breast:

Extended variants
information (count: 38 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:28)

rs_ID	r²[population]
rs10129085	0.96[CEU][hapmap];0.90[CHB][hapmap];0.95[CHD][hapmap];1.00[JPT][hapmap];0.82[MEX][hapmap];0.84[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs10161943	0.81[CHB][hapmap];0.89[CHD][hapmap];0.95[JPT][hapmap];0.89[ASN][1000 genomes]
rs1328821	0.80[CHB][hapmap];0.95[JPT][hapmap];0.89[ASN][1000 genomes]
rs1328822	0.81[CHB][hapmap];0.92[CHD][hapmap];0.95[JPT][hapmap];0.89[ASN][1000 genomes]
rs1328823	0.82[CEU][hapmap];0.82[ASN][1000 genomes]
rs16949545	0.96[CEU][hapmap];0.90[CHB][hapmap];0.94[CHD][hapmap];1.00[JPT][hapmap];0.87[MEX][hapmap];0.86[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs475933	0.86[AFR][1000 genomes];0.98[AMR][1000 genomes];0.92[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs494817	1.00[AFR][1000 genomes];0.98[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs497636	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[YRI][hapmap];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs502029	0.86[AFR][1000 genomes];0.98[AMR][1000 genomes];0.92[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs504825	0.93[AMR][1000 genomes];0.92[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs541134	0.88[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.89[GIH][hapmap];1.00[JPT][hapmap];0.85[LWK][hapmap];1.00[MEX][hapmap];0.91[MKK][hapmap];0.97[TSI][hapmap];0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs543744	0.83[ASW][hapmap];1.00[CEU][hapmap];0.90[CHB][hapmap];0.97[CHD][hapmap];0.89[GIH][hapmap];0.81[JPT][hapmap];0.97[TSI][hapmap];0.96[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs588792	0.99[AFR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs589258	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];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs591981	1.00[CEU][hapmap];0.90[CHB][hapmap];0.86[CHD][hapmap];0.93[GIH][hapmap];0.81[JPT][hapmap];0.88[MKK][hapmap];0.97[TSI][hapmap];0.96[YRI][hapmap];1.00[AFR][1000 genomes];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs603741	0.94[ASW][hapmap];1.00[CEU][hapmap];0.90[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.81[JPT][hapmap];0.82[LWK][hapmap];0.96[MEX][hapmap];0.97[TSI][hapmap];1.00[YRI][hapmap];0.89[AFR][1000 genomes];0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs605033	0.91[AMR][1000 genomes];0.96[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs61570339	0.85[AMR][1000 genomes];0.92[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs618895	0.91[CEU][hapmap];0.81[CHB][hapmap];0.81[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs622908	0.94[AMR][1000 genomes];0.92[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs637086	0.86[AFR][1000 genomes];0.84[AMR][1000 genomes];0.92[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs638325	0.86[AFR][1000 genomes];0.98[AMR][1000 genomes];0.92[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs685049	1.00[CEU][hapmap];0.90[CHB][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs7991937	0.92[CHD][hapmap];0.81[ASN][1000 genomes]
rs9561507	0.95[CHD][hapmap];0.95[JPT][hapmap];0.84[ASN][1000 genomes]
rs9589918	0.95[JPT][hapmap];0.86[ASN][1000 genomes]
rs9589922	0.91[CEU][hapmap];1.00[JPT][hapmap];0.81[AMR][1000 genomes];0.89[EUR][1000 genomes];0.91[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:10 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv933807	chr13:94187158-94845505	Weak transcription Enhancers ZNF genes & repeats Active TSS Flanking Active TSS Bivalent Enhancer Strong transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
2	nsv948455	chr13:94451368-94988900	Enhancers Weak transcription Flanking Active TSS ZNF genes & repeats Bivalent Enhancer Genic enhancers Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
3	nsv916640	chr13:94521959-95101443	Enhancers Flanking Active TSS Weak transcription ZNF genes & repeats Active TSS Strong transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
4	nsv533063	chr13:94560362-95101443	Enhancers Flanking Active TSS Bivalent Enhancer Weak transcription Active TSS Flanking Bivalent TSS/Enh Strong transcription ZNF genes & repeats Bivalent/Poised TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
5	nsv430599	chr13:94699399-94934930	Flanking Active TSS Enhancers Weak transcription Bivalent Enhancer Bivalent/Poised TSS Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
6	nsv933263	chr13:94711183-94897124	Enhancers Flanking Active TSS Bivalent Enhancer Weak transcription Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
7	nsv900924	chr13:94714981-94819307	Enhancers Active TSS Weak transcription Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS	Chromatin interactive region lncRNA	n/a	inside rSNPs	diseases
8	nsv1051276	chr13:94745995-94872494	Enhancers Weak transcription Bivalent Enhancer Bivalent/Poised TSS Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
9	nsv526048	chr13:94767311-94880219	Enhancers Weak transcription Active TSS Bivalent Enhancer Flanking Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
10	nsv562754	chr13:94770794-94895346	Active TSS Weak transcription Enhancers Flanking Active TSS Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs497836	CLDN10	cis	parietal	SCAN

Chromatin state (count:12 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr13:94800400-94814000	Weak transcription	Fetal Intestine Small	intestine
2	chr13:94805400-94808200	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
3	chr13:94805800-94807600	Enhancers	Cortex derived primary cultured neurospheres	brain
4	chr13:94805800-94808200	Enhancers	Liver	Liver
5	chr13:94806400-94807800	Enhancers	Adipose Nuclei	Adipose
6	chr13:94806600-94807800	Enhancers	Breast Myoepithelial Primary Cells	Breast
7	chr13:94806800-94809600	Weak transcription	Psoas Muscle	Psoas
8	chr13:94807000-94810200	Weak transcription	Fetal Lung	lung
9	chr13:94807400-94809600	Weak transcription	Right Atrium	heart
10	chr13:94807400-94810000	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
11	chr13:94807400-94810000	Weak transcription	Skeletal Muscle Female	skeletal muscle
12	chr13:94807400-94823400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived

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