Variant report

Variant	rs2028787
Chromosome Location	chr13:94162371-94162372
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	chr13:94151315..94153018-chr13:94160965..94162525,2	MCF-7	breast:

Extended variants
information (count: 32 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:24)

rs_ID	r²[population]
rs1445245	0.83[ASW][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];0.93[LWK][hapmap];0.87[MKK][hapmap];0.81[TSI][hapmap];0.82[YRI][hapmap];0.83[AFR][1000 genomes];0.81[AMR][1000 genomes];0.96[ASN][1000 genomes]
rs1445248	0.90[AMR][1000 genomes];0.87[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs17300394	0.81[CHB][hapmap];0.94[CHD][hapmap];0.94[JPT][hapmap];0.87[ASN][1000 genomes]
rs1900047	1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[AMR][1000 genomes];0.80[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2028788	0.90[AFR][1000 genomes];0.88[AMR][1000 genomes];0.83[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2388977	0.82[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7327116	0.90[AMR][1000 genomes];0.87[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7331487	0.89[ASN][1000 genomes]
rs7333716	0.81[CHB][hapmap];0.94[JPT][hapmap];0.87[ASN][1000 genomes]
rs7338160	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.83[YRI][hapmap];0.87[AMR][1000 genomes];0.83[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7339321	0.95[CEU][hapmap];1.00[CHB][hapmap];0.94[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.93[TSI][hapmap];0.89[AMR][1000 genomes];0.86[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7988171	0.95[CEU][hapmap];1.00[CHB][hapmap];0.89[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];0.91[MEX][hapmap];0.93[TSI][hapmap];0.84[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs9301887	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.95[GIH][hapmap];0.94[JPT][hapmap];0.86[LWK][hapmap];0.91[MEX][hapmap];0.88[MKK][hapmap];0.82[TSI][hapmap];0.82[YRI][hapmap];0.84[AMR][1000 genomes];0.82[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs9301889	0.95[CEU][hapmap];1.00[CHB][hapmap];0.94[JPT][hapmap];1.00[YRI][hapmap];0.87[AFR][1000 genomes];0.87[AMR][1000 genomes];0.84[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs9301890	0.88[ASW][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.95[GIH][hapmap];0.94[JPT][hapmap];0.89[LWK][hapmap];0.95[MKK][hapmap];1.00[YRI][hapmap];0.87[AFR][1000 genomes];0.96[ASN][1000 genomes]
rs9301891	0.83[ASW][hapmap];1.00[CHB][hapmap];0.91[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];0.91[LWK][hapmap];0.90[MKK][hapmap];0.81[TSI][hapmap];0.86[YRI][hapmap];0.88[AFR][1000 genomes];0.86[AMR][1000 genomes];0.80[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs9301893	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[AMR][1000 genomes];0.87[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs9301894	0.89[AMR][1000 genomes];0.87[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs9516248	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[AMR][1000 genomes];0.87[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs9516252	0.95[CEU][hapmap];1.00[CHB][hapmap];0.94[CHD][hapmap];0.92[GIH][hapmap];1.00[JPT][hapmap];0.83[MEX][hapmap];0.86[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs9524129	0.89[AMR][1000 genomes];0.83[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs9584123	0.86[CEU][hapmap];0.91[CHB][hapmap];1.00[JPT][hapmap];0.90[AMR][1000 genomes];0.87[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs9584124	0.90[AMR][1000 genomes];0.86[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs9589762	0.95[CEU][hapmap];1.00[CHB][hapmap];0.94[JPT][hapmap];0.90[AMR][1000 genomes];0.87[EUR][1000 genomes];0.99[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:8 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv869070	chr13:93347616-94286933	Enhancers Weak transcription Genic enhancers Bivalent Enhancer Flanking Active TSS Active TSS ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases
2	nsv1053035	chr13:93842576-94229732	Enhancers Flanking Active TSS Active TSS Weak transcription ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Strong transcription Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
3	nsv541880	chr13:93842576-94229732	Active TSS Flanking Active TSS Weak transcription Enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer Strong transcription Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
4	nsv530636	chr13:93997311-94281707	Enhancers Weak transcription Flanking Active TSS Active TSS ZNF genes & repeats Strong transcription Genic enhancers Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
5	nsv916039	chr13:94035909-94191105	Enhancers Weak transcription ZNF genes & repeats Flanking Active TSS Active TSS Bivalent Enhancer Genic enhancers Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
6	nsv562749	chr13:94083352-94263206	Weak transcription Enhancers ZNF genes & repeats Active TSS Flanking Active TSS Genic enhancers Bivalent Enhancer Strong transcription	Chromatin interactive region lncRNA	n/a	inside rSNPs	diseases
7	nsv948714	chr13:94100104-94699435	Weak transcription Enhancers Flanking Active TSS Active TSS ZNF genes & repeats Genic enhancers Bivalent Enhancer Strong transcription Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
8	nsv900922	chr13:94105666-94281492	Weak transcription Enhancers Flanking Active TSS ZNF genes & repeats Genic enhancers Strong transcription Active TSS Bivalent Enhancer	Chromatin interactive region lncRNA	n/a	inside rSNPs	diseases

No data

Chromatin state (count:14 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr13:94152600-94168400	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
2	chr13:94158200-94165400	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
3	chr13:94158400-94165400	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
4	chr13:94160400-94163000	Enhancers	iPS-20b Cell Line	embryonic stem cell
5	chr13:94160400-94163600	Enhancers	HUES48 Cell Line	embryonic stem cell
6	chr13:94160600-94163000	Enhancers	ES-I3 Cell Line	embryonic stem cell
7	chr13:94160600-94163000	Enhancers	iPS-15b Cell Line	embryonic stem cell
8	chr13:94160800-94162400	Enhancers	HUES64 Cell Line	embryonic stem cell
9	chr13:94160800-94163000	Enhancers	iPS-18 Cell Line	embryonic stem cell
10	chr13:94161200-94163000	Enhancers	HUES6 Cell Line	embryonic stem cell
11	chr13:94161400-94162400	Weak transcription	Brain Germinal Matrix	brain
12	chr13:94161400-94168400	Weak transcription	H1 Cell Line	embryonic stem cell
13	chr13:94161600-94162800	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
14	chr13:94161800-94176200	Weak transcription	H9 Cell Line	embryonic stem cell

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