Variant report

Variant	rs6787547
Chromosome Location	chr3:112023078-112023079
allele	A/G
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	YY1	chr3:112022832-112023122	GM12878	blood:	n/a	n/a
2	MAX	chr3:112023021-112023232	GM12878	blood:	n/a	n/a
3	YY1	chr3:112022689-112023199	GM12891	blood:	n/a	n/a

Variant related genes	Relation type
ENSG00000239482	TF binding region

Extended variants
information (count: 34 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:31)

rs_ID	r²[population]
rs10804500	0.83[JPT][hapmap]
rs12106967	0.86[CHB][hapmap];0.81[ASN][1000 genomes]
rs13069751	0.89[ASN][1000 genomes]
rs13069935	0.97[ASN][1000 genomes]
rs13070091	0.97[ASN][1000 genomes]
rs1317243	0.86[CHB][hapmap];0.95[JPT][hapmap];0.90[ASN][1000 genomes]
rs1879513	0.97[ASN][1000 genomes]
rs1879514	0.90[AFR][1000 genomes];0.91[AMR][1000 genomes];0.93[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2895395	0.83[JPT][hapmap]
rs4355254	0.83[JPT][hapmap]
rs4682101	0.86[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs6438064	0.97[ASN][1000 genomes]
rs6438065	0.97[ASN][1000 genomes]
rs6762106	0.97[ASN][1000 genomes]
rs6773206	0.97[ASN][1000 genomes]
rs6780745	0.96[ASN][1000 genomes]
rs6798354	0.97[ASN][1000 genomes]
rs6798486	0.97[ASN][1000 genomes]
rs6805117	0.97[ASN][1000 genomes]
rs6805142	0.94[ASN][1000 genomes]
rs6808365	0.93[AFR][1000 genomes];0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7639471	0.82[CHB][hapmap];0.82[JPT][hapmap]
rs8179913	0.97[ASN][1000 genomes]
rs9755930	0.98[ASN][1000 genomes]
rs9814721	0.97[ASN][1000 genomes]
rs9823309	0.87[AFR][1000 genomes];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs9834347	0.82[CHB][hapmap]
rs9852176	0.97[ASN][1000 genomes]
rs9856838	0.97[ASN][1000 genomes]
rs9876973	0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs9990215	0.84[CHB][hapmap]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv10307	chr3:111903974-112087686	Enhancers Active TSS Weak transcription Flanking Active TSS Strong transcription Genic enhancers Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
2	nsv3949	chr3:111998512-112044060	Enhancers Weak transcription Active TSS Flanking Active TSS ZNF genes & repeats Strong transcription Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
3	nsv967052	chr3:112020436-112027937	Flanking Active TSS Active TSS Enhancers Weak transcription Transcr. at gene 5' and 3' ZNF genes & repeats Genic enhancers	TF binding region CpG island lncRNA	2 gene(s)	inside rSNPs	n/a

No data

Chromatin state (count:118 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:112021200-112023400	Flanking Active TSS	Cortex derived primary cultured neurospheres	brain
2	chr3:112021400-112023200	Active TSS	Colon Smooth Muscle	Colon
3	chr3:112021400-112023200	Flanking Active TSS	Fetal Thymus	thymus
4	chr3:112021400-112023400	Active TSS	ES-WA7 Cell Line	embryonic stem cell
5	chr3:112021400-112025200	Enhancers	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
6	chr3:112021600-112023200	Active TSS	Brain Dorsolateral Prefrontal Cortex	brain
7	chr3:112021600-112023400	Active TSS	Fetal Brain Female	brain
8	chr3:112021600-112023400	Active TSS	Rectal Smooth Muscle	rectum
9	chr3:112021600-112023600	Active TSS	ES-I3 Cell Line	embryonic stem cell
10	chr3:112021800-112023200	Active TSS	Colonic Mucosa	Colon
11	chr3:112021800-112023400	Flanking Active TSS	Fetal Muscle Leg	muscle
12	chr3:112021800-112023400	Active TSS	Left Ventricle	heart
13	chr3:112021800-112023400	Flanking Active TSS	HUVEC	blood vessel
14	chr3:112021800-112023600	Flanking Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
15	chr3:112021800-112023600	Flanking Active TSS	Adipose Nuclei	Adipose
16	chr3:112021800-112023600	Enhancers	Lung	lung
17	chr3:112021800-112023600	Active TSS	Psoas Muscle	Psoas
18	chr3:112022000-112023200	Enhancers	Liver	Liver
19	chr3:112022000-112023200	Active TSS	Brain Hippocampus Middle	brain
20	chr3:112022000-112023200	Active TSS	Fetal Intestine Large	intestine
21	chr3:112022000-112023200	Active TSS	Fetal Muscle Trunk	muscle
22	chr3:112022000-112023400	Flanking Active TSS	Primary T helper cells fromperipheralblood	blood
23	chr3:112022000-112023400	Flanking Active TSS	Muscle Satellite Cultured Cells	--
24	chr3:112022000-112023400	Flanking Active TSS	Foreskin Fibroblast Primary Cells skin02	Skin
25	chr3:112022000-112023400	Flanking Active TSS	Foreskin Keratinocyte Primary Cells skin03	Skin
26	chr3:112022000-112023400	Flanking Active TSS	Duodenum Mucosa	Duodenum
27	chr3:112022000-112023400	Active TSS	Fetal Kidney	kidney
28	chr3:112022000-112023400	Flanking Active TSS	Skeletal Muscle Male	skeletal muscle
29	chr3:112022000-112023600	Active TSS	Fetal Intestine Small	intestine
30	chr3:112022200-112023200	Flanking Active TSS	Primary hematopoietic stem cells short term culture	blood
31	chr3:112022200-112023200	Flanking Active TSS	Primary T regulatory cells fromperipheralblood	blood
32	chr3:112022200-112023200	Active TSS	Primary T cells effector/memory enriched fromperipheralblood	blood
33	chr3:112022200-112023200	Flanking Active TSS	Monocytes-CD14+_RO01746	blood
34	chr3:112022200-112023400	Flanking Active TSS	Primary B cells from cord blood	blood
35	chr3:112022200-112023400	Flanking Active TSS	Primary B cells from peripheral blood	blood
36	chr3:112022200-112023400	Flanking Active TSS	Primary T cells from cord blood	blood
37	chr3:112022200-112023400	Flanking Active TSS	Primary hematopoietic stem cells	blood
38	chr3:112022200-112023400	Flanking Active TSS	Primary T helper memory cells from peripheral blood 2	blood
39	chr3:112022200-112023400	Flanking Active TSS	Primary T helper cells PMA-I stimulated	--
40	chr3:112022200-112023400	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Female	--
41	chr3:112022200-112023400	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
42	chr3:112022200-112023400	Active TSS	Pancreatic Islets	Pancreatic Islet
43	chr3:112022200-112023400	Active TSS	Ovary	ovary
44	chr3:112022200-112023400	Flanking Active TSS	Rectal Mucosa Donor 31	rectum
45	chr3:112022200-112023400	Enhancers	Spleen	Spleen
46	chr3:112022200-112023600	Flanking Active TSS	Duodenum Smooth Muscle	Duodenum
47	chr3:112022200-112023600	Flanking Active TSS	Skeletal Muscle Female	skeletal muscle
48	chr3:112022400-112023200	Active TSS	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
49	chr3:112022400-112023200	Flanking Active TSS	Primary monocytes fromperipheralblood	blood
50	chr3:112022400-112023200	Flanking Active TSS	Primary neutrophils fromperipheralblood	blood

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links