Variant report

Variant	rs310437
Chromosome Location	chr19:56177696-56177697
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:30)
CpG islands
(count:0)
Chromatin interactive
region (count:3)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:30 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	POLR2A	chr19:56177320-56182238	SK-N-MC	brain:	n/a	n/a
2	POLR2A	chr19:56177451-56179117	H1-hESC	embryonic stem cell:	n/a	n/a
3	POLR2A	chr19:56177314-56179149	GM12891	blood:	n/a	n/a
4	POLR2A	chr19:56177599-56179192	K562	blood:	n/a	n/a
5	POLR2A	chr19:56177344-56179067	GM12891	blood:	n/a	n/a
6	POLR2A	chr19:56177313-56179103	HepG2	liver:	n/a	n/a
7	POLR2A	chr19:56174024-56180333	GM12878	blood:	n/a	n/a
8	POLR2A	chr19:56177638-56179209	HL-60	blood:	n/a	n/a
9	POLR2A	chr19:56177676-56179214	GM12892	blood:	n/a	n/a
10	POLR2A	chr19:56177297-56179149	K562	blood:	n/a	n/a
11	POLR2A	chr19:56177383-56182464	GM12892	blood:	n/a	n/a
12	POLR2A	chr19:56177424-56179176	GM12891	blood:	n/a	n/a
13	POLR2A	chr19:56177589-56179159	GM12878	blood:	n/a	n/a
14	POLR2A	chr19:56177250-56179179	Hela-S3	cervix:	n/a	n/a
15	POLR2A	chr19:56177227-56182460	K562	blood:	n/a	n/a
16	POLR2A	chr19:56177289-56177712	H1-hESC	embryonic stem cell:	n/a	n/a
17	POLR2A	chr19:56177150-56179360	H1-hESC	embryonic stem cell:	n/a	n/a
18	POLR2A	chr19:56176947-56180628	HepG2	liver:	n/a	n/a
19	POLR2A	chr19:56177651-56180685	K562	blood:	n/a	n/a
20	POLR2A	chr19:56177219-56179201	K562	blood:	n/a	n/a
21	POLR2A	chr19:56177579-56178069	PFSK-1	brain:	n/a	n/a
22	POLR2A	chr19:56177444-56177771	GM12878	blood:	n/a	n/a
23	POLR2A	chr19:56177299-56179232	GM12878	blood:	n/a	n/a
24	POLR2A	chr19:56177567-56179074	GM12878	blood:	n/a	n/a
25	POLR2A	chr19:56177308-56179201	GM12891	blood:	n/a	n/a
26	POLR2A	chr19:56177574-56182562	GM12892	blood:	n/a	n/a
27	POLR2A	chr19:56177312-56183116	A549	lung:	n/a	n/a
28	POLR2A	chr19:56177127-56183356	PANC-1	pancreas:	n/a	n/a
29	POLR2A	chr19:56177308-56178516	Hela-S3	cervix:	n/a	n/a
30	POLR2A	chr19:56176298-56179984	GM12892	blood:	n/a	n/a

No data

(count:3 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr19:56164975..56168855-chr19:56176069..56182259,9	MCF-7	breast:
2	chr19:56176017..56178095-chr19:56199906..56202183,2	K562	blood:
3	chr19:56146402..56147911-chr19:56177195..56179470,2	MCF-7	breast:

No data

Variant related genes	Relation type
ENSG00000267096	TF binding region
ENSG00000171425	Chromatin interaction
ENSG00000063244	Chromatin interaction

Extended variants
information (count: 41 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:34)

rs_ID	r²[population]
rs10402618	0.91[ASN][1000 genomes]
rs10403866	0.84[ASN][1000 genomes]
rs10408613	0.81[ASN][1000 genomes]
rs10410404	1.00[CHB][hapmap]
rs10410802	0.91[CEU][hapmap];0.95[CHB][hapmap];1.00[MEX][hapmap];0.93[TSI][hapmap];0.88[AMR][1000 genomes];0.95[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs10410886	0.89[CHB][hapmap]
rs10412050	0.91[CEU][hapmap];0.95[CHB][hapmap];1.00[MEX][hapmap];0.93[TSI][hapmap];0.83[EUR][1000 genomes]
rs10415521	0.91[CEU][hapmap];0.95[CHB][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];1.00[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs10417539	0.84[ASN][1000 genomes]
rs10421319	1.00[CHB][hapmap]
rs11882031	0.91[CEU][hapmap];0.95[CHB][hapmap];1.00[MEX][hapmap];0.93[TSI][hapmap];0.88[AMR][1000 genomes];0.95[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2280255	0.81[ASN][1000 genomes]
rs2287791	0.91[CEU][hapmap];0.95[CHB][hapmap];0.87[CHD][hapmap];0.95[GIH][hapmap];1.00[TSI][hapmap];0.84[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs28385383	0.85[AMR][1000 genomes];0.95[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs28595590	0.85[AMR][1000 genomes];0.89[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs28668166	0.82[AMR][1000 genomes];0.84[ASN][1000 genomes]
rs310441	0.82[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs3745446	0.83[ASN][1000 genomes]
rs4801526	0.83[ASN][1000 genomes]
rs523509	0.88[ASN][1000 genomes]
rs575274	0.84[CHB][hapmap];0.84[CHD][hapmap];0.89[GIH][hapmap]
rs57544196	0.85[AMR][1000 genomes];0.84[ASN][1000 genomes]
rs584405	0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs58490076	0.90[ASN][1000 genomes]
rs60873246	0.82[ASN][1000 genomes]
rs610811	0.89[GIH][hapmap]
rs617073	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.95[GIH][hapmap];1.00[TSI][hapmap];0.83[YRI][hapmap];0.82[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs648651	0.84[AFR][1000 genomes];0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs681804	0.93[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7256441	0.83[EUR][1000 genomes]
rs73613281	0.84[ASN][1000 genomes]
rs8100143	0.91[CEU][hapmap];0.95[CHB][hapmap];1.00[MEX][hapmap];0.93[TSI][hapmap];0.88[AMR][1000 genomes];0.95[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs8104242	0.91[CEU][hapmap];0.95[CHB][hapmap];1.00[MEX][hapmap];0.93[TSI][hapmap];0.81[AMR][1000 genomes];0.95[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs8109983	0.85[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:7 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv912487	chr19:55977909-56215184	Enhancers Weak transcription Transcr. at gene 5' and 3' Flanking Active TSS Active TSS Strong transcription Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	109 gene(s)	inside rSNPs	diseases
2	nsv912494	chr19:56026072-56215184	Genic enhancers Bivalent Enhancer Flanking Active TSS Active TSS Enhancers Weak transcription Transcr. at gene 5' and 3' Strong transcription ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	97 gene(s)	inside rSNPs	diseases
3	nsv912498	chr19:56041848-56215184	Active TSS Enhancers Weak transcription Strong transcription Flanking Active TSS Transcr. at gene 5' and 3' Genic enhancers ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	97 gene(s)	inside rSNPs	diseases
4	nsv912501	chr19:56093365-56215184	Flanking Active TSS Weak transcription Strong transcription Active TSS Transcr. at gene 5' and 3' Enhancers Genic enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	92 gene(s)	inside rSNPs	diseases
5	nsv428026	chr19:56130849-56423514	Flanking Active TSS Enhancers Genic enhancers Transcr. at gene 5' and 3' Active TSS Strong transcription Weak transcription ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	82 gene(s)	inside rSNPs	diseases
6	nsv833882	chr19:56158633-56326564	Enhancers Active TSS Flanking Active TSS Genic enhancers Strong transcription Bivalent Enhancer Weak transcription Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	66 gene(s)	inside rSNPs	diseases
7	nsv1061024	chr19:56167101-56217359	Active TSS Weak transcription Transcr. at gene 5' and 3' Strong transcription Genic enhancers Enhancers ZNF genes & repeats Flanking Active TSS Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	37 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs310437	ZNF580	cis	lymphoblastoid	seeQTL

Chromatin state (count:126 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr19:56169600-56181600	Strong transcription	Cortex derived primary cultured neurospheres	brain
2	chr19:56170000-56181600	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
3	chr19:56170000-56181600	Strong transcription	Aorta	Aorta
4	chr19:56170000-56181800	Strong transcription	H9 Cell Line	embryonic stem cell
5	chr19:56170000-56184800	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
6	chr19:56170200-56178400	Strong transcription	NHEK	skin
7	chr19:56170200-56181600	Strong transcription	HUES6 Cell Line	embryonic stem cell
8	chr19:56170200-56181800	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
9	chr19:56170200-56182200	Strong transcription	HUES48 Cell Line	embryonic stem cell
10	chr19:56170200-56182400	Strong transcription	iPS-15b Cell Line	embryonic stem cell
11	chr19:56170200-56182400	Strong transcription	Rectal Smooth Muscle	rectum
12	chr19:56170200-56184000	Strong transcription	Primary T cells from cord blood	blood
13	chr19:56170200-56185200	Strong transcription	Fetal Thymus	thymus
14	chr19:56170200-56185400	Strong transcription	Monocytes-CD14+_RO01746	blood
15	chr19:56170200-56185800	Strong transcription	Fetal Stomach	stomach
16	chr19:56170400-56179800	Strong transcription	Hela-S3	cervix
17	chr19:56170400-56181600	Strong transcription	iPS DF 6.9 Cell Line	embryonic stem cell
18	chr19:56170400-56181600	Strong transcription	Fetal Muscle Leg	muscle
19	chr19:56170400-56182200	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
20	chr19:56170400-56183000	Strong transcription	Sigmoid Colon	Sigmoid Colon
21	chr19:56170400-56185600	Strong transcription	Primary neutrophils fromperipheralblood	blood
22	chr19:56170400-56185800	Strong transcription	Fetal Brain Female	brain
23	chr19:56170600-56177800	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
24	chr19:56170600-56178400	Strong transcription	HepG2	liver
25	chr19:56170600-56178600	Strong transcription	Brain Angular Gyrus	brain
26	chr19:56170600-56178800	Strong transcription	Esophagus	oesophagus
27	chr19:56170600-56181600	Strong transcription	H1 Cell Line	embryonic stem cell
28	chr19:56170600-56181600	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
29	chr19:56170600-56181600	Strong transcription	Thymus	Thymus
30	chr19:56170600-56182400	Strong transcription	HUES64 Cell Line	embryonic stem cell
31	chr19:56170600-56182400	Strong transcription	iPS-20b Cell Line	embryonic stem cell
32	chr19:56170800-56178200	Strong transcription	Fetal Intestine Large	intestine
33	chr19:56170800-56179000	Strong transcription	Rectal Mucosa Donor 31	rectum
34	chr19:56170800-56181600	Strong transcription	Ganglion Eminence derived primary cultured neurospheres	brain
35	chr19:56170800-56181600	Strong transcription	Colonic Mucosa	Colon
36	chr19:56170800-56182600	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
37	chr19:56170800-56182800	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
38	chr19:56170800-56185400	Strong transcription	Rectal Mucosa Donor 29	rectum
39	chr19:56170800-56185800	Weak transcription	Psoas Muscle	Psoas
40	chr19:56170800-56186000	Weak transcription	Right Atrium	heart
41	chr19:56171000-56178200	Strong transcription	Duodenum Mucosa	Duodenum
42	chr19:56171000-56181400	Strong transcription	Primary T killer memory cells from peripheral blood	blood
43	chr19:56171000-56181600	Strong transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
44	chr19:56171000-56181600	Strong transcription	Duodenum Smooth Muscle	Duodenum
45	chr19:56171000-56181600	Strong transcription	Left Ventricle	heart
46	chr19:56171000-56181800	Strong transcription	Brain Germinal Matrix	brain
47	chr19:56171000-56182000	Strong transcription	iPS-18 Cell Line	embryonic stem cell
48	chr19:56171000-56182800	Strong transcription	NHLF	lung
49	chr19:56171200-56178000	Strong transcription	Brain Dorsolateral Prefrontal Cortex	brain
50	chr19:56171200-56178000	Strong transcription	HMEC	breast

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