Variant report

Variant	rs2868688
Chromosome Location	chr19:53022362-53022363
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 52 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:39)

rs_ID	r²[population]
rs10582148	0.89[AFR][1000 genomes];0.97[AMR][1000 genomes];0.94[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs11084170	0.84[ASN][1000 genomes]
rs11667348	0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs11668903	0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs12462347	0.88[ASN][1000 genomes]
rs12463002	0.86[ASN][1000 genomes]
rs12610240	0.95[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs12610532	0.86[ASN][1000 genomes]
rs12974840	0.86[ASN][1000 genomes]
rs12982862	0.84[ASN][1000 genomes]
rs12984325	0.92[ASN][1000 genomes]
rs162277	0.85[ASN][1000 genomes]
rs162278	0.85[ASN][1000 genomes]
rs1677467	0.80[ASN][1000 genomes]
rs172956	0.80[ASN][1000 genomes]
rs2011702	0.93[ASN][1000 genomes]
rs2615588	0.84[EUR][1000 genomes]
rs2633517	0.85[EUR][1000 genomes]
rs324745	0.80[ASN][1000 genomes]
rs326452	0.80[ASN][1000 genomes]
rs326458	0.84[ASN][1000 genomes]
rs329929	0.85[ASN][1000 genomes]
rs34222822	0.87[ASN][1000 genomes]
rs36039960	0.87[ASN][1000 genomes]
rs414595	0.81[ASN][1000 genomes]
rs4802964	0.85[AFR][1000 genomes];0.97[AMR][1000 genomes];0.92[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs4802965	0.85[ASN][1000 genomes]
rs4802966	0.95[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs4802967	0.95[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs4802971	0.82[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs490663	0.93[AMR][1000 genomes];0.94[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs62117197	0.80[EUR][1000 genomes]
rs62117199	0.84[EUR][1000 genomes]
rs62119356	0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs621469	0.80[ASN][1000 genomes]
rs633763	0.80[ASN][1000 genomes]
rs7257823	0.88[AMR][1000 genomes];0.95[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs781129	0.85[EUR][1000 genomes]
rs802878	0.80[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:26 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr19:53003400-53022600	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
2	chr19:53009000-53022600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
3	chr19:53015400-53029600	Weak transcription	Fetal Brain Male	brain
4	chr19:53016400-53030000	Weak transcription	Brain Germinal Matrix	brain
5	chr19:53018200-53023200	Weak transcription	Fetal Muscle Leg	muscle
6	chr19:53019800-53030000	Weak transcription	Right Ventricle	heart
7	chr19:53020400-53022800	Weak transcription	Fetal Stomach	stomach
8	chr19:53020600-53025200	Enhancers	HUES6 Cell Line	embryonic stem cell
9	chr19:53020600-53030000	Weak transcription	Fetal Brain Female	brain
10	chr19:53021200-53023600	Enhancers	iPS-18 Cell Line	embryonic stem cell
11	chr19:53021200-53024000	Enhancers	iPS-15b Cell Line	embryonic stem cell
12	chr19:53021200-53024400	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
13	chr19:53021400-53023600	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
14	chr19:53021400-53024000	Enhancers	iPS DF 19.11 Cell Line	embryonic stem cell
15	chr19:53021400-53025800	Enhancers	HUES64 Cell Line	embryonic stem cell
16	chr19:53021600-53023800	Enhancers	iPS-20b Cell Line	embryonic stem cell
17	chr19:53021800-53022400	Enhancers	ES-I3 Cell Line	embryonic stem cell
18	chr19:53021800-53023000	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
19	chr19:53021800-53023000	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
20	chr19:53022000-53023000	Weak transcription	HUES48 Cell Line	embryonic stem cell
21	chr19:53022000-53023200	Weak transcription	H1 Cell Line	embryonic stem cell
22	chr19:53022000-53023200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
23	chr19:53022000-53023200	Weak transcription	H9 Cell Line	embryonic stem cell
24	chr19:53022000-53023200	Weak transcription	HepG2	liver
25	chr19:53022000-53030200	Weak transcription	Placenta Amnion	Placenta Amnion
26	chr19:53022200-53023000	Weak transcription	ES-WA7 Cell Line	embryonic stem cell

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