Variant report

Variant	rs536342
Chromosome Location	chr19:56612423-56612424
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:22)
CpG islands
(count:0)
Chromatin interactive
region (count:5)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:22 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	POLR2A	chr19:56612215-56612811	K562	blood:	n/a	n/a
2	POLR2A	chr19:56612257-56612731	H1-hESC	embryonic stem cell:	n/a	n/a
3	POLR2A	chr19:56611900-56612728	H1-hESC	embryonic stem cell:	n/a	n/a
4	POLR2A	chr19:56611302-56612865	GM12878	blood:	n/a	n/a
5	POLR2A	chr19:56611399-56612657	GM12892	blood:	n/a	n/a
6	POLR2A	chr19:56611422-56612928	PANC-1	pancreas:	n/a	n/a
7	POLR2A	chr19:56611417-56612605	K562	blood:	n/a	n/a
8	POLR2A	chr19:56611981-56612646	GM12878	blood:	n/a	n/a
9	POLR2A	chr19:56611989-56612695	H1-hESC	embryonic stem cell:	n/a	n/a
10	POLR2A	chr19:56611958-56612692	Hela-S3	cervix:	n/a	n/a
11	POLR2A	chr19:56612194-56612424	K562	blood:	n/a	n/a
12	POLR2A	chr19:56611831-56612649	GM12892	blood:	n/a	n/a
13	POLR2A	chr19:56612329-56612648	Hela-S3	cervix:	n/a	n/a
14	POLR2A	chr19:56611950-56612787	GM12878	blood:	n/a	n/a
15	POLR2A	chr19:56611124-56613783	HepG2	liver:	n/a	n/a
16	POLR2A	chr19:56611436-56612715	GM12891	blood:	n/a	n/a
17	POLR2A	chr19:56612129-56612554	H1-hESC	embryonic stem cell:	n/a	n/a
18	POLR2A	chr19:56611283-56612868	GM12892	blood:	n/a	n/a
19	POLR2A	chr19:56611919-56612808	GM12878	blood:	n/a	n/a
20	POLR2A	chr19:56612010-56612802	GM12891	blood:	n/a	n/a
21	POLR2A	chr19:56611838-56612710	GM12891	blood:	n/a	n/a
22	POLR2A	chr19:56612299-56612703	HepG2	liver:	n/a	n/a

No data

(count:5 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr19:56596947..56599631-chr19:56611713..56614011,2	K562	blood:
2	chr19:56609509..56612797-chr19:56648982..56652625,3	K562	blood:
3	chr19:56611899..56614833-chr19:56653450..56656107,2	MCF-7	breast:
4	chr19:56612388..56614679-chr19:57790987..57792726,2	K562	blood:
5	chr19:56609156..56614023-chr19:56614843..56617057,5	K562	blood:

No data

Variant related genes	Relation type
ENSG00000223060	TF binding region
ENSG00000197714	Chromatin interaction
ENSG00000167685	Chromatin interaction
ENSG00000267871	Chromatin interaction
ENSG00000223060	Chromatin interaction
ENSG00000142409	Chromatin interaction

Extended variants
information (count: 96 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:78)

rs_ID	r²[population]
rs1007851	0.85[ASN][1000 genomes]
rs12459102	0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2450439	0.81[ASN][1000 genomes]
rs2631627	0.81[AMR][1000 genomes];0.81[ASN][1000 genomes]
rs2631628	0.81[ASN][1000 genomes]
rs2631631	0.83[ASN][1000 genomes]
rs2631637	0.89[AMR][1000 genomes];0.88[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2631640	0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2637092	0.81[AMR][1000 genomes];0.81[ASN][1000 genomes]
rs2637094	0.82[ASN][1000 genomes]
rs2637097	0.84[AMR][1000 genomes];0.84[ASN][1000 genomes]
rs2932757	0.82[ASN][1000 genomes]
rs35766803	0.85[ASN][1000 genomes]
rs473953	0.87[AMR][1000 genomes];0.84[ASN][1000 genomes]
rs478402	0.89[AMR][1000 genomes];0.88[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs481936	0.89[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs490345	0.81[AMR][1000 genomes];0.81[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs492078	0.94[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs501798	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs504350	0.90[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs506547	0.84[AMR][1000 genomes];0.84[ASN][1000 genomes]
rs506782	0.94[EUR][1000 genomes]
rs509897	0.84[AMR][1000 genomes];0.92[ASN][1000 genomes]
rs517021	0.81[AMR][1000 genomes]
rs517582	0.89[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs521092	0.89[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs522980	0.81[AMR][1000 genomes]
rs524778	0.89[AMR][1000 genomes];1.00[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs524829	0.89[AMR][1000 genomes];1.00[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs524988	0.82[ASN][1000 genomes]
rs525827	0.83[ASN][1000 genomes]
rs526275	0.87[EUR][1000 genomes]
rs527715	0.83[ASN][1000 genomes]
rs530102	1.00[EUR][1000 genomes]
rs533640	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs533734	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs535393	0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs536414	0.97[AMR][1000 genomes];0.94[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs537425	0.90[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs540900	1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs554681	1.00[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs564050	0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs570210	0.93[ASN][1000 genomes]
rs572851	0.84[ASN][1000 genomes]
rs578990	0.90[AMR][1000 genomes];1.00[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs578991	0.89[AMR][1000 genomes];0.84[ASN][1000 genomes]
rs582271	0.89[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs583330	0.83[AMR][1000 genomes];0.84[ASN][1000 genomes]
rs588574	0.89[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs592827	0.84[AMR][1000 genomes];0.88[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs604364	0.85[ASN][1000 genomes]
rs609736	1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs609755	1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs619934	0.89[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs626821	0.83[AMR][1000 genomes];0.84[ASN][1000 genomes]
rs629544	0.84[AMR][1000 genomes];0.83[ASN][1000 genomes]
rs630704	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs640654	0.83[AMR][1000 genomes];0.84[ASN][1000 genomes]
rs642776	0.83[AMR][1000 genomes];0.84[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs643133	0.83[ASN][1000 genomes]
rs643174	0.81[ASN][1000 genomes]
rs648352	0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6509982	0.85[ASN][1000 genomes]
rs659424	0.86[AMR][1000 genomes];0.83[ASN][1000 genomes]
rs662308	0.81[AMR][1000 genomes];0.81[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs662763	0.81[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs665082	0.83[AMR][1000 genomes];0.81[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs665846	0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs665857	0.81[AMR][1000 genomes];0.81[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs667438	0.90[AMR][1000 genomes];1.00[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs667974	0.86[AMR][1000 genomes];0.84[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs668056	1.00[EUR][1000 genomes]
rs677127	0.81[AMR][1000 genomes];0.81[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs677142	0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs678540	0.81[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs684653	0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs685117	0.84[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs7250351	0.85[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:18 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1056598	chr19:56331762-56703428	Flanking Active TSS Active TSS Bivalent Enhancer ZNF genes & repeats Enhancers Weak transcription Strong transcription Transcr. at gene 5' and 3' Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	50 gene(s)	inside rSNPs	diseases
2	nsv1064371	chr19:56418215-56842450	ZNF genes & repeats Strong transcription Enhancers Active TSS Flanking Bivalent TSS/Enh Flanking Active TSS Weak transcription Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	65 gene(s)	inside rSNPs	diseases
3	nsv1057316	chr19:56418215-56849458	Strong transcription Enhancers ZNF genes & repeats Weak transcription Genic enhancers Flanking Active TSS Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	65 gene(s)	inside rSNPs	diseases
4	nsv580354	chr19:56505685-56723492	Weak transcription Genic enhancers Enhancers Strong transcription Active TSS Flanking Bivalent TSS/Enh Flanking Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	48 gene(s)	inside rSNPs	diseases
5	nsv833883	chr19:56512601-56640089	Strong transcription Flanking Active TSS Enhancers Weak transcription Bivalent Enhancer Active TSS Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	41 gene(s)	inside rSNPs	diseases
6	nsv523651	chr19:56537528-56707048	Weak transcription Enhancers Genic enhancers Active TSS Strong transcription Flanking Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	47 gene(s)	inside rSNPs	diseases
7	nsv1057820	chr19:56555942-56720262	Weak transcription Genic enhancers Flanking Active TSS Enhancers Strong transcription Transcr. at gene 5' and 3' Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	47 gene(s)	inside rSNPs	diseases
8	nsv528998	chr19:56578238-56707048	Active TSS Genic enhancers Weak transcription Strong transcription Flanking Active TSS Enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	47 gene(s)	inside rSNPs	diseases
9	nsv912512	chr19:56592286-56636759	Enhancers Genic enhancers Weak transcription Active TSS ZNF genes & repeats Strong transcription Flanking Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	33 gene(s)	inside rSNPs	diseases
10	nsv517365	chr19:56592286-56674548	Strong transcription Transcr. at gene 5' and 3' Flanking Active TSS Genic enhancers Weak transcription Enhancers Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	38 gene(s)	inside rSNPs	diseases
11	nsv912513	chr19:56592286-56685463	Flanking Active TSS Weak transcription Genic enhancers Strong transcription Transcr. at gene 5' and 3' Enhancers Active TSS ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	39 gene(s)	inside rSNPs	diseases
12	nsv521744	chr19:56592286-56686953	Enhancers Flanking Bivalent TSS/Enh Weak transcription Strong transcription Genic enhancers Flanking Active TSS Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	39 gene(s)	inside rSNPs	diseases
13	nsv912514	chr19:56596815-56636759	Flanking Active TSS Genic enhancers Enhancers Weak transcription Transcr. at gene 5' and 3' Strong transcription Active TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	32 gene(s)	inside rSNPs	diseases
14	nsv912515	chr19:56598829-56623710	Weak transcription Genic enhancers Strong transcription Flanking Active TSS Enhancers ZNF genes & repeats Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region	11 gene(s)	inside rSNPs	diseases
15	nsv912516	chr19:56601298-56981382	Weak transcription Strong transcription Flanking Active TSS ZNF genes & repeats Enhancers Genic enhancers Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	93 gene(s)	inside rSNPs	diseases
16	esv1809307	chr19:56604027-56633623	Enhancers Transcr. at gene 5' and 3' Weak transcription Strong transcription Active TSS Flanking Active TSS Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	29 gene(s)	inside rSNPs	diseases
17	esv1811581	chr19:56609313-56631618	Flanking Active TSS Active TSS Enhancers Weak transcription Strong transcription ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region	17 gene(s)	inside rSNPs	diseases
18	esv1824038	chr19:56610449-56636632	Weak transcription Strong transcription Active TSS Enhancers Genic enhancers ZNF genes & repeats Flanking Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	29 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:124 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr19:56592600-56620000	Weak transcription	HSMMtube	muscle
2	chr19:56592800-56622600	Weak transcription	Primary T helper naive cells from peripheral blood	blood
3	chr19:56593000-56616200	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
4	chr19:56593000-56616600	Weak transcription	Primary T killer memory cells from peripheral blood	blood
5	chr19:56593000-56616800	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
6	chr19:56593000-56631200	Weak transcription	Pancreatic Islets	Pancreatic Islet
7	chr19:56593600-56616000	Weak transcription	Stomach Mucosa	stomach
8	chr19:56594800-56616800	Weak transcription	HUVEC	blood vessel
9	chr19:56596600-56614800	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
10	chr19:56597200-56619400	Weak transcription	ES-I3 Cell Line	embryonic stem cell
11	chr19:56599800-56615200	Strong transcription	Liver	Liver
12	chr19:56600000-56619000	ZNF genes & repeats	H9 Derived Neuron Cultured Cells	ES cell derived
13	chr19:56600400-56614400	Strong transcription	HepG2	liver
14	chr19:56600800-56616800	Weak transcription	Small Intestine	intestine
15	chr19:56602800-56614400	ZNF genes & repeats	Fetal Stomach	stomach
16	chr19:56602800-56620000	Weak transcription	NH-A	brain
17	chr19:56603000-56616600	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
18	chr19:56603200-56619800	Weak transcription	NHDF-Ad	bronchial
19	chr19:56603800-56616800	Weak transcription	Psoas Muscle	Psoas
20	chr19:56604000-56614800	Strong transcription	Rectal Mucosa Donor 29	rectum
21	chr19:56604800-56616200	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
22	chr19:56604800-56616800	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
23	chr19:56605000-56612600	Weak transcription	HMEC	breast
24	chr19:56605000-56614400	Strong transcription	Duodenum Mucosa	Duodenum
25	chr19:56605000-56615000	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
26	chr19:56605000-56616400	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
27	chr19:56605200-56615000	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
28	chr19:56605200-56615000	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
29	chr19:56605200-56617000	Weak transcription	Brain Angular Gyrus	brain
30	chr19:56605200-56619800	Weak transcription	HSMM	muscle
31	chr19:56605200-56620000	Weak transcription	Fetal Kidney	kidney
32	chr19:56605400-56612600	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
33	chr19:56605400-56615000	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
34	chr19:56605600-56615000	Strong transcription	Cortex derived primary cultured neurospheres	brain
35	chr19:56605600-56615000	Strong transcription	Ganglion Eminence derived primary cultured neurospheres	brain
36	chr19:56606000-56615800	Strong transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
37	chr19:56606200-56614200	Strong transcription	Rectal Mucosa Donor 31	rectum
38	chr19:56606200-56615000	Strong transcription	Sigmoid Colon	Sigmoid Colon
39	chr19:56606200-56615200	Strong transcription	Colonic Mucosa	Colon
40	chr19:56606200-56615200	Strong transcription	Thymus	Thymus
41	chr19:56606400-56613000	Strong transcription	Breast Myoepithelial Primary Cells	Breast
42	chr19:56606400-56615200	Strong transcription	Esophagus	oesophagus
43	chr19:56606400-56615200	Strong transcription	A549	lung
44	chr19:56606400-56616600	Strong transcription	Foreskin Fibroblast Primary Cells skin01	Skin
45	chr19:56606600-56614400	Strong transcription	Stomach Smooth Muscle	stomach
46	chr19:56606800-56614000	Strong transcription	HUES64 Cell Line	embryonic stem cell
47	chr19:56606800-56614000	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
48	chr19:56606800-56614200	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
49	chr19:56606800-56614600	Strong transcription	Primary neutrophils fromperipheralblood	blood
50	chr19:56607000-56613000	Strong transcription	Primary hematopoietic stem cells short term culture	blood

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