Variant report

Variant	rs778339
Chromosome Location	chr2:233739678-233739679
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:5)
CpG islands
(count:0)
Chromatin interactive
region (count:7)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

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

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	HEY1	chr2:233738290-233739730	HepG2	liver:	n/a	n/a
2	POLR2A	chr2:233738814-233739688	HepG2	liver:	n/a	n/a
3	POLR2A	chr2:233739530-233739682	A549	lung:	n/a	n/a
4	POLR2A	chr2:233735463-233740850	HepG2	liver:	n/a	n/a
5	POLR2A	chr2:233737594-233750472	HepG2	liver:	n/a	n/a

No data

(count:7 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr2:233733606..233736578-chr2:233738541..233742093,3	K562	blood:
2	chr2:233739500..233741658-chr2:234118418..234121019,2	MCF-7	breast:
3	chr2:233738643..233740986-chr2:234158854..234161597,2	MCF-7	breast:
4	chr2:233739591..233745527-chr2:233747956..233752237,8	MCF-7	breast:
5	chr2:233739669..233741368-chr2:233754744..233756796,2	MCF-7	breast:
6	chr2:233739634..233741752-chr2:234762062..234763820,2	MCF-7	breast:
7	chr2:233733606..233736774-chr2:233738541..233741120,3	K562	blood:

No data

Variant related genes	Relation type
C2orf82	TF binding region
ENSG00000123485	Chromatin interaction
ENSG00000085978	Chromatin interaction
ENSG00000182600	Chromatin interaction
ENSG00000066248	Chromatin interaction

Extended variants
information (count: 66 )
Associated
traits (count: 8 )

rSNPs within LD-proxies of this variant (count:57)

rs_ID	r²[population]
rs10933411	0.89[AFR][1000 genomes];0.94[ASN][1000 genomes]
rs10933412	0.94[ASN][1000 genomes]
rs11676216	0.89[AFR][1000 genomes];0.94[ASN][1000 genomes]
rs12694917	0.94[ASN][1000 genomes]
rs1446310	0.84[ASN][1000 genomes]
rs1446311	0.89[AFR][1000 genomes];0.94[ASN][1000 genomes]
rs1867778	0.84[ASN][1000 genomes]
rs1947105	0.93[AFR][1000 genomes];0.96[ASN][1000 genomes]
rs2044449	0.96[ASN][1000 genomes]
rs2100053	0.93[AFR][1000 genomes];0.96[ASN][1000 genomes]
rs2250654	0.98[AMR][1000 genomes];0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2250665	0.98[AMR][1000 genomes];0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2305137	0.94[ASN][1000 genomes]
rs2305141	0.84[ASN][1000 genomes]
rs2592102	0.91[AFR][1000 genomes];0.97[ASN][1000 genomes]
rs2592113	0.84[ASN][1000 genomes]
rs2592115	0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2592116	0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2592117	0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2592126	0.86[AFR][1000 genomes];0.96[AMR][1000 genomes];0.94[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2674839	0.84[ASN][1000 genomes]
rs2675957	0.98[AMR][1000 genomes];0.94[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2675966	0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2675967	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2675971	0.93[AFR][1000 genomes];0.97[ASN][1000 genomes]
rs2675973	0.93[AFR][1000 genomes];0.94[ASN][1000 genomes]
rs2675974	0.94[ASN][1000 genomes]
rs283466	0.84[ASN][1000 genomes]
rs283468	0.82[ASN][1000 genomes]
rs283469	0.81[ASN][1000 genomes]
rs283471	0.82[ASN][1000 genomes]
rs283474	0.81[ASN][1000 genomes]
rs283475	0.81[ASN][1000 genomes]
rs3816334	0.93[AFR][1000 genomes];0.94[ASN][1000 genomes]
rs4973053	0.84[ASN][1000 genomes]
rs4973054	0.94[ASN][1000 genomes]
rs4973055	0.94[ASN][1000 genomes]
rs4973056	0.93[ASN][1000 genomes]
rs4973560	0.82[ASN][1000 genomes]
rs4973561	0.84[ASN][1000 genomes]
rs6437074	0.93[AFR][1000 genomes];0.94[ASN][1000 genomes]
rs6719061	0.85[ASN][1000 genomes]
rs709933	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs709934	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs709938	0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs7558609	0.81[AFR][1000 genomes];0.85[ASN][1000 genomes]
rs7573208	0.85[ASN][1000 genomes]
rs7587309	0.94[ASN][1000 genomes]
rs7589201	0.97[ASN][1000 genomes]
rs778338	0.85[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs778340	0.84[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs778368	0.87[AMR][1000 genomes];0.93[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs809639	0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs812383	0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs895430	0.97[ASN][1000 genomes]
rs9653383	0.82[ASN][1000 genomes]
rs991873	0.93[AFR][1000 genomes];0.94[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:9 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv948470	chr2:233166262-233886732	Enhancers Strong transcription Weak transcription Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS Flanking Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	61 gene(s)	inside rSNPs	diseases
2	nsv1005123	chr2:233227729-233920152	Enhancers Strong transcription Weak transcription Bivalent Enhancer Bivalent/Poised TSS Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	58 gene(s)	inside rSNPs	diseases
3	nsv536173	chr2:233227729-233920152	Bivalent Enhancer Strong transcription Enhancers Weak transcription Flanking Bivalent TSS/Enh Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' Active TSS ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	58 gene(s)	inside rSNPs	diseases
4	nsv834570	chr2:233639160-233805067	Weak transcription Bivalent Enhancer Enhancers Bivalent/Poised TSS Strong transcription Active TSS Genic enhancers Transcr. at gene 5' and 3' Flanking Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	12 gene(s)	inside rSNPs	diseases
5	nsv1009825	chr2:233709566-233763470	Weak transcription Bivalent Enhancer Strong transcription Genic enhancers Bivalent/Poised TSS Enhancers Flanking Bivalent TSS/Enh Flanking Active TSS ZNF genes & repeats Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
6	nsv984452	chr2:233725452-233762965	Active TSS Weak transcription Enhancers Flanking Bivalent TSS/Enh Strong transcription Genic enhancers Flanking Active TSS Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
7	nsv999116	chr2:233733352-233759864	Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer Strong transcription Weak transcription Active TSS Enhancers Flanking Active TSS Genic enhancers Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
8	nsv1007029	chr2:233733352-233760519	Enhancers Strong transcription Active TSS Weak transcription Flanking Active TSS Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
9	nsv536179	chr2:233735380-233757170	Enhancers Bivalent Enhancer Weak transcription Bivalent/Poised TSS Flanking Bivalent TSS/Enh Active TSS Flanking Active TSS Strong transcription Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases

mRNA abundance (count:8)

SNP	Gene	Cis/trans	Tissue	Source
rs778339	C2orf82	cis	Skin Sun Exposed Lower leg	GTEx
rs778339	C2orf82	cis	hippocampus	BrainEAC
rs778339	C2orf82	cis	intralobular white matter	BrainEAC
rs778339	C2orf82	cis	frontal cortex	BrainEAC
rs778339	C2orf82	cis	brain	BrainEAC
rs778339	C2orf82	cis	thalamus	BrainEAC
rs778339	C2orf82	cis	putamen	BrainEAC
rs778339	C2orf82	cis	substantia nigra	BrainEAC

Chromatin state (count:43 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:233723000-233740400	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
2	chr2:233726000-233740400	Weak transcription	HMEC	breast
3	chr2:233726400-233740200	Weak transcription	Primary B cells from cord blood	blood
4	chr2:233726400-233740400	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
5	chr2:233726400-233740800	Weak transcription	HSMM	muscle
6	chr2:233726600-233739800	Weak transcription	Muscle Satellite Cultured Cells	--
7	chr2:233726600-233740000	Weak transcription	Pancreas	Pancrea
8	chr2:233726600-233740200	Weak transcription	Rectal Smooth Muscle	rectum
9	chr2:233726600-233740400	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
10	chr2:233726600-233740400	Weak transcription	Lung	lung
11	chr2:233726600-233740400	Weak transcription	NHEK	skin
12	chr2:233726800-233755600	Weak transcription	HSMMtube	muscle
13	chr2:233734400-233740400	Enhancers	Brain Inferior Temporal Lobe	brain
14	chr2:233734600-233740200	Enhancers	Brain Cingulate Gyrus	brain
15	chr2:233734600-233740200	Enhancers	Brain Substantia Nigra	brain
16	chr2:233734800-233740200	Weak transcription	ES-I3 Cell Line	embryonic stem cell
17	chr2:233735000-233740000	Enhancers	Brain Dorsolateral Prefrontal Cortex	brain
18	chr2:233735000-233740000	Genic enhancers	Fetal Intestine Small	intestine
19	chr2:233736400-233740200	Enhancers	Fetal Intestine Large	intestine
20	chr2:233736600-233740200	Enhancers	Brain Hippocampus Middle	brain
21	chr2:233736800-233740200	Weak transcription	Fetal Brain Male	brain
22	chr2:233738000-233740000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
23	chr2:233738000-233740000	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
24	chr2:233738000-233740200	Enhancers	Colonic Mucosa	Colon
25	chr2:233738200-233740400	Enhancers	Liver	Liver
26	chr2:233738600-233740000	Weak transcription	Breast Myoepithelial Primary Cells	Breast
27	chr2:233738600-233740200	Enhancers	A549	lung
28	chr2:233738600-233740600	Enhancers	Spleen	Spleen
29	chr2:233738800-233740200	Enhancers	Hela-S3	cervix
30	chr2:233738800-233741000	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
31	chr2:233739000-233740000	Weak transcription	Brain Anterior Caudate	brain
32	chr2:233739200-233740200	Weak transcription	Brain Angular Gyrus	brain
33	chr2:233739400-233739800	Bivalent Enhancer	Primary monocytes fromperipheralblood	blood
34	chr2:233739400-233739800	Bivalent Enhancer	Monocytes-CD14+_RO01746	blood
35	chr2:233739400-233740000	Enhancers	Rectal Mucosa Donor 29	rectum
36	chr2:233739400-233740200	Bivalent Enhancer	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
37	chr2:233739400-233740400	Weak transcription	Esophagus	oesophagus
38	chr2:233739400-233740600	Enhancers	Gastric	stomach
39	chr2:233739400-233740600	Bivalent Enhancer	Sigmoid Colon	Sigmoid Colon
40	chr2:233739400-233740600	Bivalent Enhancer	Stomach Mucosa	stomach
41	chr2:233739600-233740000	Flanking Active TSS	Duodenum Mucosa	Duodenum
42	chr2:233739600-233740000	Enhancers	Rectal Mucosa Donor 31	rectum
43	chr2:233739600-233740000	Enhancers	HepG2	liver

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links