Variant report

Variant	rs9837520
Chromosome Location	chr3:49722356-49722357
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:21)
CpG islands
(count:0)
Chromatin interactive
region (count:3)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:21 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	RXRA	chr3:49721628-49722410	HepG2	liver:	n/a	n/a
2	POLR2A	chr3:49721456-49727648	H1-hESC	embryonic stem cell:	n/a	n/a
3	PAX5	chr3:49722095-49722435	GM12878	blood:	n/a	n/a
4	POLR2A	chr3:49717503-49727239	HepG2	liver:	n/a	n/a
5	POLR2A	chr3:49721269-49722516	HepG2	liver:	n/a	n/a
6	POLR2A	chr3:49720128-49724935	GM12878	blood:	n/a	n/a
7	POLR2A	chr3:49718663-49722661	HepG2	liver:	n/a	n/a
8	POLR2A	chr3:49721728-49722496	H1-hESC	embryonic stem cell:	n/a	n/a
9	POLR2A	chr3:49716580-49724829	HepG2	liver:	n/a	n/a
10	JUND	chr3:49721387-49723325	HepG2	liver:	n/a	n/a
11	IRF4	chr3:49722277-49722605	GM12878	blood:	n/a	n/a
12	POLR2A	chr3:49721295-49723518	GM12892	blood:	n/a	n/a
13	POLR2A	chr3:49721760-49722612	SK-N-MC	brain:	n/a	n/a
14	POLR2A	chr3:49721601-49723433	GM12891	blood:	n/a	n/a
15	POLR2A	chr3:49716518-49723590	HepG2	liver:	n/a	n/a
16	FOSL2	chr3:49721509-49723262	HepG2	liver:	n/a	n/a
17	HEY1	chr3:49718256-49727412	HepG2	liver:	n/a	n/a
18	POU2F2	chr3:49722143-49723345	GM12878	blood:	n/a	n/a
19	POLR2A	chr3:49721241-49724664	GM12892	blood:	n/a	n/a
20	POLR2A	chr3:49721694-49724714	GM12878	blood:	n/a	n/a
21	POLR2A	chr3:49721676-49723718	GM12878	blood:	n/a	n/a

No data

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

No.	Distal block	Cell Line	Cell type
1	chr3:49710552..49715225-chr3:49718907..49727364,14	MCF-7	breast:
2	chr3:49720877..49722933-chr3:49723247..49725096,3	K562	blood:
3	chr3:49719726..49722448-chr3:49723596..49725872,2	K562	blood:

No data

Variant related genes	Relation type
RNF123	TF binding region
ENSG00000173531	Chromatin interaction
ENSG00000164062	Chromatin interaction

Extended variants
information (count: 50 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:40)

rs_ID	r²[population]
rs11130212	0.92[ASN][1000 genomes]
rs11130213	0.85[AMR][1000 genomes];0.86[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs1131095	0.85[AMR][1000 genomes];0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11709525	0.82[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs11710037	0.94[ASN][1000 genomes]
rs11718165	0.83[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs11917431	0.89[ASN][1000 genomes]
rs11919311	0.82[ASN][1000 genomes]
rs11921590	0.89[ASN][1000 genomes]
rs13085791	0.83[AMR][1000 genomes];0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13316695	0.82[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1352890	0.86[ASN][1000 genomes]
rs1873625	0.89[ASN][1000 genomes]
rs1873626	0.87[ASN][1000 genomes]
rs2172252	0.81[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2329020	0.87[ASN][1000 genomes]
rs2960548	0.92[ASN][1000 genomes]
rs3197999	0.86[AMR][1000 genomes];0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34762726	0.82[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs35007338	0.87[ASN][1000 genomes]
rs35404120	0.87[ASN][1000 genomes]
rs4283605	0.82[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4855847	0.87[ASN][1000 genomes]
rs4855852	0.82[ASN][1000 genomes]
rs4855881	0.92[ASN][1000 genomes]
rs4855883	0.81[ASN][1000 genomes]
rs6770670	0.82[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6803222	0.89[ASN][1000 genomes]
rs7614725	0.89[ASN][1000 genomes]
rs9812791	0.82[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs9822268	0.83[AMR][1000 genomes];0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9823546	0.83[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs9824092	0.94[ASN][1000 genomes]
rs9827708	0.89[ASN][1000 genomes]
rs9833611	0.89[ASN][1000 genomes]
rs9836291	0.83[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs9837341	0.89[ASN][1000 genomes]
rs9858542	0.83[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs9862080	0.94[ASN][1000 genomes]
rs9882740	0.81[EUR][1000 genomes];0.94[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:10 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv508217	chr3:49615446-49769896	Weak transcription Enhancers Flanking Active TSS Genic enhancers Strong transcription Active TSS Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	55 gene(s)	inside rSNPs	diseases
2	esv1796352	chr3:49687101-49949959	Genic enhancers Weak transcription Enhancers Active TSS Flanking Active TSS Bivalent Enhancer Strong transcription Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	90 gene(s)	inside rSNPs	diseases
3	esv1825898	chr3:49688948-49764849	Weak transcription Enhancers Flanking Active TSS Active TSS Bivalent Enhancer Strong transcription Genic enhancers 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 miRNA target site	53 gene(s)	inside rSNPs	diseases
4	esv1808511	chr3:49689880-49744825	Active TSS Flanking Active TSS Weak transcription Genic enhancers Strong transcription Bivalent/Poised TSS Enhancers Transcr. at gene 5' and 3' Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	40 gene(s)	inside rSNPs	diseases
5	nsv820990	chr3:49720651-49735911	Flanking Active TSS Weak transcription Strong transcription Transcr. at gene 5' and 3' Bivalent Enhancer Enhancers Flanking Bivalent TSS/Enh Genic enhancers Active TSS Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region	14 gene(s)	inside rSNPs	diseases
6	esv12377	chr3:49720751-49735851	Flanking Active TSS Weak transcription Strong transcription Bivalent Enhancer Enhancers Active TSS Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region	14 gene(s)	inside rSNPs	diseases
7	esv11877	chr3:49721171-49727086	Enhancers Transcr. at gene 5' and 3' Weak transcription Strong transcription Flanking Active TSS Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Active TSS ZNF genes & repeats Genic enhancers	TF binding region CpG island Chromatin interactive region	14 gene(s)	inside rSNPs	diseases
8	nsv471425	chr3:49721381-49726196	Enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Strong transcription Flanking Active TSS Bivalent Enhancer Weak transcription Active TSS Transcr. at gene 5' and 3' Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region	11 gene(s)	inside rSNPs	diseases
9	nsv482080	chr3:49721381-49726196	Active TSS Weak transcription Enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Strong transcription Bivalent/Poised TSS Genic enhancers Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region	11 gene(s)	inside rSNPs	diseases
10	nsv822077	chr3:49721400-49734526	Flanking Active TSS Weak transcription Flanking Bivalent TSS/Enh Active TSS Enhancers Strong transcription Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region	14 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs9837520	RBM6	Cis_1M	lymphoblastoid	RTeQTL
rs9837520	IHPK2	Cis_1M	lymphoblastoid	RTeQTL
rs9837520	FAM212A	cis	Muscle Skeletal	GTEx

Chromatin state (count:113 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:49712200-49723800	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
2	chr3:49712800-49723600	Weak transcription	Right Atrium	heart
3	chr3:49712800-49726200	Weak transcription	Small Intestine	intestine
4	chr3:49713000-49722400	Strong transcription	H9 Cell Line	embryonic stem cell
5	chr3:49713000-49722400	Strong transcription	Cortex derived primary cultured neurospheres	brain
6	chr3:49713000-49722600	Strong transcription	HUES6 Cell Line	embryonic stem cell
7	chr3:49713000-49722800	Strong transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
8	chr3:49713000-49722800	Strong transcription	Thymus	Thymus
9	chr3:49713000-49723200	Weak transcription	Stomach Mucosa	stomach
10	chr3:49713000-49723400	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
11	chr3:49713000-49723800	Weak transcription	Fetal Heart	heart
12	chr3:49713200-49722400	Strong transcription	iPS-20b Cell Line	embryonic stem cell
13	chr3:49713200-49722400	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
14	chr3:49713200-49722400	Strong transcription	Primary hematopoietic stem cells short term culture	blood
15	chr3:49713200-49722400	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
16	chr3:49713200-49722400	Strong transcription	Monocytes-CD14+_RO01746	blood
17	chr3:49713200-49722600	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
18	chr3:49713200-49722600	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
19	chr3:49713200-49722600	Strong transcription	Brain Germinal Matrix	brain
20	chr3:49713200-49722800	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
21	chr3:49713200-49723000	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
22	chr3:49713200-49723000	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
23	chr3:49713400-49722400	Strong transcription	Adipose Nuclei	Adipose
24	chr3:49713400-49722400	Strong transcription	Duodenum Mucosa	Duodenum
25	chr3:49713400-49722400	Strong transcription	Fetal Brain Female	brain
26	chr3:49713400-49722600	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
27	chr3:49713400-49722800	Strong transcription	Primary neutrophils fromperipheralblood	blood
28	chr3:49713400-49723000	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
29	chr3:49713600-49722400	Strong transcription	Ovary	ovary
30	chr3:49713800-49722400	Strong transcription	Ganglion Eminence derived primary cultured neurospheres	brain
31	chr3:49713800-49722400	Strong transcription	Brain Hippocampus Middle	brain
32	chr3:49713800-49723000	Strong transcription	Fetal Intestine Small	intestine
33	chr3:49714000-49723200	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
34	chr3:49714200-49722400	Strong transcription	Skeletal Muscle Male	skeletal muscle
35	chr3:49714200-49723000	Strong transcription	Gastric	stomach
36	chr3:49714200-49723200	Strong transcription	Dnd41	blood
37	chr3:49714600-49722400	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
38	chr3:49714600-49723800	Strong transcription	Liver	Liver
39	chr3:49714800-49722400	Strong transcription	Brain Dorsolateral Prefrontal Cortex	brain
40	chr3:49715800-49722600	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
41	chr3:49716000-49722600	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
42	chr3:49717400-49723800	Weak transcription	Pancreatic Islets	Pancreatic Islet
43	chr3:49717600-49723800	Weak transcription	Primary T helper naive cells from peripheral blood	blood
44	chr3:49718400-49722400	Strong transcription	Skeletal Muscle Female	skeletal muscle
45	chr3:49719000-49723000	Weak transcription	Fetal Kidney	kidney
46	chr3:49719000-49726200	Weak transcription	Primary T killer memory cells from peripheral blood	blood
47	chr3:49719800-49722400	ZNF genes & repeats	Lung	lung
48	chr3:49719800-49723200	Weak transcription	Psoas Muscle	Psoas
49	chr3:49719800-49723600	Genic enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
50	chr3:49719800-49724400	Weak transcription	NHDF-Ad	bronchial

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links