Variant report

Variant	rs2303947
Chromosome Location	chr2:128281469-128281470
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr2:128280281..128282755-chr6:127809233..127811638,2	MCF-7	breast:
2	chr2:128278204..128279874-chr2:128280067..128281749,2	K562	blood:
3	chr2:128272088..128276196-chr2:128278536..128286742,8	K562	blood:
4	chr2:128280589..128286553-chr2:128394118..128400117,7	K562	blood:
5	chr2:128145128..128146772-chr2:128281228..128284838,3	MCF-7	breast:
6	chr2:128271568..128276709-chr2:128278536..128286742,13	K562	blood:

Variant related genes	Relation type
ENSG00000236682	Chromatin interaction
ENSG00000163166	Chromatin interaction
ENSG00000072163	Chromatin interaction
ENSG00000169967	Chromatin interaction

Extended variants
information (count: 29 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:27)

rs_ID	r²[population]
rs10432384	0.91[AFR][1000 genomes];0.99[ASN][1000 genomes]
rs10460269	0.80[AMR][1000 genomes];0.81[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs10928770	0.80[AMR][1000 genomes];0.81[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs11690009	0.82[ASN][1000 genomes]
rs11694581	0.98[AFR][1000 genomes];0.92[AMR][1000 genomes];0.93[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs12463949	0.85[ASN][1000 genomes]
rs12464981	1.00[CHB][hapmap];0.86[JPT][hapmap]
rs12466957	1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs12475191	0.91[AFR][1000 genomes];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs12475389	1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs12476558	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs13013022	0.83[AMR][1000 genomes];0.81[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs13026187	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs13029611	0.82[AMR][1000 genomes];0.80[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs13035004	0.84[ASN][1000 genomes]
rs1864553	0.88[CEU][hapmap]
rs1968396	0.90[AFR][1000 genomes];0.84[EUR][1000 genomes]
rs2052953	0.80[AMR][1000 genomes];0.81[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2099209	0.85[MEX][hapmap]
rs3732207	0.98[AFR][1000 genomes];0.92[AMR][1000 genomes];0.93[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs4507043	0.86[ASN][1000 genomes]
rs4662733	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs56398807	0.88[ASN][1000 genomes]
rs7583571	0.88[ASN][1000 genomes]
rs7590705	0.94[ASW][hapmap];0.95[CHB][hapmap];1.00[CHD][hapmap];0.86[GIH][hapmap];0.82[JPT][hapmap];1.00[LWK][hapmap];0.88[MKK][hapmap];1.00[YRI][hapmap];0.91[AFR][1000 genomes]
rs777556	0.88[CEU][hapmap]
rs873099	0.88[CEU][hapmap];0.85[MEX][hapmap]

Variant overlapped rSNPs/rCNVs (count:2 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv875014	chr2:128178415-128328375	Strong transcription Flanking Bivalent TSS/Enh Weak transcription Enhancers Flanking Active TSS Genic enhancers Bivalent/Poised TSS Bivalent Enhancer Active TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	28 gene(s)	inside rSNPs	diseases
2	nsv2912	chr2:128281152-128307830	Enhancers Flanking Active TSS Active TSS Genic enhancers Weak transcription Strong transcription Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	16 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs2303947	ERCC3	cis	cerebellum	SCAN

Chromatin state (count:126 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:128262600-128283000	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
2	chr2:128263200-128282800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
3	chr2:128266000-128282800	Weak transcription	Pancreatic Islets	Pancreatic Islet
4	chr2:128267200-128282000	Weak transcription	Fetal Brain Male	brain
5	chr2:128267600-128282000	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
6	chr2:128268400-128281600	Strong transcription	Primary hematopoietic stem cells short term culture	blood
7	chr2:128268600-128281600	Strong transcription	Fetal Thymus	thymus
8	chr2:128270200-128282600	Weak transcription	Small Intestine	intestine
9	chr2:128271400-128281800	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
10	chr2:128271400-128281800	Strong transcription	Rectal Mucosa Donor 31	rectum
11	chr2:128272400-128282800	Weak transcription	H9 Cell Line	embryonic stem cell
12	chr2:128272400-128282800	Weak transcription	Colonic Mucosa	Colon
13	chr2:128272800-128282800	Weak transcription	Placenta Amnion	Placenta Amnion
14	chr2:128273600-128281600	Strong transcription	Primary B cells from cord blood	blood
15	chr2:128273600-128281800	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
16	chr2:128273600-128281800	Strong transcription	iPS-20b Cell Line	embryonic stem cell
17	chr2:128273600-128282800	Weak transcription	Gastric	stomach
18	chr2:128273800-128281600	Weak transcription	Primary T helper naive cells from peripheral blood	blood
19	chr2:128273800-128281600	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
20	chr2:128274000-128281600	Weak transcription	Fetal Heart	heart
21	chr2:128274000-128281800	Strong transcription	Primary B cells from peripheral blood	blood
22	chr2:128274000-128282200	Weak transcription	Pancreas	Pancrea
23	chr2:128274200-128281600	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
24	chr2:128274200-128281800	Strong transcription	HUES64 Cell Line	embryonic stem cell
25	chr2:128274200-128281800	Strong transcription	K562	blood
26	chr2:128274200-128282000	Strong transcription	Placenta	Placenta
27	chr2:128274200-128282200	Weak transcription	Lung	lung
28	chr2:128274200-128282200	Weak transcription	Spleen	Spleen
29	chr2:128274200-128282600	Weak transcription	iPS-15b Cell Line	embryonic stem cell
30	chr2:128274200-128282600	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
31	chr2:128274200-128282800	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
32	chr2:128274200-128283000	Weak transcription	Aorta	Aorta
33	chr2:128274400-128281600	Strong transcription	HUES6 Cell Line	embryonic stem cell
34	chr2:128274400-128281600	Strong transcription	HSMM	muscle
35	chr2:128274400-128281800	Strong transcription	HUES48 Cell Line	embryonic stem cell
36	chr2:128274400-128282200	Weak transcription	Left Ventricle	heart
37	chr2:128274400-128282800	Weak transcription	Brain Cingulate Gyrus	brain
38	chr2:128274400-128282800	Weak transcription	Ovary	ovary
39	chr2:128274400-128282800	Weak transcription	Rectal Smooth Muscle	rectum
40	chr2:128274400-128282800	Weak transcription	Right Atrium	heart
41	chr2:128274400-128282800	Weak transcription	Right Ventricle	heart
42	chr2:128274600-128281600	Weak transcription	Colon Smooth Muscle	Colon
43	chr2:128274600-128282800	Weak transcription	NHLF	lung
44	chr2:128275000-128281600	Strong transcription	iPS-18 Cell Line	embryonic stem cell
45	chr2:128275600-128281600	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
46	chr2:128275800-128282800	Weak transcription	Fetal Brain Female	brain
47	chr2:128275800-128282800	Weak transcription	HSMMtube	muscle
48	chr2:128276200-128281600	Strong transcription	Primary monocytes fromperipheralblood	blood
49	chr2:128276400-128282400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
50	chr2:128276600-128281800	Strong transcription	Osteobl	bone

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