Variant report

Variant	rs16853564
Chromosome Location	chr3:143128922-143128923
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	chr3:143127774..143129299-chr3:143137124..143139731,2	MCF-7	breast:
2	chr3:143047507..143050166-chr3:143127472..143129524,2	K562	blood:

Extended variants
information (count: 28 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:24)

rs_ID	r²[population]
rs12630579	0.85[CHB][hapmap];1.00[JPT][hapmap];0.84[ASN][1000 genomes]
rs12631011	0.88[TSI][hapmap]
rs12638374	1.00[CEU][hapmap]
rs16853472	0.88[TSI][hapmap]
rs16853475	0.88[TSI][hapmap]
rs16853550	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs16853555	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.91[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.84[AFR][1000 genomes];0.85[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs16853570	0.85[CHB][hapmap];1.00[JPT][hapmap];0.91[YRI][hapmap];0.84[AFR][1000 genomes];0.81[AMR][1000 genomes];0.88[ASN][1000 genomes]
rs2293326	1.00[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs57014448	0.84[ASN][1000 genomes]
rs59309029	1.00[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs59545496	0.84[ASN][1000 genomes]
rs6765286	1.00[CEU][hapmap];0.85[CHB][hapmap];1.00[JPT][hapmap];0.90[YRI][hapmap];0.83[AFR][1000 genomes];0.85[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6765388	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.80[MKK][hapmap];1.00[TSI][hapmap];0.83[YRI][hapmap];0.85[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6767272	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.83[AFR][1000 genomes];0.85[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6773090	1.00[CEU][hapmap];0.82[CHB][hapmap];1.00[JPT][hapmap];0.89[YRI][hapmap];0.84[AFR][1000 genomes];0.85[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6778621	1.00[CEU][hapmap];1.00[CHB][hapmap];0.85[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6797479	0.81[AFR][1000 genomes];0.85[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6805036	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.83[AFR][1000 genomes];0.85[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6805667	0.85[CHB][hapmap];0.91[YRI][hapmap];0.81[AMR][1000 genomes];0.84[ASN][1000 genomes]
rs7620504	1.00[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs7642550	0.84[EUR][1000 genomes]
rs7642639	1.00[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs950427	0.88[TSI][hapmap]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv949288	chr3:142793323-143585882	Enhancers Flanking Active TSS Weak transcription ZNF genes & repeats Strong transcription Active TSS Transcr. at gene 5' and 3' Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	24 gene(s)	inside rSNPs	diseases
2	esv2757894	chr3:142992697-143285979	Enhancers Weak transcription Strong transcription Active TSS Flanking Active TSS ZNF genes & repeats Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
3	esv2759184	chr3:142992697-143285979	Enhancers Weak transcription Flanking Active TSS ZNF genes & repeats Strong transcription Bivalent Enhancer Active TSS Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
4	nsv999000	chr3:143086325-143136128	Enhancers Flanking Active TSS ZNF genes & repeats Weak transcription Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	2 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	chr3:143100600-143142600	Weak transcription	Primary T cells from cord blood	blood
2	chr3:143126600-143129000	Enhancers	HUES48 Cell Line	embryonic stem cell
3	chr3:143126600-143130800	Weak transcription	Dnd41	blood
4	chr3:143126800-143129000	Enhancers	H1 Cell Line	embryonic stem cell
5	chr3:143126800-143129200	Enhancers	HUES6 Cell Line	embryonic stem cell
6	chr3:143127200-143129000	Enhancers	iPS-20b Cell Line	embryonic stem cell
7	chr3:143127200-143129200	Enhancers	iPS-15b Cell Line	embryonic stem cell
8	chr3:143127200-143129400	Enhancers	HUES64 Cell Line	embryonic stem cell
9	chr3:143127400-143129200	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
10	chr3:143127600-143129200	Enhancers	H9 Cell Line	embryonic stem cell
11	chr3:143128200-143129000	Enhancers	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
12	chr3:143128200-143129200	Enhancers	iPS-18 Cell Line	embryonic stem cell
13	chr3:143128800-143129000	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
14	chr3:143128800-143130400	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell

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