Variant report

Variant	rs12148826
Chromosome Location	chr15:93419892-93419893
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr15:93394513..93396310-chr15:93417417..93419914,2	MCF-7	breast:
2	chr15:93333327..93367027-chr15:93419774..93462750,363	K562	blood:
3	chr15:93344712..93371031-chr15:93418700..93467618,365	MCF-7	breast:
4	chr15:93345383..93371459-chr15:93416796..93454653,318	MCF-7	breast:

Variant related genes	Relation type
ENSG00000258527	Chromatin interaction
ENSG00000185442	Chromatin interaction
ENSG00000258922	Chromatin interaction

Extended variants
information (count: 11 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:4)

rs_ID	r²[population]
rs11074120	0.81[CHB][hapmap]
rs2304655	0.87[CHB][hapmap]
rs60753138	0.87[AFR][1000 genomes];0.94[AMR][1000 genomes];0.92[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs8042632	0.81[CHB][hapmap]

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	nsv904499	chr15:92914795-93472582	Bivalent Enhancer Flanking Active TSS Genic enhancers Strong transcription Active TSS Transcr. at gene 5' and 3' Weak transcription Enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA	163 gene(s)	inside rSNPs	diseases
2	nsv948738	chr15:93070742-93728147	Strong transcription Weak transcription Flanking Active TSS Enhancers Genic enhancers Active TSS 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 miRNA target site	169 gene(s)	inside rSNPs	diseases
3	nsv1049490	chr15:93134405-93591660	Enhancers Genic enhancers Weak transcription Strong transcription Active TSS ZNF genes & repeats Flanking Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	151 gene(s)	inside rSNPs	diseases
4	nsv530846	chr15:93323949-94030462	Active TSS Strong transcription Flanking Active TSS Enhancers Weak transcription Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	153 gene(s)	inside rSNPs	diseases
5	nsv948881	chr15:93383740-93603608	Genic enhancers Strong transcription Weak transcription Transcr. at gene 5' and 3' Enhancers Flanking Active TSS Active TSS ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	91 gene(s)	inside rSNPs	diseases
6	nsv1047496	chr15:93412778-93475878	Enhancers Flanking Active TSS Active TSS Strong transcription Transcr. at gene 5' and 3' Genic enhancers Weak transcription ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA	87 gene(s)	inside rSNPs	diseases
7	nsv1036560	chr15:93413594-93462163	Enhancers Flanking Active TSS Transcr. at gene 5' and 3' Weak transcription Genic enhancers Strong transcription Active TSS ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA	87 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs12148826	CHD2	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:20 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:93412600-93425000	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
2	chr15:93413600-93421800	Weak transcription	Gastric	stomach
3	chr15:93413600-93421800	Weak transcription	Skeletal Muscle Male	skeletal muscle
4	chr15:93413600-93425200	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
5	chr15:93413800-93421600	Weak transcription	HUES6 Cell Line	embryonic stem cell
6	chr15:93413800-93421600	Weak transcription	Pancreas	Pancrea
7	chr15:93413800-93421600	Weak transcription	Skeletal Muscle Female	skeletal muscle
8	chr15:93413800-93425200	Weak transcription	Left Ventricle	heart
9	chr15:93414000-93424200	Weak transcription	Rectal Smooth Muscle	rectum
10	chr15:93415400-93420000	Weak transcription	Hela-S3	cervix
11	chr15:93418200-93423200	Weak transcription	ES-I3 Cell Line	embryonic stem cell
12	chr15:93419400-93420000	Enhancers	A549	lung
13	chr15:93419400-93420200	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
14	chr15:93419400-93421000	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
15	chr15:93419400-93421600	Enhancers	K562	blood
16	chr15:93419600-93420200	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
17	chr15:93419600-93420800	Weak transcription	Aorta	Aorta
18	chr15:93419600-93421000	Enhancers	Placenta	Placenta
19	chr15:93419800-93420600	Enhancers	Placenta Amnion	Placenta Amnion
20	chr15:93419800-93424200	Enhancers	HepG2	liver

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links