Variant report

Variant	rs16986548
Chromosome Location	chr22:29001380-29001381
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	chr22:28997050..28999545-chr22:28999902..29002703,2	MCF-7	breast:

Extended variants
information (count: 39 )
Associated
traits (count: 0)

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

rs_ID	r²[population]
rs12157518	1.00[AMR][1000 genomes];0.82[ASN][1000 genomes]
rs12159502	1.00[CEU][hapmap];1.00[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs12165475	1.00[CEU][hapmap];0.86[JPT][hapmap]
rs12167378	1.00[CEU][hapmap];0.89[JPT][hapmap]
rs16986377	0.83[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs16986462	1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs16986656	1.00[CEU][hapmap]
rs17878936	1.00[ASW][hapmap];1.00[CEU][hapmap];0.90[TSI][hapmap]
rs2073326	1.00[ASW][hapmap];1.00[CEU][hapmap];0.89[JPT][hapmap];0.90[TSI][hapmap]
rs35731009	1.00[AFR][1000 genomes];0.94[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs58427200	0.82[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs5997363	0.86[ASN][1000 genomes]
rs5997365	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AMR][1000 genomes];0.82[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs5997367	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AMR][1000 genomes];0.82[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs5997369	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs5997372	0.88[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs6005758	1.00[AMR][1000 genomes];0.82[ASN][1000 genomes]
rs6005765	0.82[ASN][1000 genomes]
rs6005779	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[TSI][hapmap];0.88[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs6005780	0.85[EUR][1000 genomes]
rs6005783	1.00[CEU][hapmap];1.00[YRI][hapmap];0.85[EUR][1000 genomes]
rs6005789	0.80[AFR][1000 genomes];0.88[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs6005793	0.80[AFR][1000 genomes];0.88[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs6005822	0.85[AFR][1000 genomes]
rs6005829	1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6005833	0.82[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs6005834	1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs6005843	1.00[CEU][hapmap];0.89[JPT][hapmap];0.82[TSI][hapmap]
rs73428082	0.86[ASN][1000 genomes]
rs73428096	0.88[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs73430108	0.88[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs9625544	0.86[JPT][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	nsv1067544	chr22:28755418-29055246	Enhancers Weak transcription Flanking Active TSS Active TSS Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh Genic enhancers Strong transcription Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	4 gene(s)	inside rSNPs	diseases
2	nsv544674	chr22:28755418-29055246	ZNF genes & repeats Weak transcription Enhancers Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh Strong transcription Bivalent Enhancer Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	4 gene(s)	inside rSNPs	diseases
3	nsv588880	chr22:28807277-29001789	Weak transcription Enhancers ZNF genes & repeats Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Strong transcription Bivalent/Poised TSS Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region miRNA	3 gene(s)	inside rSNPs	diseases
4	nsv916473	chr22:28837041-29215603	Weak transcription Bivalent Enhancer Active TSS Enhancers Strong transcription Flanking Active TSS Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	83 gene(s)	inside rSNPs	diseases
5	nsv459867	chr22:28993183-29109036	Weak transcription Enhancers Strong transcription Bivalent/Poised TSS Bivalent Enhancer Active TSS Flanking Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
6	nsv588881	chr22:28993183-29109036	Weak transcription Enhancers Bivalent Enhancer Strong transcription Bivalent/Poised TSS Active TSS Flanking Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
7	esv3408790	chr22:28999302-29001500	Weak transcription Enhancers	Chromatin interactive region	2 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:16 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr22:28991400-29003600	Weak transcription	NHLF	lung
2	chr22:28991400-29004200	Weak transcription	Duodenum Smooth Muscle	Duodenum
3	chr22:28991800-29007600	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
4	chr22:28996200-29002800	Weak transcription	Rectal Smooth Muscle	rectum
5	chr22:28998200-29004000	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
6	chr22:29000600-29002000	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
7	chr22:29000800-29001600	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
8	chr22:29000800-29001600	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
9	chr22:29000800-29001600	Enhancers	HUVEC	blood vessel
10	chr22:29001000-29001400	Enhancers	Brain Hippocampus Middle	brain
11	chr22:29001000-29001600	Enhancers	iPS-15b Cell Line	embryonic stem cell
12	chr22:29001000-29001600	Enhancers	Fetal Lung	lung
13	chr22:29001000-29001800	Enhancers	HUES64 Cell Line	embryonic stem cell
14	chr22:29001000-29001800	Enhancers	Cortex derived primary cultured neurospheres	brain
15	chr22:29001200-29001600	Enhancers	ES-I3 Cell Line	embryonic stem cell
16	chr22:29001200-29001600	Enhancers	iPS-18 Cell Line	embryonic stem cell

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