Variant report

Variant	rs2287431
Chromosome Location	chr2:211320288-211320289
allele	G/T
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	CEBPB	chr2:211320230-211320472	HepG2	liver:	n/a	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr2:211320066..211322209-chr2:211344355..211345928,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000234281	TF binding region

Extended variants
information (count: 48 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:45)

rs_ID	r²[population]
rs10490318	0.81[CHB][hapmap];0.84[CHD][hapmap];0.94[MEX][hapmap]
rs10804182	1.00[ASN][1000 genomes]
rs10804183	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.98[ASN][1000 genomes]
rs10804185	0.81[CHB][hapmap]
rs11690895	1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs11889228	1.00[CHB][hapmap];1.00[JPT][hapmap];0.99[ASN][1000 genomes]
rs12466705	0.81[CHB][hapmap]
rs12477237	0.83[ASN][1000 genomes]
rs12611623	0.81[CHB][hapmap]
rs16844534	0.81[CHB][hapmap]
rs17771664	0.90[CHB][hapmap];0.84[CHD][hapmap];0.88[MEX][hapmap]
rs17772042	0.80[CHB][hapmap]
rs17822981	0.81[CHB][hapmap];0.84[CHD][hapmap];0.88[MEX][hapmap]
rs2287424	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs2287425	1.00[ASN][1000 genomes]
rs2287429	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs2287430	1.00[ASN][1000 genomes]
rs2287432	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs2287433	0.89[JPT][hapmap];0.84[ASN][1000 genomes]
rs2370949	1.00[CHB][hapmap];1.00[JPT][hapmap];0.99[ASN][1000 genomes]
rs2887899	0.91[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs3755184	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs3770689	0.99[ASN][1000 genomes]
rs3770694	1.00[ASN][1000 genomes]
rs3770695	0.98[ASN][1000 genomes]
rs3770699	0.88[CHD][hapmap];1.00[JPT][hapmap];0.91[ASN][1000 genomes]
rs3845633	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs3856339	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs41272663	0.95[AFR][1000 genomes]
rs4372818	0.81[CHB][hapmap]
rs4673526	0.84[ASN][1000 genomes]
rs4673528	0.92[ASN][1000 genomes]
rs4673529	0.92[ASN][1000 genomes]
rs6711129	0.81[CHB][hapmap]
rs6725303	0.81[CHB][hapmap];0.84[CHD][hapmap]
rs6725770	0.81[CHB][hapmap];0.84[CHD][hapmap];0.88[MEX][hapmap]
rs6727182	0.86[ASN][1000 genomes]
rs6729280	0.81[CHB][hapmap]
rs6752320	0.81[CHB][hapmap]
rs6756422	1.00[ASN][1000 genomes]
rs725379	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs72930503	0.89[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs72930539	0.94[ASN][1000 genomes]
rs7578688	1.00[ASN][1000 genomes]
rs7595022	1.00[ASN][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	nsv875767	chr2:211119233-211334647	Weak transcription Enhancers Genic enhancers ZNF genes & repeats Strong transcription Flanking Active TSS Active TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	5 gene(s)	inside rSNPs	diseases
2	nsv3147	chr2:211281479-211326844	Weak transcription Enhancers Genic enhancers Strong transcription ZNF genes & repeats Flanking Active TSS Bivalent Enhancer Active TSS Transcr. at gene 5' and 3'	TF binding region Chromatin interactive region lncRNA miRNA target site	2 gene(s)	inside rSNPs	diseases
3	esv3398091	chr2:211315261-211634200	Active TSS Flanking Active TSS Weak transcription Strong transcription Enhancers Genic enhancers ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	12 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs2287431	CPS1	cis	parietal	SCAN
rs2287431	LANCL1	cis	cerebellum	SCAN

Chromatin state (count:123 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:211292400-211323000	Weak transcription	Fetal Brain Male	brain
2	chr2:211293800-211335400	Weak transcription	ES-I3 Cell Line	embryonic stem cell
3	chr2:211294800-211322200	Weak transcription	K562	blood
4	chr2:211294800-211333200	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
5	chr2:211295000-211330400	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
6	chr2:211295000-211336000	Weak transcription	Colonic Mucosa	Colon
7	chr2:211295000-211340600	Weak transcription	HUVEC	blood vessel
8	chr2:211296000-211340200	Weak transcription	Small Intestine	intestine
9	chr2:211296400-211341000	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
10	chr2:211297400-211321400	Weak transcription	Primary neutrophils fromperipheralblood	blood
11	chr2:211297800-211336200	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
12	chr2:211299400-211322600	Weak transcription	H9 Cell Line	embryonic stem cell
13	chr2:211299600-211322400	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
14	chr2:211299800-211330000	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
15	chr2:211300200-211326000	Weak transcription	NHDF-Ad	bronchial
16	chr2:211300400-211329800	Weak transcription	A549	lung
17	chr2:211301200-211322400	Weak transcription	Aorta	Aorta
18	chr2:211301200-211322600	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
19	chr2:211301200-211322600	Weak transcription	Pancreas	Pancrea
20	chr2:211301200-211322600	Weak transcription	Spleen	Spleen
21	chr2:211301200-211325400	Weak transcription	Esophagus	oesophagus
22	chr2:211301200-211330000	Weak transcription	Gastric	stomach
23	chr2:211301200-211340200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
24	chr2:211301200-211340600	Weak transcription	Fetal Intestine Small	intestine
25	chr2:211301200-211340800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
26	chr2:211301400-211330000	Weak transcription	Muscle Satellite Cultured Cells	--
27	chr2:211301400-211330800	Weak transcription	Right Ventricle	heart
28	chr2:211301400-211334400	Weak transcription	NHEK	skin
29	chr2:211301400-211336000	Weak transcription	Primary T killer memory cells from peripheral blood	blood
30	chr2:211305600-211326600	Weak transcription	Brain Germinal Matrix	brain
31	chr2:211306000-211330000	Weak transcription	Rectal Smooth Muscle	rectum
32	chr2:211306200-211322200	Weak transcription	Colon Smooth Muscle	Colon
33	chr2:211306200-211326800	Weak transcription	Sigmoid Colon	Sigmoid Colon
34	chr2:211308000-211322600	Weak transcription	H1 Cell Line	embryonic stem cell
35	chr2:211308000-211332400	Weak transcription	Primary monocytes fromperipheralblood	blood
36	chr2:211311000-211322600	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
37	chr2:211312000-211322000	Weak transcription	Cortex derived primary cultured neurospheres	brain
38	chr2:211313000-211320600	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
39	chr2:211314200-211328800	Strong transcription	Primary T cells from cord blood	blood
40	chr2:211314400-211327000	Strong transcription	Primary T cells fromperipheralblood	blood
41	chr2:211315400-211327200	Strong transcription	Primary hematopoietic stem cells	blood
42	chr2:211315400-211340000	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
43	chr2:211315600-211320400	Strong transcription	Primary hematopoietic stem cells short term culture	blood
44	chr2:211315600-211320600	Strong transcription	Duodenum Smooth Muscle	Duodenum
45	chr2:211315600-211321200	Strong transcription	Primary T helper naive cells fromperipheralblood	blood
46	chr2:211315600-211323400	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
47	chr2:211315600-211323400	Strong transcription	Breast Myoepithelial Primary Cells	Breast
48	chr2:211315600-211325600	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
49	chr2:211315600-211337800	Strong transcription	Fetal Thymus	thymus
50	chr2:211315600-211339600	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived

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