Variant report

Variant	rs10513200
Chromosome Location	chr3:143128798-143128799
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: 48 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:44)

rs_ID	r²[population]
rs10446278	0.84[JPT][hapmap]
rs10513201	0.84[CHB][hapmap];0.94[JPT][hapmap];0.95[ASN][1000 genomes]
rs10935491	0.85[AMR][1000 genomes];0.92[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs10935492	0.95[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11707045	0.91[CEU][hapmap];0.92[CHB][hapmap];1.00[JPT][hapmap];0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11707857	0.91[CEU][hapmap];0.84[CHB][hapmap];0.90[CHD][hapmap];1.00[JPT][hapmap];0.95[TSI][hapmap];0.82[AMR][1000 genomes];0.90[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs11719681	0.91[CEU][hapmap];0.92[CHB][hapmap];0.94[JPT][hapmap];0.87[YRI][hapmap];0.95[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11927016	0.83[CEU][hapmap]
rs16846341	0.94[JPT][hapmap];0.96[ASN][1000 genomes]
rs16853522	0.92[JPT][hapmap];0.96[ASN][1000 genomes]
rs16853578	0.84[CHB][hapmap];0.94[JPT][hapmap];0.95[ASN][1000 genomes]
rs17757146	0.87[CEU][hapmap];0.92[CHB][hapmap];0.89[CHD][hapmap];1.00[JPT][hapmap];0.89[MEX][hapmap];0.89[TSI][hapmap];0.89[AMR][1000 genomes];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17757182	0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1875459	1.00[ASW][hapmap];0.91[CEU][hapmap];0.92[CHB][hapmap];0.90[CHD][hapmap];0.84[GIH][hapmap];1.00[JPT][hapmap];0.94[MEX][hapmap];0.95[TSI][hapmap];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2360255	1.00[ASW][hapmap];0.91[CEU][hapmap];0.84[CHB][hapmap];0.84[CHD][hapmap];1.00[JPT][hapmap];0.89[MEX][hapmap];0.97[TSI][hapmap];0.91[AMR][1000 genomes];0.94[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs35233571	0.91[AMR][1000 genomes];0.95[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs35358995	0.80[AMR][1000 genomes];0.91[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs36125349	0.89[AMR][1000 genomes];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4311209	0.96[ASN][1000 genomes]
rs4521222	0.96[ASN][1000 genomes]
rs56080141	0.96[ASN][1000 genomes]
rs56152928	0.85[AMR][1000 genomes];0.93[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs61301417	0.96[ASN][1000 genomes]
rs6770293	0.83[CHB][hapmap];0.94[JPT][hapmap];0.96[ASN][1000 genomes]
rs6782465	0.94[JPT][hapmap];0.96[ASN][1000 genomes]
rs6795522	0.84[JPT][hapmap]
rs73144740	0.85[ASN][1000 genomes]
rs73144743	0.91[ASN][1000 genomes]
rs73144745	0.90[ASN][1000 genomes]
rs73144749	0.96[ASN][1000 genomes]
rs73144760	0.97[ASN][1000 genomes]
rs73144769	0.93[ASN][1000 genomes]
rs73144770	0.96[ASN][1000 genomes]
rs73144771	0.96[ASN][1000 genomes]
rs73144772	0.96[ASN][1000 genomes]
rs73144773	0.96[ASN][1000 genomes]
rs73144774	0.96[ASN][1000 genomes]
rs73144777	0.96[ASN][1000 genomes]
rs7374585	0.84[CHB][hapmap];0.94[JPT][hapmap];0.93[ASN][1000 genomes]
rs7617737	0.91[CEU][hapmap];0.92[CHB][hapmap];1.00[JPT][hapmap];0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7624553	0.80[JPT][hapmap]
rs7627844	0.89[AMR][1000 genomes];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7652087	0.91[CEU][hapmap];0.92[CHB][hapmap];1.00[JPT][hapmap];0.95[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7652557	0.89[AMR][1000 genomes];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]

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:15 , 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	chr3:143127000-143128800	Enhancers	ES-WA7 Cell Line	embryonic stem cell
7	chr3:143127200-143128800	Enhancers	ES-I3 Cell Line	embryonic stem cell
8	chr3:143127200-143129000	Enhancers	iPS-20b Cell Line	embryonic stem cell
9	chr3:143127200-143129200	Enhancers	iPS-15b Cell Line	embryonic stem cell
10	chr3:143127200-143129400	Enhancers	HUES64 Cell Line	embryonic stem cell
11	chr3:143127400-143129200	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
12	chr3:143127600-143129200	Enhancers	H9 Cell Line	embryonic stem cell
13	chr3:143127800-143128800	Enhancers	iPS DF 6.9 Cell Line	embryonic stem cell
14	chr3:143128200-143129000	Enhancers	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
15	chr3:143128200-143129200	Enhancers	iPS-18 Cell Line	embryonic stem cell

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