Variant report

Variant	rs2403020
Chromosome Location	chr12:83344190-83344191
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 44 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:35)

rs_ID	r²[population]
rs10746259	0.84[GIH][hapmap];0.88[JPT][hapmap]
rs10746261	0.84[GIH][hapmap];0.88[JPT][hapmap]
rs10862525	0.97[AFR][1000 genomes];0.92[AMR][1000 genomes];0.98[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs10862526	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[YRI][hapmap];0.86[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs10862527	1.00[CHB][hapmap];1.00[CHD][hapmap];0.92[GIH][hapmap];1.00[JPT][hapmap];0.97[ASN][1000 genomes]
rs10862528	0.96[ASN][1000 genomes]
rs10862529	0.92[CHB][hapmap];1.00[JPT][hapmap];0.80[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10862530	1.00[CHB][hapmap];1.00[CHD][hapmap];0.88[GIH][hapmap];1.00[JPT][hapmap];0.97[ASN][1000 genomes]
rs10862532	0.87[ASN][1000 genomes]
rs12297736	0.86[JPT][hapmap];0.85[ASN][1000 genomes]
rs12320912	0.85[ASN][1000 genomes]
rs12809082	0.83[GIH][hapmap];0.82[JPT][hapmap]
rs1471781	0.85[CEU][hapmap];0.89[ASN][1000 genomes]
rs1484991	0.82[JPT][hapmap]
rs1625397	0.96[ASN][1000 genomes]
rs1682590	0.81[AMR][1000 genomes];0.82[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1682592	0.81[AMR][1000 genomes];0.80[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1682593	0.92[CHB][hapmap];1.00[CHD][hapmap];0.96[GIH][hapmap];1.00[JPT][hapmap];0.84[MEX][hapmap];0.84[MKK][hapmap];0.89[TSI][hapmap];0.98[ASN][1000 genomes]
rs1682594	0.98[ASN][1000 genomes]
rs1682595	0.96[ASN][1000 genomes]
rs17010139	0.82[JPT][hapmap]
rs17010268	0.88[JPT][hapmap];0.84[ASN][1000 genomes]
rs1796188	0.92[CHB][hapmap];0.94[JPT][hapmap];0.98[ASN][1000 genomes]
rs1796189	0.98[ASN][1000 genomes]
rs2019384	0.81[JPT][hapmap]
rs2403021	1.00[CHB][hapmap];0.94[JPT][hapmap];0.96[YRI][hapmap];0.98[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2403023	0.92[CHB][hapmap];1.00[CHD][hapmap];0.88[GIH][hapmap];0.94[JPT][hapmap];0.97[ASN][1000 genomes]
rs3993374	0.97[ASN][1000 genomes]
rs4346030	0.86[AFR][1000 genomes];0.90[AMR][1000 genomes];0.98[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs4346031	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7295699	0.87[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7957916	1.00[CHB][hapmap];1.00[JPT][hapmap];0.98[ASN][1000 genomes]
rs7965229	0.95[AFR][1000 genomes];0.91[AMR][1000 genomes];0.96[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs7970086	0.84[CHB][hapmap];0.90[CHD][hapmap];0.95[GIH][hapmap];0.94[JPT][hapmap];0.90[ASN][1000 genomes]
rs7971263	0.80[CEU][hapmap];0.98[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:9 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv521849	chr12:83013783-83991479	Weak transcription ZNF genes & repeats Enhancers Strong transcription Active TSS Flanking Active TSS Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	16 gene(s)	inside rSNPs	diseases
2	nsv469490	chr12:83089431-83507269	Enhancers Weak transcription Strong transcription ZNF genes & repeats Genic enhancers Flanking Active TSS Bivalent Enhancer Active TSS	TF binding region CpG island Chromatin interactive region	6 gene(s)	inside rSNPs	diseases
3	nsv559542	chr12:83089431-83507269	Weak transcription Enhancers Flanking Active TSS Strong transcription ZNF genes & repeats Active TSS Genic enhancers Bivalent Enhancer	TF binding region CpG island Chromatin interactive region	6 gene(s)	inside rSNPs	diseases
4	esv2758315	chr12:83101045-83357621	Enhancers Weak transcription Strong transcription ZNF genes & repeats Flanking Active TSS Bivalent Enhancer Genic enhancers Active TSS	TF binding region CpG island Chromatin interactive region	2 gene(s)	inside rSNPs	diseases
5	esv2759911	chr12:83101045-83357621	Enhancers Weak transcription Active TSS Genic enhancers ZNF genes & repeats Strong transcription Flanking Active TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region	2 gene(s)	inside rSNPs	diseases
6	nsv832472	chr12:83248283-83419753	Weak transcription ZNF genes & repeats Enhancers Flanking Active TSS Active TSS Genic enhancers Strong transcription Bivalent Enhancer	TF binding region CpG island Chromatin interactive region	4 gene(s)	inside rSNPs	n/a
7	nsv559557	chr12:83334204-83453620	ZNF genes & repeats Weak transcription Enhancers Strong transcription Flanking Active TSS Active TSS Genic enhancers	TF binding region CpG island Chromatin interactive region	4 gene(s)	inside rSNPs	n/a
8	nsv469495	chr12:83339933-83374779	Weak transcription Enhancers Strong transcription ZNF genes & repeats Flanking Active TSS Active TSS	Chromatin interactive region	1 gene(s)	inside rSNPs	n/a
9	nsv559558	chr12:83339933-83374779	Enhancers Weak transcription Strong transcription Flanking Active TSS ZNF genes & repeats Active TSS	Chromatin interactive region	1 gene(s)	inside rSNPs	n/a

No data

Chromatin state (count:8 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:83325000-83346400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
2	chr12:83325600-83348000	Weak transcription	Colon Smooth Muscle	Colon
3	chr12:83331400-83348000	Weak transcription	Brain Hippocampus Middle	brain
4	chr12:83340400-83348200	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
5	chr12:83340800-83348400	Weak transcription	Primary monocytes fromperipheralblood	blood
6	chr12:83342000-83352600	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
7	chr12:83343800-83346400	Weak transcription	Breast Myoepithelial Primary Cells	Breast
8	chr12:83343800-83347600	Weak transcription	Brain Substantia Nigra	brain

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links