Variant report

Variant	rs1920430
Chromosome Location	chr12:67829963-67829964
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr12:67827399..67830001-chr12:67831925..67834912,2	MCF-7	breast:
2	chr12:67803758..67807464-chr12:67826851..67830325,3	K562	blood:
3	chr12:67828571..67831280-chr12:67896110..67898028,2	MCF-7	breast:
4	chr12:67822398..67825852-chr12:67826641..67830656,5	MCF-7	breast:
5	chr12:67663101..67664698-chr12:67829162..67831006,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000111530	Chromatin interaction

Extended variants
information (count: 27 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:25)

rs_ID	r²[population]
rs10506549	1.00[CEU][hapmap];0.93[CHB][hapmap];0.94[CHD][hapmap];0.91[GIH][hapmap];1.00[JPT][hapmap];0.91[MEX][hapmap];0.93[TSI][hapmap];0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs10878616	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.88[MKK][hapmap];1.00[TSI][hapmap];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11176738	0.81[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs11176739	0.93[CHB][hapmap];1.00[JPT][hapmap];0.81[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs11176744	0.81[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12828359	0.85[CEU][hapmap];1.00[CHB][hapmap];0.84[CHD][hapmap];0.88[GIH][hapmap];1.00[JPT][hapmap];0.95[MEX][hapmap];0.86[TSI][hapmap];0.89[AMR][1000 genomes];0.92[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1882033	0.91[JPT][hapmap];0.80[ASN][1000 genomes]
rs1882280	0.81[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.85[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1882282	1.00[CEU][hapmap];0.96[AMR][1000 genomes];0.95[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1882283	0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2870937	0.82[JPT][hapmap]
rs35583684	0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4913247	0.93[CHB][hapmap];1.00[JPT][hapmap];0.81[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4913248	0.93[CHB][hapmap];1.00[JPT][hapmap];0.81[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4913249	0.93[CHB][hapmap];0.94[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];0.81[MKK][hapmap];0.81[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4913323	0.93[CHB][hapmap];1.00[JPT][hapmap];0.81[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4913324	0.93[CHB][hapmap];0.94[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];0.81[MKK][hapmap];0.81[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs67939426	0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7132295	0.81[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7132301	0.93[CHB][hapmap];0.91[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];0.81[MKK][hapmap];0.81[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7298082	0.81[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7312115	0.81[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7312371	0.81[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7312608	0.81[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7958866	0.85[CEU][hapmap];0.81[CHB][hapmap];0.92[JPT][hapmap];0.95[MEX][hapmap];0.86[TSI][hapmap];0.89[AMR][1000 genomes];0.92[EUR][1000 genomes];0.87[ASN][1000 genomes]

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	nsv559212	chr12:67373549-67850925	Flanking Active TSS Enhancers Weak transcription Strong transcription Bivalent Enhancer Bivalent/Poised TSS Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	24 gene(s)	inside rSNPs	diseases
2	nsv1054111	chr12:67556780-67865542	Enhancers Weak transcription Flanking Active TSS Strong transcription Active TSS Genic enhancers ZNF genes & repeats Bivalent Enhancer 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	20 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs1920430	CAND1	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:47 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:67817800-67830600	Enhancers	Rectal Mucosa Donor 31	rectum
2	chr12:67818600-67832000	Enhancers	Fetal Intestine Large	intestine
3	chr12:67819600-67831400	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
4	chr12:67821400-67830600	Enhancers	Rectal Mucosa Donor 29	rectum
5	chr12:67825400-67835200	Weak transcription	Ovary	ovary
6	chr12:67825600-67835400	Weak transcription	Fetal Kidney	kidney
7	chr12:67826400-67831200	Enhancers	NHLF	lung
8	chr12:67826600-67835200	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
9	chr12:67827200-67830200	Enhancers	Sigmoid Colon	Sigmoid Colon
10	chr12:67827200-67830600	Enhancers	Fetal Intestine Small	intestine
11	chr12:67827200-67830800	Enhancers	NH-A	brain
12	chr12:67827200-67831000	Enhancers	Foreskin Melanocyte Primary Cells skin01	Skin
13	chr12:67827200-67831000	Enhancers	Skeletal Muscle Female	skeletal muscle
14	chr12:67827200-67831200	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
15	chr12:67827400-67830000	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
16	chr12:67827400-67830200	Enhancers	Duodenum Mucosa	Duodenum
17	chr12:67827400-67831200	Enhancers	HSMM	muscle
18	chr12:67827400-67831400	Enhancers	HSMMtube	muscle
19	chr12:67827600-67830400	Enhancers	Stomach Mucosa	stomach
20	chr12:67827600-67830600	Enhancers	Small Intestine	intestine
21	chr12:67827600-67831200	Enhancers	Primary hematopoietic stem cells short term culture	blood
22	chr12:67827600-67831200	Enhancers	Muscle Satellite Cultured Cells	--
23	chr12:67827800-67830800	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
24	chr12:67827800-67835400	Weak transcription	NHEK	skin
25	chr12:67828000-67831000	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
26	chr12:67828200-67830400	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
27	chr12:67829000-67830000	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
28	chr12:67829000-67830000	Enhancers	Foreskin Fibroblast Primary Cells skin02	Skin
29	chr12:67829000-67831200	Enhancers	Osteobl	bone
30	chr12:67829000-67835400	Weak transcription	Liver	Liver
31	chr12:67829200-67830000	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
32	chr12:67829200-67830400	Weak transcription	Fetal Heart	heart
33	chr12:67829200-67831400	Weak transcription	Right Atrium	heart
34	chr12:67829200-67835200	Weak transcription	Rectal Smooth Muscle	rectum
35	chr12:67829200-67835400	Weak transcription	Fetal Lung	lung
36	chr12:67829400-67830000	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
37	chr12:67829400-67830400	Enhancers	NHDF-Ad	bronchial
38	chr12:67829400-67831200	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
39	chr12:67829400-67835400	Weak transcription	Colon Smooth Muscle	Colon
40	chr12:67829600-67830000	Weak transcription	Skeletal Muscle Male	skeletal muscle
41	chr12:67829600-67830200	Enhancers	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
42	chr12:67829600-67830600	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
43	chr12:67829800-67830000	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
44	chr12:67829800-67830000	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
45	chr12:67829800-67830000	Enhancers	Colonic Mucosa	Colon
46	chr12:67829800-67830000	Enhancers	Placenta	Placenta
47	chr12:67829800-67830000	Enhancers	Psoas Muscle	Psoas

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links