Variant report

Variant	rs3748024
Chromosome Location	chr2:113346413-113346414
allele	C/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	NR2F2	chr2:113345798-113346583	MCF-7	breast:	n/a	n/a
2	CEBPB	chr2:113346233-113346467	A549	lung:	n/a	chr2:113346315-113346326
3	HA-E2F1	chr2:113345882-113346509	MCF-7	breast:	n/a	n/a
4	HDAC2	chr2:113345877-113346513	MCF-7	breast:	n/a	n/a
5	POLR2A	chr2:113346344-113346428	GM12878	blood:	n/a	n/a
6	MAX	chr2:113345867-113346558	MCF-7	breast:	n/a	n/a
7	CEBPB	chr2:113346179-113346459	IMR90	lung:	n/a	chr2:113346315-113346326
8	CEBPB	chr2:113346033-113346566	MCF-7	breast:	n/a	chr2:113346315-113346326
9	CEBPB	chr2:113345971-113346577	MCF-7	breast:	n/a	chr2:113346315-113346326
10	CEBPB	chr2:113346150-113346472	K562	blood:	n/a	chr2:113346315-113346326
11	FOXP2	chr2:113346184-113346574	PFSK-1	brain:	n/a	n/a
12	CEBPB	chr2:113346157-113346491	HepG2	liver:	n/a	chr2:113346315-113346326
13	NR3C1	chr2:113345909-113346467	A549	lung:	n/a	n/a
14	CEBPB	chr2:113346156-113346458	Hela-S3	cervix:	n/a	chr2:113346315-113346326
15	GATA3	chr2:113345820-113346544	MCF-7	breast:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr2:113344320..113346442-chr2:113363758..113365916,2	MCF-7	breast:
2	chr2:113345940..113348650-chr2:113401824..113404479,3	MCF-7	breast:
3	chr2:113344897..113346779-chr2:113377975..113380310,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000243389	TF binding region
ENSG00000228251	TF binding region
ENSG00000237753	Chromatin interaction
ENSG00000144136	Chromatin interaction
ENSG00000231747	Chromatin interaction

Extended variants
information (count: 20 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:17)

rs_ID	r²[population]
rs10864905	0.88[CEU][hapmap];0.86[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs11677050	0.89[CEU][hapmap];0.96[MEX][hapmap];0.89[TSI][hapmap];0.86[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs11687159	0.88[CHB][hapmap];0.87[CHD][hapmap];0.94[JPT][hapmap];0.86[ASN][1000 genomes]
rs11689338	0.84[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs12618882	0.87[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs3789722	0.80[AFR][1000 genomes];0.85[ASN][1000 genomes]
rs3789723	0.82[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs3816141	0.89[CEU][hapmap];0.91[MEX][hapmap];0.89[TSI][hapmap];0.82[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs41278940	0.80[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs41280572	0.88[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs4849075	0.94[EUR][1000 genomes]
rs4849076	0.92[EUR][1000 genomes]
rs56081241	0.86[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs6732422	0.85[ASN][1000 genomes]
rs719667	0.87[CHD][hapmap];0.87[JPT][hapmap];0.92[LWK][hapmap];0.83[ASN][1000 genomes]
rs719668	0.81[CHB][hapmap];0.87[CHD][hapmap];0.87[JPT][hapmap];0.83[ASN][1000 genomes]
rs7578724	0.89[CEU][hapmap];0.88[EUR][1000 genomes]

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	nsv874877	chr2:113287964-113382054	Enhancers Strong transcription Genic enhancers Flanking Active TSS Active TSS Weak transcription Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	36 gene(s)	inside rSNPs	diseases
2	nsv458997	chr2:113313794-113431092	Flanking Active TSS Strong transcription Weak transcription Genic enhancers Enhancers Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	73 gene(s)	inside rSNPs	diseases
3	nsv582708	chr2:113313794-113431092	Strong transcription Weak transcription Enhancers Flanking Active TSS Genic enhancers Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	73 gene(s)	inside rSNPs	diseases

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs3748024	LOC653596	cis	multi-tissue	Pritchard
rs3748024	POLR1B	cis	cerebellum	SCAN
rs3748024	FBLN7	cis	parietal	SCAN
rs3748024	POLR1B	cis	parietal	SCAN

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:113343000-113348600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
2	chr2:113343000-113348800	Genic enhancers	Fetal Muscle Leg	muscle
3	chr2:113343000-113349400	Enhancers	Pancreas	Pancrea
4	chr2:113343000-113350000	Weak transcription	H9 Cell Line	embryonic stem cell
5	chr2:113343200-113348400	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
6	chr2:113343200-113349000	Weak transcription	Colonic Mucosa	Colon
7	chr2:113343200-113353000	Weak transcription	NH-A	brain
8	chr2:113343200-113357400	Weak transcription	ES-I3 Cell Line	embryonic stem cell
9	chr2:113343200-113357400	Weak transcription	Rectal Mucosa Donor 31	rectum
10	chr2:113343200-113357400	Weak transcription	A549	lung
11	chr2:113343200-113357400	Weak transcription	HMEC	breast
12	chr2:113343200-113357400	Weak transcription	NHDF-Ad	bronchial
13	chr2:113343400-113346800	Genic enhancers	Foreskin Fibroblast Primary Cells skin02	Skin
14	chr2:113343400-113349600	Strong transcription	Primary T cells from cord blood	blood
15	chr2:113343400-113357400	Weak transcription	Primary hematopoietic stem cells	blood
16	chr2:113343600-113347400	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
17	chr2:113343600-113347600	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
18	chr2:113343600-113348400	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
19	chr2:113343600-113348800	Strong transcription	Fetal Stomach	stomach
20	chr2:113343600-113349000	Strong transcription	Monocytes-CD14+_RO01746	blood
21	chr2:113343600-113349400	Strong transcription	Fetal Intestine Large	intestine
22	chr2:113343600-113357400	Weak transcription	K562	blood
23	chr2:113343600-113357600	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
24	chr2:113343800-113346800	Strong transcription	HUES64 Cell Line	embryonic stem cell
25	chr2:113343800-113346800	Strong transcription	Primary monocytes fromperipheralblood	blood
26	chr2:113343800-113346800	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
27	chr2:113343800-113346800	Strong transcription	NHLF	lung
28	chr2:113343800-113347000	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
29	chr2:113343800-113347200	Strong transcription	NHEK	skin
30	chr2:113343800-113347400	Strong transcription	HUES6 Cell Line	embryonic stem cell
31	chr2:113343800-113347400	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
32	chr2:113343800-113347400	Genic enhancers	Fetal Muscle Trunk	muscle
33	chr2:113343800-113347400	Strong transcription	Rectal Smooth Muscle	rectum
34	chr2:113343800-113347600	Strong transcription	Stomach Smooth Muscle	stomach
35	chr2:113343800-113347800	Strong transcription	Primary hematopoietic stem cells short term culture	blood
36	chr2:113343800-113348600	Strong transcription	Fetal Thymus	thymus
37	chr2:113343800-113348800	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
38	chr2:113343800-113348800	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
39	chr2:113343800-113348800	Strong transcription	Fetal Intestine Small	intestine
40	chr2:113343800-113349000	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
41	chr2:113343800-113349400	Strong transcription	Thymus	Thymus
42	chr2:113343800-113349600	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
43	chr2:113343800-113357600	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
44	chr2:113344000-113346800	Strong transcription	Fetal Brain Female	brain
45	chr2:113344000-113346800	Strong transcription	Ovary	ovary
46	chr2:113344000-113347400	Strong transcription	Lung	lung
47	chr2:113344000-113347600	Strong transcription	Rectal Mucosa Donor 29	rectum
48	chr2:113344000-113348800	Strong transcription	Sigmoid Colon	Sigmoid Colon
49	chr2:113344000-113349000	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
50	chr2:113344000-113349000	Strong transcription	Primary B cells from peripheral blood	blood

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