Variant report

Variant	rs4802968
Chromosome Location	chr19:53024983-53024984
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr19:53024234..53025826-chr19:53029049..53030597,2	MCF-7	breast:

Extended variants
information (count: 40 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:27)

rs_ID	r²[population]
rs11084170	0.90[ASN][1000 genomes]
rs11665734	0.81[AFR][1000 genomes]
rs11669969	0.92[AFR][1000 genomes];0.88[AMR][1000 genomes];0.92[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs12610532	0.91[ASN][1000 genomes]
rs12984325	0.83[ASN][1000 genomes]
rs161932	0.90[ASN][1000 genomes]
rs1677467	0.94[ASN][1000 genomes]
rs172956	0.94[ASN][1000 genomes]
rs2011702	0.84[ASN][1000 genomes]
rs324745	0.94[ASN][1000 genomes]
rs324747	0.90[ASN][1000 genomes]
rs324748	0.92[ASN][1000 genomes]
rs326452	0.94[ASN][1000 genomes]
rs326456	0.87[ASN][1000 genomes]
rs378790	0.89[ASN][1000 genomes]
rs389503	0.90[ASN][1000 genomes]
rs400278	0.93[ASN][1000 genomes]
rs414595	0.83[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs414804	0.82[AMR][1000 genomes];0.97[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs419317	0.92[ASN][1000 genomes]
rs4802969	0.82[AFR][1000 genomes];0.90[AMR][1000 genomes];0.88[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4802970	0.87[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs621469	0.94[ASN][1000 genomes]
rs633763	0.94[ASN][1000 genomes]
rs650885	0.86[ASN][1000 genomes]
rs650937	0.85[ASN][1000 genomes]
rs802878	0.94[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:13 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1066537	chr19:52794424-53044977	Active TSS ZNF genes & repeats Weak transcription Enhancers Strong transcription Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	24 gene(s)	inside rSNPs	diseases
2	nsv544060	chr19:52794424-53044977	ZNF genes & repeats Weak transcription Enhancers Flanking Bivalent TSS/Enh Flanking Active TSS Active TSS Strong transcription Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	24 gene(s)	inside rSNPs	diseases
3	nsv580026	chr19:52937100-53059872	Weak transcription Enhancers Active TSS ZNF genes & repeats Flanking Active TSS Transcr. at gene 5' and 3' Genic enhancers Strong transcription Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
4	nsv1063648	chr19:52938131-53041119	ZNF genes & repeats Weak transcription Active TSS Flanking Active TSS Strong transcription Bivalent/Poised TSS Enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
5	nsv1057296	chr19:52950339-53396986	Weak transcription Active TSS ZNF genes & repeats Strong transcription Enhancers Flanking Active TSS Transcr. at gene 5' and 3' Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	34 gene(s)	inside rSNPs	diseases
6	nsv978841	chr19:52983057-53088237	ZNF genes & repeats Weak transcription Enhancers Strong transcription Active TSS Flanking Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer Genic enhancers Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
7	esv3404701	chr19:52986895-53035152	Weak transcription Active TSS Enhancers Flanking Active TSS Strong transcription ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
8	esv3440535	chr19:52993529-53035203	ZNF genes & repeats Enhancers Flanking Active TSS Weak transcription Active TSS Strong transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
9	nsv1066717	chr19:52993620-53041995	Active TSS ZNF genes & repeats Flanking Active TSS Enhancers Weak transcription Strong transcription Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS Genic enhancers Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
10	nsv1064342	chr19:52996710-53041119	ZNF genes & repeats Active TSS Weak transcription Enhancers Bivalent/Poised TSS Flanking Active TSS Strong transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
11	nsv1055825	chr19:53001299-53037378	Active TSS Weak transcription Strong transcription ZNF genes & repeats Flanking Active TSS Enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
12	nsv1055859	chr19:53001299-53041119	Enhancers Active TSS Weak transcription Strong transcription ZNF genes & repeats Flanking Active TSS Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
13	nsv1060656	chr19:53001299-53041995	Weak transcription Active TSS Enhancers Flanking Active TSS Strong transcription ZNF genes & repeats Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:20 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr19:53015400-53029600	Weak transcription	Fetal Brain Male	brain
2	chr19:53016400-53030000	Weak transcription	Brain Germinal Matrix	brain
3	chr19:53019800-53030000	Weak transcription	Right Ventricle	heart
4	chr19:53020600-53025200	Enhancers	HUES6 Cell Line	embryonic stem cell
5	chr19:53020600-53030000	Weak transcription	Fetal Brain Female	brain
6	chr19:53021400-53025800	Enhancers	HUES64 Cell Line	embryonic stem cell
7	chr19:53022000-53030200	Weak transcription	Placenta Amnion	Placenta Amnion
8	chr19:53023000-53025200	Enhancers	K562	blood
9	chr19:53023600-53027000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
10	chr19:53023600-53029600	Weak transcription	H9 Cell Line	embryonic stem cell
11	chr19:53023600-53030200	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
12	chr19:53023600-53030200	Weak transcription	iPS-18 Cell Line	embryonic stem cell
13	chr19:53023600-53030200	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
14	chr19:53023800-53027400	Weak transcription	H1 Cell Line	embryonic stem cell
15	chr19:53024000-53025600	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
16	chr19:53024400-53025600	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
17	chr19:53024400-53026400	Enhancers	iPS-15b Cell Line	embryonic stem cell
18	chr19:53024600-53025000	Flanking Active TSS	HepG2	liver
19	chr19:53024800-53025000	Enhancers	Placenta	Placenta
20	chr19:53024800-53025400	Weak transcription	ES-I3 Cell Line	embryonic stem cell

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