Variant report

Variant	rs2271976
Chromosome Location	chr12:123751726-123751727
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr12:123460655..123463100-chr12:123749736..123752602,2	MCF-7	breast:
2	chr12:123717082..123719698-chr12:123751267..123753093,2	K562	blood:
3	chr12:123736848..123739836-chr12:123749677..123753155,4	K562	blood:
4	chr12:123749757..123758492-chr12:123844437..123851411,15	MCF-7	breast:

Variant related genes	Relation type
ENSG00000139697	Chromatin interaction
ENSG00000111325	Chromatin interaction
ENSG00000130921	Chromatin interaction
ENSG00000256092	Chromatin interaction
ENSG00000051825	Chromatin interaction

Extended variants
information (count: 65 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:61)

rs_ID	r²[population]
rs10444439	0.94[JPT][hapmap]
rs10732573	0.85[JPT][hapmap];0.82[ASN][1000 genomes]
rs10734901	0.82[ASN][1000 genomes]
rs10744150	0.82[CHB][hapmap];0.85[JPT][hapmap]
rs10744151	0.82[CHB][hapmap];0.82[JPT][hapmap]
rs10744152	0.80[JPT][hapmap]
rs10772997	0.80[JPT][hapmap]
rs10773000	0.91[CHB][hapmap];1.00[JPT][hapmap];0.91[ASN][1000 genomes]
rs10773002	0.82[CHB][hapmap];0.84[JPT][hapmap]
rs10773003	1.00[CEU][hapmap];0.94[JPT][hapmap]
rs10773005	1.00[CEU][hapmap];0.94[JPT][hapmap]
rs10846489	1.00[CHB][hapmap];1.00[JPT][hapmap];0.99[ASN][1000 genomes]
rs11057219	0.98[ASN][1000 genomes]
rs11057223	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.87[AFR][1000 genomes];0.97[AMR][1000 genomes];0.91[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs11057224	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11057251	0.94[JPT][hapmap]
rs11057273	1.00[CEU][hapmap];0.86[JPT][hapmap]
rs11057276	0.94[JPT][hapmap]
rs11057287	0.80[JPT][hapmap]
rs1109559	1.00[CHB][hapmap];1.00[JPT][hapmap];0.98[ASN][1000 genomes]
rs1109560	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.98[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11554169	0.80[ASN][1000 genomes]
rs11608305	0.95[JPT][hapmap]
rs12317452	1.00[CEU][hapmap];0.95[JPT][hapmap]
rs12366872	1.00[CEU][hapmap];0.95[JPT][hapmap]
rs1568427	0.83[CHB][hapmap];0.84[JPT][hapmap]
rs1568428	1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[ASN][1000 genomes]
rs1609520	0.84[JPT][hapmap]
rs1727293	0.84[JPT][hapmap]
rs1727301	0.90[CHB][hapmap];0.90[JPT][hapmap]
rs1727331	0.84[JPT][hapmap]
rs1790104	0.91[CHB][hapmap];0.90[JPT][hapmap]
rs1879379	1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[ASN][1000 genomes]
rs1969355	0.81[ASN][1000 genomes]
rs1980251	0.82[ASN][1000 genomes]
rs2030401	0.99[ASN][1000 genomes]
rs2280424	0.84[JPT][hapmap]
rs2337630	0.89[ASN][1000 genomes]
rs2337631	0.89[ASN][1000 genomes]
rs2682427	0.91[CHB][hapmap];0.90[JPT][hapmap]
rs28410096	1.00[CEU][hapmap];0.94[JPT][hapmap]
rs28532037	1.00[CEU][hapmap];0.94[JPT][hapmap]
rs28533432	0.94[JPT][hapmap]
rs28660993	1.00[CEU][hapmap];0.94[JPT][hapmap]
rs3088303	1.00[CEU][hapmap];0.94[JPT][hapmap]
rs34841857	0.88[ASN][1000 genomes]
rs3759114	0.84[JPT][hapmap];0.82[ASN][1000 genomes]
rs4553407	1.00[ASN][1000 genomes]
rs4759372	0.81[ASN][1000 genomes]
rs4759377	0.93[CEU][hapmap];0.94[JPT][hapmap]
rs4759411	0.85[JPT][hapmap];0.80[ASN][1000 genomes]
rs4759413	0.82[ASN][1000 genomes]
rs4759414	0.85[JPT][hapmap];0.82[ASN][1000 genomes]
rs61953394	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7139321	1.00[CHB][hapmap];1.00[JPT][hapmap];0.84[ASN][1000 genomes]
rs7304782	0.84[JPT][hapmap]
rs7312955	0.90[ASN][1000 genomes]
rs7315453	1.00[CEU][hapmap];0.94[JPT][hapmap]
rs73231928	0.84[ASN][1000 genomes]
rs7959415	0.83[JPT][hapmap]
rs7972811	1.00[CEU][hapmap];0.94[JPT][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	esv1825473	chr12:123582855-123822503	Weak transcription Strong transcription Flanking Active TSS Genic enhancers Enhancers Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	73 gene(s)	inside rSNPs	diseases
2	esv1803368	chr12:123640853-123822503	Weak transcription Strong transcription Flanking Active TSS Genic enhancers Enhancers Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	70 gene(s)	inside rSNPs	diseases
3	esv1830566	chr12:123640853-123822503	Flanking Active TSS Strong transcription Enhancers Weak transcription Genic enhancers Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	70 gene(s)	inside rSNPs	diseases
4	esv1836043	chr12:123709409-123822503	Weak transcription Flanking Active TSS Strong transcription Enhancers Genic enhancers Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	70 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs2271976	CDK2AP1	cis	Whole Blood	GTEx
rs2271976	RP11-282O18.3	cis	Whole Blood	GTEx

Chromatin state (count:127 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:123734600-123753200	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
2	chr12:123735200-123751800	Strong transcription	Fetal Stomach	stomach
3	chr12:123735600-123752400	Strong transcription	Thymus	Thymus
4	chr12:123736000-123752200	Strong transcription	Dnd41	blood
5	chr12:123736400-123752200	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
6	chr12:123736400-123752600	Strong transcription	NHLF	lung
7	chr12:123737000-123753000	Strong transcription	Fetal Intestine Small	intestine
8	chr12:123737200-123752000	Strong transcription	A549	lung
9	chr12:123738000-123751800	Strong transcription	Liver	Liver
10	chr12:123738000-123751800	Strong transcription	Fetal Intestine Large	intestine
11	chr12:123738000-123752000	Strong transcription	Duodenum Mucosa	Duodenum
12	chr12:123738000-123752000	Strong transcription	HUVEC	blood vessel
13	chr12:123738000-123752600	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
14	chr12:123738000-123752800	Strong transcription	Placenta Amnion	Placenta Amnion
15	chr12:123738200-123751800	Strong transcription	Sigmoid Colon	Sigmoid Colon
16	chr12:123738200-123752000	Strong transcription	Rectal Mucosa Donor 29	rectum
17	chr12:123738600-123752200	Strong transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
18	chr12:123739200-123751800	Strong transcription	Adipose Nuclei	Adipose
19	chr12:123739200-123752600	Weak transcription	Psoas Muscle	Psoas
20	chr12:123739200-123753000	Weak transcription	Right Atrium	heart
21	chr12:123739200-123753200	Weak transcription	Fetal Heart	heart
22	chr12:123739200-123754200	Weak transcription	Pancreatic Islets	Pancreatic Islet
23	chr12:123739400-123751800	Strong transcription	Stomach Smooth Muscle	stomach
24	chr12:123739800-123752400	Strong transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
25	chr12:123739800-123753200	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
26	chr12:123740000-123753600	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
27	chr12:123741000-123752200	Strong transcription	Osteobl	bone
28	chr12:123741000-123753600	Weak transcription	Primary T killer memory cells from peripheral blood	blood
29	chr12:123742000-123752600	Strong transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
30	chr12:123742400-123753400	Weak transcription	Primary T helper naive cells from peripheral blood	blood
31	chr12:123742400-123754600	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
32	chr12:123742400-123754600	Weak transcription	Small Intestine	intestine
33	chr12:123743000-123754200	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
34	chr12:123743200-123751800	Strong transcription	Aorta	Aorta
35	chr12:123743400-123751800	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
36	chr12:123743400-123752400	Weak transcription	Primary B cells from peripheral blood	blood
37	chr12:123743400-123754000	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
38	chr12:123743600-123752200	Weak transcription	Primary T cells fromperipheralblood	blood
39	chr12:123743600-123753600	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
40	chr12:123743800-123752000	Strong transcription	Fetal Thymus	thymus
41	chr12:123743800-123752200	Weak transcription	Primary T helper cells PMA-I stimulated	--
42	chr12:123743800-123752600	Weak transcription	Primary T helper cells fromperipheralblood	blood
43	chr12:123743800-123752600	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
44	chr12:123744000-123752400	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
45	chr12:123744000-123753800	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
46	chr12:123744000-123753800	Weak transcription	K562	blood
47	chr12:123744600-123752600	Weak transcription	Primary B cells from cord blood	blood
48	chr12:123745000-123753000	Weak transcription	Stomach Mucosa	stomach
49	chr12:123745400-123754000	Genic enhancers	ES-UCSF4 Cell Line	embryonic stem cell
50	chr12:123746000-123752400	Strong transcription	HUES64 Cell Line	embryonic stem cell

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links