Variant report

Variant	rs11065374
Chromosome Location	chr12:121400205-121400206
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr12:121398625..121400416-chr12:121405425..121406992,2	K562	blood:

Extended variants
information (count: 23 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:16)

rs_ID	r²[population]
rs11065363	0.87[ASN][1000 genomes]
rs11065367	0.90[ASN][1000 genomes]
rs11065373	0.98[ASN][1000 genomes]
rs11065375	0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11065376	0.98[ASN][1000 genomes]
rs11065393	0.81[CHB][hapmap]
rs1169280	0.82[JPT][hapmap]
rs1169307	0.82[CHB][hapmap]
rs12814766	0.98[ASN][1000 genomes]
rs1971318	0.90[ASN][1000 genomes]
rs2393802	0.84[ASN][1000 genomes]
rs3999413	0.82[CHB][hapmap]
rs6489787	0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7305428	0.98[ASN][1000 genomes]
rs7962595	0.86[ASN][1000 genomes]
rs7966322	0.94[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:7 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv521928	chr12:121041728-121761800	Genic enhancers Flanking Active TSS Weak transcription Transcr. at gene 5' and 3' Enhancers Strong transcription ZNF genes & repeats Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	68 gene(s)	inside rSNPs	diseases
2	nsv1037070	chr12:121069938-121459047	Weak transcription Enhancers Active TSS Genic enhancers Flanking Active TSS Bivalent/Poised TSS Strong transcription Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	45 gene(s)	inside rSNPs	diseases
3	nsv899559	chr12:121324727-121592689	Active TSS Enhancers Weak transcription Flanking Bivalent TSS/Enh Flanking Active TSS Genic enhancers Bivalent/Poised TSS Strong transcription Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	31 gene(s)	inside rSNPs	diseases
4	esv1838192	chr12:121363589-121402932	Weak transcription Active TSS ZNF genes & repeats Enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	Chromatin interactive region	3 gene(s)	inside rSNPs	diseases
5	nsv899560	chr12:121371233-121560581	Strong transcription Weak transcription Enhancers Flanking Active TSS Active TSS Genic enhancers Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	23 gene(s)	inside rSNPs	diseases
6	nsv899561	chr12:121376416-121525591	Enhancers Flanking Active TSS Active TSS Genic enhancers Weak transcription Strong transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	20 gene(s)	inside rSNPs	diseases
7	nsv899562	chr12:121376416-121565870	Weak transcription Flanking Active TSS Active TSS Strong transcription Enhancers Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	24 gene(s)	inside rSNPs	diseases

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs11065374	FLJ12448	cis	multi-tissue	Pritchard
rs11065374	CABP1	cis	cerebellum	SCAN
rs11065374	RNF34	cis	cerebellum	SCAN
rs11065374	HPD	cis	parietal	SCAN

Chromatin state (count:28 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:121393600-121400600	Enhancers	Fetal Intestine Large	intestine
2	chr12:121394600-121408200	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
3	chr12:121395800-121408200	Weak transcription	Fetal Kidney	kidney
4	chr12:121396600-121400600	Enhancers	Duodenum Mucosa	Duodenum
5	chr12:121397000-121400600	Enhancers	Stomach Mucosa	stomach
6	chr12:121397600-121401000	Enhancers	Fetal Intestine Small	intestine
7	chr12:121397600-121406800	Weak transcription	ES-I3 Cell Line	embryonic stem cell
8	chr12:121397800-121400400	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
9	chr12:121397800-121405400	Weak transcription	Pancreas	Pancrea
10	chr12:121398000-121400600	Enhancers	K562	blood
11	chr12:121398000-121400800	Enhancers	A549	lung
12	chr12:121398600-121401000	Enhancers	Liver	Liver
13	chr12:121398600-121401400	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
14	chr12:121398800-121401000	Enhancers	NHEK	skin
15	chr12:121399200-121401000	Enhancers	Rectal Mucosa Donor 31	rectum
16	chr12:121399400-121401600	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
17	chr12:121399600-121400800	Enhancers	HepG2	liver
18	chr12:121399600-121401400	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
19	chr12:121399600-121403200	Weak transcription	Thymus	Thymus
20	chr12:121399800-121400400	Enhancers	Rectal Mucosa Donor 29	rectum
21	chr12:121399800-121401400	Enhancers	HMEC	breast
22	chr12:121400000-121400600	Weak transcription	Colonic Mucosa	Colon
23	chr12:121400000-121400600	Enhancers	Small Intestine	intestine
24	chr12:121400000-121400800	Enhancers	NHDF-Ad	bronchial
25	chr12:121400000-121402200	Weak transcription	Esophagus	oesophagus
26	chr12:121400000-121405400	Weak transcription	Sigmoid Colon	Sigmoid Colon
27	chr12:121400000-121406600	Weak transcription	Gastric	stomach
28	chr12:121400200-121400600	Bivalent Enhancer	Foreskin Fibroblast Primary Cells skin01	Skin

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links