Variant report

Variant	rs2230593
Chromosome Location	chr3:49940078-49940079
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:9)
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	POLR2A	chr3:49939501-49941825	HCT-116	colon:	n/a	n/a
2	POLR2A	chr3:49939484-49941805	Hela-S3	cervix:	n/a	n/a
3	POLR2A	chr3:49939864-49941766	HCT-116	colon:	n/a	n/a
4	POLR2A	chr3:49939517-49941790	Hela-S3	cervix:	n/a	n/a
5	SMARCB1	chr3:49939531-49941759	Hela-S3	cervix:	n/a	n/a

No data

(count:9 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr3:49907025..49909566-chr3:49939184..49940917,2	K562	blood:
2	chr19:2475693..2476461-chr3:49939604..49940586,2	Hela-S3	cervix:
3	chr3:49839049..49842350-chr3:49936029..49940414,4	K562	blood:
4	chr3:49937512..49940184-chr3:49951912..49954370,2	MCF-7	breast:
5	chr3:49844713..49846618-chr3:49938018..49940554,2	K562	blood:
6	chr3:49838036..49840305-chr3:49938057..49940452,2	MCF-7	breast:
7	chr3:49936090..49937594-chr3:49939320..49940938,2	K562	blood:
8	chr3:49837665..49841605-chr3:49939148..49941365,3	K562	blood:
9	chr3:49933351..49938041-chr3:49938966..49942332,9	K562	blood:

No data

Variant related genes	Relation type
ENSG00000228008	TF binding region
ENSG00000164076	Chromatin interaction
ENSG00000185614	Chromatin interaction
ENSG00000230698	Chromatin interaction
ENSG00000164078	Chromatin interaction
ENSG00000099860	Chromatin interaction

Extended variants
information (count: 9 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:5)

rs_ID	r²[population]
rs12486358	1.00[CHB][hapmap]
rs13072748	1.00[CHB][hapmap]
rs13078735	1.00[CHB][hapmap]
rs2230591	1.00[CHB][hapmap];1.00[YRI][hapmap]
rs7433231	1.00[CHB][hapmap]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	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
2	nsv834688	chr3:49811115-50019299	Weak transcription Active TSS Flanking Active TSS Strong transcription Enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer Genic enhancers Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	60 gene(s)	inside rSNPs	diseases
3	nsv876766	chr3:49817450-49961780	Weak transcription Strong transcription Enhancers Flanking Active TSS Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Genic enhancers 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	47 gene(s)	inside rSNPs	diseases
4	nsv876767	chr3:49918751-50153356	Active TSS Genic enhancers Weak transcription Transcr. at gene 5' and 3' Strong transcription Flanking Active TSS Enhancers Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	54 gene(s)	inside rSNPs	diseases

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs2230593	RBM6	cis	cerebellum	SCAN
rs2230593	RNF123	cis	parietal	SCAN
rs2230593	QARS	cis	parietal	SCAN
rs2230593	GMPPB	cis	parietal	SCAN

Chromatin state (count:76 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:49920000-49943000	Weak transcription	Brain Anterior Caudate	brain
2	chr3:49925200-49941200	Weak transcription	Brain Germinal Matrix	brain
3	chr3:49927600-49940400	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
4	chr3:49928600-49943000	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
5	chr3:49929600-49941200	Weak transcription	Ovary	ovary
6	chr3:49931400-49943600	Weak transcription	Brain Hippocampus Middle	brain
7	chr3:49933800-49941400	Weak transcription	Brain Inferior Temporal Lobe	brain
8	chr3:49934400-49941400	Weak transcription	Brain Angular Gyrus	brain
9	chr3:49936200-49941000	Transcr. at gene 5' and 3'	Foreskin Keratinocyte Primary Cells skin02	Skin
10	chr3:49936400-49940800	Enhancers	Pancreas	Pancrea
11	chr3:49937000-49940800	Enhancers	Sigmoid Colon	Sigmoid Colon
12	chr3:49937400-49940200	Enhancers	Breast Myoepithelial Primary Cells	Breast
13	chr3:49937600-49940800	Enhancers	K562	blood
14	chr3:49937600-49941000	Enhancers	Placenta	Placenta
15	chr3:49937600-49943200	Active TSS	Rectal Smooth Muscle	rectum
16	chr3:49937800-49940400	Enhancers	iPS DF 19.11 Cell Line	embryonic stem cell
17	chr3:49938000-49941400	Enhancers	GM12878-XiMat	blood
18	chr3:49938200-49940600	Enhancers	Fetal Stomach	stomach
19	chr3:49938200-49940800	Enhancers	Fetal Muscle Leg	muscle
20	chr3:49938200-49941800	Flanking Active TSS	HMEC	breast
21	chr3:49938400-49940800	Enhancers	Colon Smooth Muscle	Colon
22	chr3:49938400-49941000	Enhancers	Fetal Muscle Trunk	muscle
23	chr3:49938600-49941200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
24	chr3:49938800-49940200	Weak transcription	Adipose Nuclei	Adipose
25	chr3:49938800-49940400	Weak transcription	Right Ventricle	heart
26	chr3:49938800-49940600	Enhancers	A549	lung
27	chr3:49938800-49940800	Weak transcription	Left Ventricle	heart
28	chr3:49938800-49941000	Weak transcription	Psoas Muscle	Psoas
29	chr3:49938800-49943200	Weak transcription	HSMMtube	muscle
30	chr3:49938800-49943200	Weak transcription	NH-A	brain
31	chr3:49939000-49940400	Weak transcription	Skeletal Muscle Female	skeletal muscle
32	chr3:49939000-49941000	Weak transcription	Osteobl	bone
33	chr3:49939000-49941200	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
34	chr3:49939000-49941200	Weak transcription	NHLF	lung
35	chr3:49939000-49941400	Active TSS	Hela-S3	cervix
36	chr3:49939000-49941600	Active TSS	Duodenum Smooth Muscle	Duodenum
37	chr3:49939000-49943200	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
38	chr3:49939000-49943200	Weak transcription	Muscle Satellite Cultured Cells	--
39	chr3:49939000-49943400	Weak transcription	HSMM	muscle
40	chr3:49939200-49940200	Weak transcription	Skeletal Muscle Male	skeletal muscle
41	chr3:49939200-49940400	Enhancers	Fetal Intestine Large	intestine
42	chr3:49939200-49940800	Enhancers	Fetal Thymus	thymus
43	chr3:49939200-49941000	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
44	chr3:49939200-49941000	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
45	chr3:49939200-49941200	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
46	chr3:49939200-49941400	Weak transcription	NHDF-Ad	bronchial
47	chr3:49939400-49940600	Enhancers	Lung	lung
48	chr3:49939400-49940800	Weak transcription	HUES6 Cell Line	embryonic stem cell
49	chr3:49939400-49940800	Flanking Active TSS	Esophagus	oesophagus
50	chr3:49939400-49940800	Weak transcription	Small Intestine	intestine

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