Variant report

Variant	rs310438
Chromosome Location	chr19:56177298-56177299
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:11)
CpG islands
(count:0)
Chromatin interactive
region (count:3)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:11 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	POLR2A	chr19:56174024-56180333	GM12878	blood:	n/a	n/a
2	POLR2A	chr19:56177291-56177455	H1-hESC	embryonic stem cell:	n/a	n/a
3	POLR2A	chr19:56177297-56179149	K562	blood:	n/a	n/a
4	POLR2A	chr19:56177250-56179179	Hela-S3	cervix:	n/a	n/a
5	POLR2A	chr19:56177227-56182460	K562	blood:	n/a	n/a
6	POLR2A	chr19:56177289-56177712	H1-hESC	embryonic stem cell:	n/a	n/a
7	POLR2A	chr19:56177150-56179360	H1-hESC	embryonic stem cell:	n/a	n/a
8	POLR2A	chr19:56176947-56180628	HepG2	liver:	n/a	n/a
9	POLR2A	chr19:56177219-56179201	K562	blood:	n/a	n/a
10	POLR2A	chr19:56177127-56183356	PANC-1	pancreas:	n/a	n/a
11	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
ENSG00000063244	Chromatin interaction
ENSG00000171425	Chromatin interaction

Extended variants
information (count: 22 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:15)

rs_ID	r²[population]
rs11545669	1.00[AMR][1000 genomes];0.83[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs310439	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs310442	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs310443	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs310444	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs507498	0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs537728	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs57063593	0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs581023	0.84[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs600106	1.00[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs630491	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs637788	0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs679577	1.00[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs680444	1.00[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs681433	1.00[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[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

No data

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	chr19:56170400-56177400	Strong transcription	Fetal Intestine Small	intestine
17	chr19:56170400-56179800	Strong transcription	Hela-S3	cervix
18	chr19:56170400-56181600	Strong transcription	iPS DF 6.9 Cell Line	embryonic stem cell
19	chr19:56170400-56181600	Strong transcription	Fetal Muscle Leg	muscle
20	chr19:56170400-56182200	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
21	chr19:56170400-56183000	Strong transcription	Sigmoid Colon	Sigmoid Colon
22	chr19:56170400-56185600	Strong transcription	Primary neutrophils fromperipheralblood	blood
23	chr19:56170400-56185800	Strong transcription	Fetal Brain Female	brain
24	chr19:56170600-56177800	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
25	chr19:56170600-56178400	Strong transcription	HepG2	liver
26	chr19:56170600-56178600	Strong transcription	Brain Angular Gyrus	brain
27	chr19:56170600-56178800	Strong transcription	Esophagus	oesophagus
28	chr19:56170600-56181600	Strong transcription	H1 Cell Line	embryonic stem cell
29	chr19:56170600-56181600	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
30	chr19:56170600-56181600	Strong transcription	Thymus	Thymus
31	chr19:56170600-56182400	Strong transcription	HUES64 Cell Line	embryonic stem cell
32	chr19:56170600-56182400	Strong transcription	iPS-20b Cell Line	embryonic stem cell
33	chr19:56170800-56177400	Strong transcription	Gastric	stomach
34	chr19:56170800-56177600	Strong transcription	Right Ventricle	heart
35	chr19:56170800-56178200	Strong transcription	Fetal Intestine Large	intestine
36	chr19:56170800-56179000	Strong transcription	Rectal Mucosa Donor 31	rectum
37	chr19:56170800-56181600	Strong transcription	Ganglion Eminence derived primary cultured neurospheres	brain
38	chr19:56170800-56181600	Strong transcription	Colonic Mucosa	Colon
39	chr19:56170800-56182600	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
40	chr19:56170800-56182800	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
41	chr19:56170800-56185400	Strong transcription	Rectal Mucosa Donor 29	rectum
42	chr19:56170800-56185800	Weak transcription	Psoas Muscle	Psoas
43	chr19:56170800-56186000	Weak transcription	Right Atrium	heart
44	chr19:56171000-56178200	Strong transcription	Duodenum Mucosa	Duodenum
45	chr19:56171000-56181400	Strong transcription	Primary T killer memory cells from peripheral blood	blood
46	chr19:56171000-56181600	Strong transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
47	chr19:56171000-56181600	Strong transcription	Duodenum Smooth Muscle	Duodenum
48	chr19:56171000-56181600	Strong transcription	Left Ventricle	heart
49	chr19:56171000-56181800	Strong transcription	Brain Germinal Matrix	brain
50	chr19:56171000-56182000	Strong transcription	iPS-18 Cell Line	embryonic stem cell

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links