Variant report

Variant	rs3803199
Chromosome Location	chr13:51658297-51658298
allele	A/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	chr13:51658271-51658388	MCF10A-Er-Src	breast:	n/a	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr13:51653499..51655024-chr13:51656882..51658497,2	MCF-7	breast:
2	chr13:51657919..51660554-chr13:51663790..51665589,3	K562	blood:

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-RNASEH2B-2	chr13:51657937-51658461	XLOC_010392

Variant related genes	Relation type
GUCY1B2	TF binding region
ENSG00000123201	Chromatin interaction

Extended variants
information (count: 26 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:25)

rs_ID	r²[population]
rs11148205	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[YRI][hapmap];0.85[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs11842080	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs12859216	0.94[CHB][hapmap];0.87[JPT][hapmap]
rs12865698	0.86[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs12868262	0.83[AFR][1000 genomes];0.91[AMR][1000 genomes];0.84[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs12871332	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[YRI][hapmap];0.85[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs12877403	0.94[CHB][hapmap];0.87[JPT][hapmap]
rs3790015	0.94[CHB][hapmap];1.00[JPT][hapmap];0.83[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs3790017	0.82[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs3803198	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];0.84[MEX][hapmap];0.93[TSI][hapmap];0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3803200	0.92[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.91[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];0.88[YRI][hapmap];0.93[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4606607	0.85[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs913467	0.88[CHB][hapmap]
rs927992	0.93[CHB][hapmap];0.85[JPT][hapmap]
rs9526717	1.00[CHB][hapmap];0.84[CHD][hapmap];1.00[JPT][hapmap]
rs9563015	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[YRI][hapmap];0.85[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs9563017	0.88[AMR][1000 genomes]
rs9563018	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[YRI][hapmap];0.90[AFR][1000 genomes];0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9563019	0.85[AFR][1000 genomes];0.85[AMR][1000 genomes];0.96[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs9563020	0.85[AFR][1000 genomes];0.85[AMR][1000 genomes];0.94[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs9568502	0.83[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];0.96[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.88[MKK][hapmap];0.90[TSI][hapmap];0.85[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs9568503	0.92[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.96[GIH][hapmap];1.00[JPT][hapmap];0.83[LWK][hapmap];1.00[MEX][hapmap];0.96[MKK][hapmap];0.90[TSI][hapmap];0.88[YRI][hapmap];0.85[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs9568504	0.84[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs9568505	0.85[AMR][1000 genomes]
rs9568511	0.88[ASN][1000 genomes]

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

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv832610	chr13:51636661-51822106	Bivalent/Poised TSS Enhancers Active TSS Weak transcription Flanking Active TSS Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:15 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr13:51652800-51667000	Weak transcription	Right Atrium	heart
2	chr13:51654800-51671600	Weak transcription	H1 Cell Line	embryonic stem cell
3	chr13:51655000-51671200	Weak transcription	iPS-15b Cell Line	embryonic stem cell
4	chr13:51656200-51670400	Weak transcription	HUES64 Cell Line	embryonic stem cell
5	chr13:51656400-51671200	Weak transcription	ES-I3 Cell Line	embryonic stem cell
6	chr13:51656600-51658400	Strong transcription	iPS-18 Cell Line	embryonic stem cell
7	chr13:51656600-51665000	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
8	chr13:51657600-51659800	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
9	chr13:51657800-51658400	Strong transcription	HUES48 Cell Line	embryonic stem cell
10	chr13:51657800-51658400	ZNF genes & repeats	iPS DF 6.9 Cell Line	embryonic stem cell
11	chr13:51657800-51659800	Strong transcription	H9 Cell Line	embryonic stem cell
12	chr13:51657800-51666000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
13	chr13:51658000-51659200	Strong transcription	HUES6 Cell Line	embryonic stem cell
14	chr13:51658000-51672000	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
15	chr13:51658200-51670600	Weak transcription	iPS-20b Cell Line	embryonic stem cell

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