Variant report

Variant	rs16831520
Chromosome Location	chr3:160541707-160541708
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr3:160395405..160397806-chr3:160539467..160541973,2	MCF-7	breast:

Extended variants
information (count: 53 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:49)

rs_ID	r²[population]
rs1159747	1.00[CEU][hapmap];0.82[GIH][hapmap];0.92[TSI][hapmap]
rs1378662	1.00[CEU][hapmap];0.82[GIH][hapmap];0.92[TSI][hapmap]
rs1378663	1.00[CEU][hapmap]
rs1455870	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.82[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];0.90[MEX][hapmap];0.96[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1455871	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.82[GIH][hapmap];1.00[JPT][hapmap];0.90[MEX][hapmap];1.00[TSI][hapmap];0.86[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs16831442	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.82[GIH][hapmap];1.00[JPT][hapmap];1.00[TSI][hapmap];0.88[EUR][1000 genomes]
rs16831457	1.00[CEU][hapmap];0.85[CHB][hapmap];1.00[JPT][hapmap];0.88[EUR][1000 genomes]
rs16831471	0.94[EUR][1000 genomes]
rs16831473	1.00[CEU][hapmap];0.85[CHB][hapmap];0.86[JPT][hapmap];0.94[EUR][1000 genomes]
rs16831516	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.82[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];0.90[MEX][hapmap];0.96[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs17236620	0.88[EUR][1000 genomes]
rs17236641	0.85[EUR][1000 genomes]
rs17236648	0.94[EUR][1000 genomes]
rs17236655	0.94[EUR][1000 genomes]
rs17236662	1.00[CEU][hapmap];0.82[CHB][hapmap];1.00[CHD][hapmap];0.82[GIH][hapmap];1.00[JPT][hapmap];1.00[TSI][hapmap];0.81[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs17289334	0.85[JPT][hapmap]
rs17826352	0.88[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs17826358	1.00[CEU][hapmap];1.00[TSI][hapmap];0.88[EUR][1000 genomes]
rs17826364	0.94[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs17826370	1.00[CEU][hapmap];0.85[CHB][hapmap];0.88[CHD][hapmap];0.82[GIH][hapmap];0.86[JPT][hapmap];1.00[TSI][hapmap];0.94[EUR][1000 genomes]
rs17826376	1.00[CEU][hapmap];0.85[CHB][hapmap];0.88[CHD][hapmap];0.82[GIH][hapmap];0.86[JPT][hapmap];1.00[TSI][hapmap];0.94[EUR][1000 genomes]
rs2068817	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.82[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];0.90[MEX][hapmap];0.96[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34035435	0.82[AFR][1000 genomes];0.91[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs3907061	0.86[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4549318	0.81[AFR][1000 genomes];0.91[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4627794	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs55891037	0.92[AFR][1000 genomes];0.94[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs55905728	0.92[AFR][1000 genomes];0.94[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs55923270	0.86[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs55997050	0.92[AFR][1000 genomes];0.94[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs56083575	0.94[EUR][1000 genomes]
rs56141155	0.92[AFR][1000 genomes];0.94[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs56157815	0.94[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs56180903	0.94[EUR][1000 genomes]
rs56331465	0.92[AFR][1000 genomes];0.94[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs57828617	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs58891820	0.94[EUR][1000 genomes]
rs6768524	1.00[CEU][hapmap];0.85[CHB][hapmap];0.86[JPT][hapmap]
rs6771910	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6779461	1.00[CEU][hapmap];0.94[EUR][1000 genomes]
rs73877952	0.94[EUR][1000 genomes]
rs73877966	0.94[EUR][1000 genomes]
rs7618082	1.00[CEU][hapmap];0.85[CHB][hapmap];0.88[CHD][hapmap];0.82[GIH][hapmap];0.86[JPT][hapmap];1.00[TSI][hapmap];0.94[EUR][1000 genomes]
rs7618596	0.94[EUR][1000 genomes]
rs7629154	1.00[CEU][hapmap];0.85[CHB][hapmap];0.88[CHD][hapmap];0.82[GIH][hapmap];0.86[JPT][hapmap];1.00[TSI][hapmap];0.94[EUR][1000 genomes]
rs7632089	0.82[CHB][hapmap]
rs7633401	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs7640802	0.82[CHB][hapmap]
rs9837945	0.87[CEU][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	nsv532666	chr3:159777847-160703202	Enhancers Weak transcription ZNF genes & repeats Strong transcription Bivalent/Poised TSS Active TSS Transcr. at gene 5' and 3' Flanking Active TSS Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	271 gene(s)	inside rSNPs	diseases
2	nsv1009249	chr3:160496237-160627378	Weak transcription Flanking Active TSS Enhancers ZNF genes & repeats Active TSS Bivalent Enhancer Genic enhancers	TF binding region CpG island Chromatin interactive region	3 gene(s)	inside rSNPs	diseases
3	nsv536780	chr3:160496237-160627378	Enhancers Flanking Active TSS Active TSS Weak transcription ZNF genes & repeats Bivalent Enhancer Genic enhancers	TF binding region CpG island Chromatin interactive region	3 gene(s)	inside rSNPs	diseases
4	nsv432495	chr3:160534298-160548298	Active TSS Enhancers Weak transcription Flanking Active TSS	Chromatin interactive region	1 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:7 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:160530800-160543200	Weak transcription	Psoas Muscle	Psoas
2	chr3:160537800-160543400	Weak transcription	HUES64 Cell Line	embryonic stem cell
3	chr3:160540200-160541800	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
4	chr3:160540800-160542600	Enhancers	Skeletal Muscle Male	skeletal muscle
5	chr3:160541000-160543200	Weak transcription	iPS-18 Cell Line	embryonic stem cell
6	chr3:160541200-160543200	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
7	chr3:160541400-160543000	Enhancers	Skeletal Muscle Female	skeletal muscle

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