Variant report

Variant	rs1820260
Chromosome Location	chr16:81374504-81374505
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 38 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:32)

rs_ID	r²[population]
rs11643932	0.82[ASN][1000 genomes]
rs12103052	1.00[CEU][hapmap];0.85[CHB][hapmap];0.89[GIH][hapmap];0.84[JPT][hapmap];0.81[MEX][hapmap];0.87[AMR][1000 genomes];0.92[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs12448813	0.92[CEU][hapmap];0.83[GIH][hapmap];0.81[MEX][hapmap];0.89[EUR][1000 genomes]
rs12918775	0.83[AFR][1000 genomes]
rs12920172	0.86[CHB][hapmap]
rs12921222	1.00[CEU][hapmap];0.93[CHB][hapmap];0.84[JPT][hapmap];0.82[AFR][1000 genomes];0.92[AMR][1000 genomes];0.92[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs12925218	0.99[AFR][1000 genomes];0.96[AMR][1000 genomes];0.94[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12927652	0.92[CEU][hapmap];1.00[CHB][hapmap];0.85[JPT][hapmap];0.82[AFR][1000 genomes];0.89[AMR][1000 genomes];0.92[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs12929924	0.92[CEU][hapmap];1.00[CHB][hapmap];0.95[YRI][hapmap];0.98[AFR][1000 genomes];0.89[AMR][1000 genomes];0.87[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12933277	1.00[CEU][hapmap];1.00[CHB][hapmap];0.82[AFR][1000 genomes];0.88[AMR][1000 genomes];0.92[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs12934500	0.92[CEU][hapmap];1.00[CHB][hapmap];0.85[JPT][hapmap];0.96[YRI][hapmap];0.98[AFR][1000 genomes];0.89[AMR][1000 genomes];0.87[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1564116	0.92[CEU][hapmap];0.86[GIH][hapmap];0.81[MEX][hapmap];0.85[MKK][hapmap];0.85[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs16955063	1.00[CEU][hapmap];1.00[CHB][hapmap];0.89[AMR][1000 genomes];0.92[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs35151165	0.97[AFR][1000 genomes];0.90[AMR][1000 genomes];0.92[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs35378839	0.82[ASN][1000 genomes]
rs4888145	0.95[AFR][1000 genomes];0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4889309	1.00[CEU][hapmap];0.88[EUR][1000 genomes]
rs6564872	0.92[CEU][hapmap];0.84[GIH][hapmap];0.86[TSI][hapmap];0.84[EUR][1000 genomes]
rs7194094	1.00[CEU][hapmap];1.00[CHB][hapmap];0.83[JPT][hapmap];0.96[YRI][hapmap];0.96[AFR][1000 genomes];0.89[AMR][1000 genomes];0.91[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7199407	0.92[CEU][hapmap];0.90[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs7199797	0.87[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs7203482	0.89[CEU][hapmap];1.00[CHB][hapmap];0.80[GIH][hapmap];0.92[JPT][hapmap];0.81[MEX][hapmap];0.80[MKK][hapmap];0.83[AMR][1000 genomes];0.88[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs7203835	0.92[CEU][hapmap];0.81[EUR][1000 genomes]
rs729181	0.92[CEU][hapmap];0.89[GIH][hapmap];0.93[TSI][hapmap];0.81[EUR][1000 genomes]
rs8051314	0.92[CEU][hapmap];0.85[CHB][hapmap];0.81[AFR][1000 genomes];0.87[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs8055288	0.89[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs8062704	0.85[LWK][hapmap];0.88[YRI][hapmap]
rs8064146	0.87[AMR][1000 genomes];0.91[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs9921359	0.92[CEU][hapmap];0.83[CHB][hapmap];0.88[GIH][hapmap];0.85[MEX][hapmap];0.86[MKK][hapmap];0.83[TSI][hapmap];0.89[AMR][1000 genomes];0.89[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs9922086	0.92[CEU][hapmap];0.83[GIH][hapmap];0.92[JPT][hapmap];0.81[MEX][hapmap];0.88[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs9934557	0.81[CHB][hapmap]
rs9938148	0.92[CEU][hapmap];0.85[CHB][hapmap];0.86[AMR][1000 genomes];0.91[EUR][1000 genomes];0.86[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:6 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv532569	chr16:80980356-81700149	Weak transcription Flanking Active TSS Genic enhancers Enhancers Strong transcription Active TSS Bivalent Enhancer ZNF genes & repeats 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	71 gene(s)	inside rSNPs	diseases
2	nsv532597	chr16:81009718-81388348	Active TSS Weak transcription Strong transcription Flanking Active TSS Enhancers 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	56 gene(s)	inside rSNPs	diseases
3	nsv1058519	chr16:81177767-81735333	Flanking Active TSS Weak transcription ZNF genes & repeats Strong transcription Enhancers Transcr. at gene 5' and 3' Active TSS Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA	36 gene(s)	inside rSNPs	diseases
4	nsv948448	chr16:81198147-81906766	Enhancers Flanking Active TSS Weak transcription Strong transcription Active TSS Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA	37 gene(s)	inside rSNPs	diseases
5	nsv1061359	chr16:81349826-81471867	Weak transcription ZNF genes & repeats Strong transcription Flanking Active TSS Enhancers Genic enhancers Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA	17 gene(s)	inside rSNPs	diseases
6	nsv542992	chr16:81349826-81471867	Weak transcription Enhancers ZNF genes & repeats Strong transcription Active TSS Flanking Active TSS Bivalent/Poised TSS Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA	17 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:14 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr16:81350000-81375000	Weak transcription	Fetal Intestine Large	intestine
2	chr16:81353400-81390400	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
3	chr16:81354200-81391600	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
4	chr16:81357800-81375800	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
5	chr16:81363800-81379400	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
6	chr16:81364000-81374600	Weak transcription	Cortex derived primary cultured neurospheres	brain
7	chr16:81366400-81379200	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
8	chr16:81366400-81380400	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
9	chr16:81366600-81374600	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
10	chr16:81369800-81374800	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
11	chr16:81369800-81379400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
12	chr16:81373600-81375000	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
13	chr16:81374200-81374600	Weak transcription	Fetal Intestine Small	intestine
14	chr16:81374400-81374600	ZNF genes & repeats	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links