Variant report

Variant	rs1914052
Chromosome Location	chr12:39295471-39295472
allele	A/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	POLR2A	chr12:39295407-39295516	MCF10A-Er-Src	breast:	n/a	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr12:39294074..39295589-chr12:39295957..39298877,2	K562	blood:

Variant related genes	Relation type
ENSG00000257718	TF binding region

Extended variants
information (count: 45 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:42)

rs_ID	r²[population]
rs10160990	0.85[CEU][hapmap];0.94[AFR][1000 genomes];0.83[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs10732735	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs1095573	0.87[CEU][hapmap];0.86[EUR][1000 genomes]
rs11169615	0.85[EUR][1000 genomes]
rs11169618	0.85[EUR][1000 genomes]
rs11537523	0.85[EUR][1000 genomes]
rs1356267	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.99[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1400281	0.91[AFR][1000 genomes];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1516553	0.90[EUR][1000 genomes]
rs1516557	0.88[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1533918	0.87[CEU][hapmap];0.88[EUR][1000 genomes]
rs1607040	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1615648	0.87[CEU][hapmap];0.89[JPT][hapmap]
rs1684426	0.81[EUR][1000 genomes]
rs1719833	0.87[CEU][hapmap];0.89[JPT][hapmap];0.85[EUR][1000 genomes]
rs1719847	0.87[CEU][hapmap];0.89[JPT][hapmap]
rs1719860	0.82[EUR][1000 genomes]
rs1878225	0.80[JPT][hapmap]
rs1996879	0.88[EUR][1000 genomes]
rs2056529	0.95[AFR][1000 genomes];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2069210	0.87[CEU][hapmap];0.89[JPT][hapmap]
rs4002228	0.84[AFR][1000 genomes];0.87[EUR][1000 genomes]
rs4768394	0.87[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[AFR][1000 genomes];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7298168	1.00[CEU][hapmap];1.00[CHB][hapmap];0.94[JPT][hapmap];0.94[AFR][1000 genomes];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7974247	0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7978838	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs826849	0.87[CEU][hapmap];0.88[JPT][hapmap];0.83[EUR][1000 genomes]
rs826853	0.85[CEU][hapmap];0.89[JPT][hapmap]
rs826860	0.89[JPT][hapmap]
rs826861	0.87[CEU][hapmap];0.89[JPT][hapmap]
rs826862	0.87[CEU][hapmap];0.89[JPT][hapmap]
rs826869	0.87[CEU][hapmap];0.89[JPT][hapmap]
rs826872	0.81[CHB][hapmap];0.93[JPT][hapmap]
rs826884	0.85[CEU][hapmap];0.85[EUR][1000 genomes]
rs826885	0.83[EUR][1000 genomes]
rs826887	0.89[JPT][hapmap]
rs826890	0.94[JPT][hapmap]
rs826894	0.89[JPT][hapmap]
rs851933	0.89[JPT][hapmap]
rs862331	0.85[CEU][hapmap];0.89[JPT][hapmap]
rs862332	0.85[EUR][1000 genomes]
rs866120	0.85[CEU][hapmap];0.89[JPT][hapmap]

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	nsv1047623	chr12:39187817-39539939	Active TSS Bivalent Enhancer Weak transcription Flanking Active TSS ZNF genes & repeats Enhancers Bivalent/Poised TSS Strong transcription Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	21 gene(s)	inside rSNPs	diseases
2	esv3389115	chr12:39221256-39448458	Flanking Active TSS Enhancers Weak transcription ZNF genes & repeats Active TSS Bivalent/Poised TSS Strong transcription Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	18 gene(s)	inside rSNPs	diseases
3	nsv899009	chr12:39284077-39441096	Active TSS Bivalent/Poised TSS Enhancers Weak transcription Flanking Active TSS Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	18 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:42 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:39271800-39297200	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
2	chr12:39285000-39296400	Weak transcription	Primary hematopoietic stem cells	blood
3	chr12:39286600-39297400	Weak transcription	Rectal Mucosa Donor 29	rectum
4	chr12:39287400-39296400	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
5	chr12:39287400-39298600	Weak transcription	Aorta	Aorta
6	chr12:39288000-39296600	Weak transcription	Liver	Liver
7	chr12:39289600-39297000	Weak transcription	HUVEC	blood vessel
8	chr12:39290200-39297600	Weak transcription	Adipose Nuclei	Adipose
9	chr12:39290400-39296200	Weak transcription	Primary hematopoietic stem cells short term culture	blood
10	chr12:39290600-39297000	Weak transcription	Right Atrium	heart
11	chr12:39290800-39297600	Weak transcription	Rectal Mucosa Donor 31	rectum
12	chr12:39290800-39298600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
13	chr12:39292200-39296400	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
14	chr12:39292200-39297200	Weak transcription	Placenta	Placenta
15	chr12:39292400-39297000	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
16	chr12:39292400-39297200	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
17	chr12:39292400-39297400	Weak transcription	HMEC	breast
18	chr12:39292400-39297600	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
19	chr12:39292400-39297600	Weak transcription	NHDF-Ad	bronchial
20	chr12:39292400-39298800	Weak transcription	Placenta Amnion	Placenta Amnion
21	chr12:39292600-39296800	Weak transcription	NHEK	skin
22	chr12:39292600-39297000	Weak transcription	A549	lung
23	chr12:39292800-39297000	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
24	chr12:39292800-39297000	Weak transcription	Pancreatic Islets	Pancreatic Islet
25	chr12:39292800-39297600	Weak transcription	H9 Cell Line	embryonic stem cell
26	chr12:39292800-39297600	Weak transcription	iPS-15b Cell Line	embryonic stem cell
27	chr12:39292800-39298000	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
28	chr12:39293000-39297400	Weak transcription	HUES6 Cell Line	embryonic stem cell
29	chr12:39293000-39297600	Weak transcription	HUES48 Cell Line	embryonic stem cell
30	chr12:39293000-39298400	Weak transcription	iPS-18 Cell Line	embryonic stem cell
31	chr12:39293200-39296400	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
32	chr12:39293200-39297000	Weak transcription	HUES64 Cell Line	embryonic stem cell
33	chr12:39293200-39297200	Weak transcription	Breast Myoepithelial Primary Cells	Breast
34	chr12:39293200-39297400	Weak transcription	ES-I3 Cell Line	embryonic stem cell
35	chr12:39293400-39297000	Weak transcription	iPS-20b Cell Line	embryonic stem cell
36	chr12:39293600-39297000	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
37	chr12:39294200-39296200	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
38	chr12:39294400-39295600	Weak transcription	Sigmoid Colon	Sigmoid Colon
39	chr12:39294600-39297000	Active TSS	GM12878-XiMat	blood
40	chr12:39295000-39298000	Weak transcription	Lung	lung
41	chr12:39295400-39296400	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
42	chr12:39295400-39297200	Enhancers	Hela-S3	cervix

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