Variant report

Variant	rs9824559
Chromosome Location	chr3:142304132-142304133
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr3:142297092..142299718-chr3:142303138..142306954,3	MCF-7	breast:
2	chr3:142304116..142308988-chr3:142313771..142316581,4	MCF-7	breast:
3	chr3:142304087..142306838-chr3:142309222..142312026,2	K562	blood:
4	chr3:142303600..142305532-chr3:142667653..142669421,2	K562	blood:

Variant related genes	Relation type
ENSG00000252745	Chromatin interaction
ENSG00000175054	Chromatin interaction
ENSG00000120756	Chromatin interaction

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

rSNPs within LD-proxies of this variant (count:31)

rs_ID	r²[population]
rs13324817	1.00[ASN][1000 genomes]
rs16852314	0.92[AFR][1000 genomes];0.86[ASN][1000 genomes]
rs28539899	1.00[ASN][1000 genomes]
rs55764539	1.00[ASN][1000 genomes]
rs56921402	1.00[ASN][1000 genomes]
rs57014591	1.00[ASN][1000 genomes]
rs57792207	0.86[ASN][1000 genomes]
rs61300208	1.00[ASN][1000 genomes]
rs6765659	1.00[ASN][1000 genomes]
rs6768692	1.00[ASN][1000 genomes]
rs6775426	1.00[ASN][1000 genomes]
rs6778183	1.00[ASN][1000 genomes]
rs6783167	1.00[ASN][1000 genomes]
rs73002081	1.00[ASN][1000 genomes]
rs73002088	1.00[ASN][1000 genomes]
rs73002089	1.00[ASN][1000 genomes]
rs73002093	1.00[ASN][1000 genomes]
rs73864409	1.00[ASN][1000 genomes]
rs7431811	1.00[ASN][1000 genomes]
rs7620319	1.00[ASN][1000 genomes]
rs7623858	1.00[ASN][1000 genomes]
rs7628187	1.00[ASN][1000 genomes]
rs7634495	0.89[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs7644891	0.86[AFR][1000 genomes];0.86[ASN][1000 genomes]
rs9815050	1.00[ASN][1000 genomes]
rs9821817	0.94[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs9829403	1.00[ASN][1000 genomes]
rs9832315	1.00[ASN][1000 genomes]
rs9835086	1.00[ASN][1000 genomes]
rs9846817	0.94[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs9867946	1.00[ASN][1000 genomes]

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	nsv877556	chr3:141898980-142331360	Flanking Active TSS Weak transcription ZNF genes & repeats Strong transcription Enhancers Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	51 gene(s)	inside rSNPs	diseases
2	nsv877558	chr3:142123841-142331360	Weak transcription Strong transcription Flanking Active TSS Enhancers ZNF genes & repeats Genic enhancers Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	36 gene(s)	inside rSNPs	diseases
3	nsv877559	chr3:142132749-142331360	Active TSS Enhancers Strong transcription Flanking Active TSS Weak transcription ZNF genes & repeats Bivalent Enhancer Genic enhancers 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	35 gene(s)	inside rSNPs	diseases
4	nsv877560	chr3:142132749-142362179	Strong transcription ZNF genes & repeats Weak transcription Active TSS Enhancers Transcr. at gene 5' and 3' Flanking Active TSS Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	35 gene(s)	inside rSNPs	diseases
5	nsv877561	chr3:142152925-142331360	Enhancers Weak transcription Strong transcription Flanking Active TSS Bivalent/Poised TSS Genic enhancers Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	34 gene(s)	inside rSNPs	diseases
6	nsv932989	chr3:142204208-142423305	Weak transcription Strong transcription Active TSS Flanking Active TSS Enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	33 gene(s)	inside rSNPs	diseases
7	nsv591919	chr3:142219542-142308070	Weak transcription Strong transcription Active TSS Enhancers Flanking Active TSS Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	26 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:6 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:142298200-142314400	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
2	chr3:142298400-142306000	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
3	chr3:142298600-142314400	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
4	chr3:142298800-142305600	Weak transcription	Liver	Liver
5	chr3:142298800-142305600	Weak transcription	A549	lung
6	chr3:142300600-142305600	Weak transcription	HUES48 Cell Line	embryonic stem cell

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