Variant report

Variant	rs12828359
Chromosome Location	chr12:67823328-67823329
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr12:67820987..67823729-chr12:67825470..67827435,2	K562	blood:
2	chr12:67822398..67825852-chr12:67826641..67830656,5	MCF-7	breast:
3	chr12:67820626..67824224-chr12:68042054..68045159,3	MCF-7	breast:
4	chr12:67820987..67824264-chr12:67824816..67827435,5	K562	blood:
5	chr12:67822502..67824353-chr12:67826994..67828756,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000127334	Chromatin interaction

Extended variants
information (count: 27 )
Associated
traits (count: 2 )

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

rs_ID	r²[population]
rs10506549	0.85[CEU][hapmap];0.93[CHB][hapmap];1.00[JPT][hapmap];0.86[MEX][hapmap];0.85[AMR][1000 genomes];0.88[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs10878616	1.00[ASW][hapmap];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]
rs11176738	0.91[ASN][1000 genomes]
rs11176739	0.93[CHB][hapmap];1.00[JPT][hapmap];0.91[ASN][1000 genomes]
rs11176744	0.91[ASN][1000 genomes]
rs1882033	0.91[JPT][hapmap];0.81[AMR][1000 genomes];0.85[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs1882280	0.88[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1882282	0.84[CEU][hapmap];0.85[AMR][1000 genomes];0.87[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs1882283	0.87[AMR][1000 genomes];0.88[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1920430	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]
rs2870937	0.82[JPT][hapmap]
rs35583684	0.86[AMR][1000 genomes];0.88[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4913247	0.93[CHB][hapmap];1.00[JPT][hapmap];0.91[ASN][1000 genomes]
rs4913248	0.93[CHB][hapmap];1.00[JPT][hapmap];0.91[ASN][1000 genomes]
rs4913249	0.93[CHB][hapmap];0.84[GIH][hapmap];1.00[JPT][hapmap];0.91[ASN][1000 genomes]
rs4913323	0.93[CHB][hapmap];1.00[JPT][hapmap];0.91[ASN][1000 genomes]
rs4913324	0.93[CHB][hapmap];0.84[GIH][hapmap];1.00[JPT][hapmap];0.91[ASN][1000 genomes]
rs67939426	0.86[AMR][1000 genomes];0.88[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7132295	0.91[ASN][1000 genomes]
rs7132301	0.93[CHB][hapmap];0.84[GIH][hapmap];1.00[JPT][hapmap];0.91[ASN][1000 genomes]
rs7298082	0.91[ASN][1000 genomes]
rs7312115	0.90[ASN][1000 genomes]
rs7312371	0.91[ASN][1000 genomes]
rs7312608	0.91[ASN][1000 genomes]
rs7958866	1.00[CEU][hapmap];0.81[CHB][hapmap];0.94[CHD][hapmap];0.92[JPT][hapmap];0.83[LWK][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.90[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:2)

SNP	Gene	Cis/trans	Tissue	Source
rs12828359	CAND1	Cis_1M	lymphoblastoid	RTeQTL
rs12828359	TBK1	cis	cerebellum	SCAN

Chromatin state (count:43 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:67809200-67824000	Weak transcription	Psoas Muscle	Psoas
2	chr12:67817800-67830600	Enhancers	Rectal Mucosa Donor 31	rectum
3	chr12:67818600-67827000	Enhancers	Fetal Intestine Small	intestine
4	chr12:67818600-67832000	Enhancers	Fetal Intestine Large	intestine
5	chr12:67819600-67825400	Enhancers	Sigmoid Colon	Sigmoid Colon
6	chr12:67819600-67831400	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
7	chr12:67820000-67828600	Weak transcription	Pancreas	Pancrea
8	chr12:67820000-67828800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
9	chr12:67820200-67824000	Weak transcription	Skeletal Muscle Male	skeletal muscle
10	chr12:67820200-67824000	Weak transcription	Skeletal Muscle Female	skeletal muscle
11	chr12:67820200-67829000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
12	chr12:67820400-67824200	Weak transcription	Rectal Smooth Muscle	rectum
13	chr12:67820600-67823400	Weak transcription	Fetal Kidney	kidney
14	chr12:67820600-67824000	Weak transcription	Fetal Lung	lung
15	chr12:67820600-67824000	Weak transcription	NHDF-Ad	bronchial
16	chr12:67820600-67824200	Weak transcription	Fetal Muscle Leg	muscle
17	chr12:67820600-67824600	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
18	chr12:67820600-67824800	Weak transcription	Fetal Heart	heart
19	chr12:67820600-67825200	Weak transcription	Stomach Smooth Muscle	stomach
20	chr12:67821000-67824200	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
21	chr12:67821000-67826000	Enhancers	Foreskin Melanocyte Primary Cells skin01	Skin
22	chr12:67821400-67830600	Enhancers	Rectal Mucosa Donor 29	rectum
23	chr12:67821800-67824800	Weak transcription	Brain Hippocampus Middle	brain
24	chr12:67822000-67825000	Weak transcription	Colonic Mucosa	Colon
25	chr12:67822000-67827200	Weak transcription	GM12878-XiMat	blood
26	chr12:67822200-67823400	Weak transcription	Fetal Stomach	stomach
27	chr12:67822200-67824600	Weak transcription	HSMMtube	muscle
28	chr12:67822200-67825000	Weak transcription	Duodenum Smooth Muscle	Duodenum
29	chr12:67822200-67827600	Weak transcription	Small Intestine	intestine
30	chr12:67822400-67824000	Weak transcription	Placenta	Placenta
31	chr12:67822400-67824200	Weak transcription	NHLF	lung
32	chr12:67822400-67824800	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
33	chr12:67822400-67827200	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
34	chr12:67822400-67827600	Weak transcription	Stomach Mucosa	stomach
35	chr12:67822800-67824200	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
36	chr12:67822800-67824800	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
37	chr12:67822800-67824800	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
38	chr12:67823000-67824200	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
39	chr12:67823000-67824800	Weak transcription	Duodenum Mucosa	Duodenum
40	chr12:67823000-67827200	Weak transcription	HMEC	breast
41	chr12:67823000-67827200	Weak transcription	NHEK	skin
42	chr12:67823200-67823400	Enhancers	Aorta	Aorta
43	chr12:67823200-67827400	Weak transcription	HepG2	liver

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