Variant report

Variant	rs73578252
Chromosome Location	chr19:53064159-53064160
allele	C/T
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	FOSL2	chr19:53064142-53064421	HepG2	liver:	n/a	chr19:53064299-53064307 chr19:53064299-53064307 chr19:53064299-53064306 chr19:53064297-53064309 chr19:53064298-53064308
2	FOXA1	chr19:53064011-53064443	HepG2	liver:	n/a	n/a
3	POLR2A	chr19:53064021-53064480	GM12878	blood:	n/a	n/a
4	SP1	chr19:53064109-53064441	HepG2	liver:	n/a	chr19:53064196-53064208 chr19:53064197-53064206 chr19:53064196-53064208 chr19:53064198-53064207

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr19:53063695..53066005-chr19:53068578..53070383,2	K562	blood:

Variant related genes	Relation type
RPL39P34	TF binding region

Extended variants
information (count: 60 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:55)

rs_ID	r²[population]
rs11879684	1.00[ASN][1000 genomes]
rs11882311	1.00[ASN][1000 genomes]
rs12461522	1.00[ASN][1000 genomes]
rs12462080	1.00[ASN][1000 genomes]
rs12971372	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.84[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12977988	0.85[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12979584	0.96[EUR][1000 genomes]
rs12985487	0.82[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12986137	0.83[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs16983943	1.00[ASN][1000 genomes]
rs2029316	0.89[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs2061355	1.00[ASN][1000 genomes]
rs28570374	1.00[ASN][1000 genomes]
rs329948	1.00[ASN][1000 genomes]
rs329949	1.00[ASN][1000 genomes]
rs34066730	0.88[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs34106830	0.85[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34203482	1.00[ASN][1000 genomes]
rs34316627	1.00[ASN][1000 genomes]
rs34529833	1.00[ASN][1000 genomes]
rs34603606	0.96[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs34724169	0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34747259	0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34866464	0.96[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs34942135	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35068231	0.96[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs35356792	1.00[ASN][1000 genomes]
rs35591322	1.00[ASN][1000 genomes]
rs35888888	0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35895760	1.00[ASN][1000 genomes]
rs35904532	1.00[ASN][1000 genomes]
rs35990292	0.96[EUR][1000 genomes]
rs35993483	0.96[EUR][1000 genomes]
rs36089907	1.00[ASN][1000 genomes]
rs382838	1.00[ASN][1000 genomes]
rs436426	1.00[ASN][1000 genomes]
rs4401146	0.96[EUR][1000 genomes]
rs557496	1.00[ASN][1000 genomes]
rs58067500	1.00[ASN][1000 genomes]
rs58494379	1.00[ASN][1000 genomes]
rs61545816	1.00[ASN][1000 genomes]
rs61746334	0.88[AFR][1000 genomes];1.00[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs71358875	1.00[ASN][1000 genomes]
rs71358876	1.00[ASN][1000 genomes]
rs71358877	1.00[ASN][1000 genomes]
rs71358878	1.00[ASN][1000 genomes]
rs71358879	1.00[ASN][1000 genomes]
rs71358884	0.82[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7252479	1.00[ASN][1000 genomes]
rs7257824	1.00[ASN][1000 genomes]
rs73578236	0.96[AMR][1000 genomes];0.84[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73590059	1.00[ASN][1000 genomes]
rs73934854	1.00[ASN][1000 genomes]
rs8104197	0.96[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs811920	1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:5 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	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
2	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
3	nsv510772	chr19:53037211-53103470	ZNF genes & repeats Weak transcription Strong transcription Enhancers Active TSS Flanking Active TSS Transcr. at gene 5' and 3' Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
4	nsv1065584	chr19:53043126-53127459	Weak transcription ZNF genes & repeats Flanking Active TSS Enhancers Strong transcription Active TSS Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	11 gene(s)	inside rSNPs	diseases
5	nsv833874	chr19:53058014-53257875	Weak transcription ZNF genes & repeats Active TSS Enhancers Strong transcription Flanking Active TSS Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	19 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:109 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr19:53042000-53070400	ZNF genes & repeats	Primary hematopoietic stem cells G-CSF-mobilized Male	--
2	chr19:53042200-53068200	ZNF genes & repeats	Primary hematopoietic stem cells short term culture	blood
3	chr19:53046400-53069200	ZNF genes & repeats	Monocytes-CD14+_RO01746	blood
4	chr19:53047400-53068200	ZNF genes & repeats	Thymus	Thymus
5	chr19:53047800-53068600	ZNF genes & repeats	IMR90 fetal lung fibroblasts Cell Line	lung
6	chr19:53048000-53066400	ZNF genes & repeats	Primary T regulatory cells fromperipheralblood	blood
7	chr19:53050400-53065400	ZNF genes & repeats	Sigmoid Colon	Sigmoid Colon
8	chr19:53050400-53069200	ZNF genes & repeats	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
9	chr19:53051000-53068000	ZNF genes & repeats	Fetal Intestine Large	intestine
10	chr19:53051400-53068200	ZNF genes & repeats	Primary T helper cells PMA-I stimulated	--
11	chr19:53051600-53068000	ZNF genes & repeats	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
12	chr19:53051600-53068200	ZNF genes & repeats	Rectal Mucosa Donor 29	rectum
13	chr19:53051600-53073200	ZNF genes & repeats	Foreskin Melanocyte Primary Cells skin03	Skin
14	chr19:53052000-53067400	ZNF genes & repeats	Primary T helper naive cells fromperipheralblood	blood
15	chr19:53052000-53067800	ZNF genes & repeats	Primary Natural Killer cells fromperipheralblood	blood
16	chr19:53052200-53067800	ZNF genes & repeats	Primary T helper cells fromperipheralblood	blood
17	chr19:53053600-53067800	ZNF genes & repeats	Primary T cells fromperipheralblood	blood
18	chr19:53054600-53064200	ZNF genes & repeats	Fetal Muscle Leg	muscle
19	chr19:53056200-53065800	ZNF genes & repeats	Foreskin Keratinocyte Primary Cells skin03	Skin
20	chr19:53056600-53065400	ZNF genes & repeats	H1 Derived Mesenchymal Stem Cells	ES cell derived
21	chr19:53057600-53064200	ZNF genes & repeats	Placenta	Placenta
22	chr19:53058400-53072600	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
23	chr19:53058600-53065200	Weak transcription	Brain Substantia Nigra	brain
24	chr19:53058600-53070000	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
25	chr19:53058600-53072800	Weak transcription	Fetal Brain Male	brain
26	chr19:53058800-53070000	Weak transcription	Hela-S3	cervix
27	chr19:53059000-53064600	Weak transcription	Brain Inferior Temporal Lobe	brain
28	chr19:53059000-53068000	Strong transcription	Dnd41	blood
29	chr19:53059000-53068600	ZNF genes & repeats	Fetal Intestine Small	intestine
30	chr19:53059200-53073000	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
31	chr19:53059400-53065600	ZNF genes & repeats	Fetal Stomach	stomach
32	chr19:53059800-53066600	ZNF genes & repeats	Colonic Mucosa	Colon
33	chr19:53060200-53064200	Strong transcription	Breast Myoepithelial Primary Cells	Breast
34	chr19:53060200-53067400	ZNF genes & repeats	Pancreatic Islets	Pancreatic Islet
35	chr19:53060400-53065400	ZNF genes & repeats	Primary B cells from cord blood	blood
36	chr19:53060800-53067200	ZNF genes & repeats	Lung	lung
37	chr19:53060800-53068600	Strong transcription	Foreskin Fibroblast Primary Cells skin02	Skin
38	chr19:53060800-53069400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
39	chr19:53060800-53072800	Weak transcription	Placenta Amnion	Placenta Amnion
40	chr19:53061000-53072600	Weak transcription	Fetal Brain Female	brain
41	chr19:53061000-53072800	Weak transcription	Brain Angular Gyrus	brain
42	chr19:53061200-53064600	Weak transcription	Fetal Lung	lung
43	chr19:53061200-53072600	Weak transcription	Fetal Heart	heart
44	chr19:53061200-53072800	Weak transcription	Brain Anterior Caudate	brain
45	chr19:53061400-53072600	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
46	chr19:53062000-53064200	ZNF genes & repeats	Foreskin Keratinocyte Primary Cells skin02	Skin
47	chr19:53062000-53064200	ZNF genes & repeats	Skeletal Muscle Female	skeletal muscle
48	chr19:53062000-53064800	ZNF genes & repeats	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
49	chr19:53062000-53065400	ZNF genes & repeats	Primary T cells from cord blood	blood
50	chr19:53062000-53065400	Strong transcription	Primary T helper naive cells from peripheral blood	blood

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