Variant report

Variant	rs2276456
Chromosome Location	chr12:48375975-48375976
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr12:48375228..48376777-chr12:48381596..48383195,2	MCF-7	breast:
2	chr12:48373823..48376376-chr12:48383731..48387007,3	MCF-7	breast:
3	chr12:48375713..48377256-chr12:48377465..48379370,2	MCF-7	breast:
4	chr12:48370423..48373200-chr12:48373445..48376245,2	K562	blood:
5	chr12:48262428..48264401-chr12:48374730..48377595,2	K562	blood:
6	chr12:48372717..48377052-chr12:48391617..48394178,3	MCF-7	breast:

Variant related genes	Relation type
ENSG00000139219	Chromatin interaction

Extended variants
information (count: 17 )
Associated
traits (count: 6 )

rSNPs within LD-proxies of this variant (count:12)

rs_ID	r²[population]
rs11168337	0.91[CHB][hapmap];0.95[CHD][hapmap];1.00[JPT][hapmap];0.82[AMR][1000 genomes];0.92[ASN][1000 genomes]
rs12721428	0.90[JPT][hapmap]
rs1635544	0.82[CHB][hapmap];0.83[CHD][hapmap];0.86[GIH][hapmap];0.85[JPT][hapmap]
rs1635550	0.88[CHD][hapmap];0.90[JPT][hapmap];0.86[ASN][1000 genomes]
rs1635553	1.00[CHB][hapmap];0.97[CHD][hapmap];0.80[GIH][hapmap];0.95[JPT][hapmap];0.82[AMR][1000 genomes];0.96[ASN][1000 genomes]
rs1793937	0.86[CEU][hapmap];0.87[EUR][1000 genomes]
rs2070739	0.90[JPT][hapmap]
rs2276454	0.83[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];0.87[GIH][hapmap];1.00[JPT][hapmap];0.93[TSI][hapmap];0.83[AMR][1000 genomes];0.91[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2276455	0.84[AMR][1000 genomes];0.91[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2276457	0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs3829736	0.90[CHB][hapmap];1.00[JPT][hapmap];0.98[ASN][1000 genomes]
rs740024	0.82[CHB][hapmap]

Variant overlapped rSNPs/rCNVs (count:5 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv832401	chr12:48347453-48477999	Weak transcription Enhancers Bivalent Enhancer Genic enhancers Active TSS Flanking Bivalent TSS/Enh Strong transcription Bivalent/Poised TSS Flanking Active TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	29 gene(s)	inside rSNPs	diseases
2	nsv899061	chr12:48360620-48389023	Bivalent Enhancer Enhancers Strong transcription Weak transcription Flanking Bivalent TSS/Enh Genic enhancers Flanking Active TSS Bivalent/Poised TSS ZNF genes & repeats Active TSS	TF binding region CpG island Chromatin interactive region	2 gene(s)	inside rSNPs	diseases
3	nsv525456	chr12:48366449-48376969	Weak transcription Strong transcription Flanking Active TSS Enhancers Bivalent Enhancer ZNF genes & repeats Active TSS Genic enhancers Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
4	nsv519659	chr12:48366449-48389245	Enhancers Weak transcription Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats Strong transcription Genic enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Active TSS	TF binding region CpG island Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
5	nsv558789	chr12:48368541-48376869	Enhancers Weak transcription Strong transcription Bivalent Enhancer Genic enhancers Flanking Active TSS Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region	1 gene(s)	inside rSNPs	diseases

mRNA abundance (count:6)

SNP	Gene	Cis/trans	Tissue	Source
rs2276456	PRKAG1	cis	parietal	SCAN
rs2276456	ASB8	cis	cerebellum	SCAN
rs2276456	RP1-228P16.1	cis	Skin Sun Exposed Lower leg	GTEx
rs2276456	PRPF40B	cis	parietal	SCAN
rs2276456	CCNT1	cis	cerebellum	SCAN
rs2276456	SNORA2A	cis	parietal	SCAN

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:48358600-48381400	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
2	chr12:48359200-48384000	Weak transcription	H9 Cell Line	embryonic stem cell
3	chr12:48363400-48383000	Weak transcription	Spleen	Spleen
4	chr12:48364400-48381200	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
5	chr12:48365200-48381600	Weak transcription	Right Atrium	heart
6	chr12:48365400-48381000	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
7	chr12:48366200-48381200	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
8	chr12:48366200-48381400	Strong transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
9	chr12:48366200-48381600	Strong transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
10	chr12:48372400-48378400	Weak transcription	Breast Myoepithelial Primary Cells	Breast
11	chr12:48373800-48376800	Enhancers	Fetal Intestine Large	intestine
12	chr12:48374200-48377600	Genic enhancers	iPS DF 19.11 Cell Line	embryonic stem cell
13	chr12:48374400-48376400	Genic enhancers	Fetal Intestine Small	intestine
14	chr12:48374800-48379000	Strong transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
15	chr12:48375000-48376000	Enhancers	Rectal Mucosa Donor 29	rectum
16	chr12:48375000-48381600	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
17	chr12:48375200-48381200	Weak transcription	Fetal Muscle Leg	muscle
18	chr12:48375800-48376000	Enhancers	HepG2	liver
19	chr12:48375800-48376200	Weak transcription	Fetal Lung	lung
20	chr12:48375800-48377000	Bivalent Enhancer	Foreskin Melanocyte Primary Cells skin01	Skin

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