Variant report

Variant	rs10181720
Chromosome Location	chr2:113838608-113838609
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr2:113838578..113840540-chr2:113849414..113851474,2	MCF-7	breast:
2	chr2:113836939..113839548-chr2:113991525..113994507,2	MCF-7	breast:
3	chr2:113835964..113840226-chr2:113955452..113959687,5	MCF-7	breast:
4	chr2:113837765..113839725-chr2:113955649..113957205,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000125618	Chromatin interaction
ENSG00000189223	Chromatin interaction
ENSG00000125637	Chromatin interaction

Extended variants
information (count: 25 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:20)

rs_ID	r²[population]
rs10169599	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.84[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];0.95[MEX][hapmap];0.98[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]
rs10184259	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.87[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];0.95[MEX][hapmap];1.00[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]
rs10186133	1.00[CHB][hapmap];0.87[CHD][hapmap];0.82[GIH][hapmap];1.00[JPT][hapmap];0.89[LWK][hapmap];0.83[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs11677088	0.93[ASN][1000 genomes]
rs11678375	1.00[CHB][hapmap];1.00[JPT][hapmap];0.83[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs11682107	0.99[ASN][1000 genomes]
rs11887823	1.00[ASN][1000 genomes]
rs11891557	0.99[ASN][1000 genomes]
rs12466799	0.83[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs12468224	0.83[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs12477866	0.83[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs12477867	0.82[AFR][1000 genomes];0.97[ASN][1000 genomes]
rs12711750	0.83[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs12711751	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12711752	0.87[CHD][hapmap];1.00[JPT][hapmap];0.83[ASN][1000 genomes]
rs13386602	1.00[CHB][hapmap];1.00[JPT][hapmap];0.83[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs13389457	0.83[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs13398125	0.83[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs6759676	1.00[CHB][hapmap];0.87[CHD][hapmap];0.82[GIH][hapmap];1.00[JPT][hapmap];0.87[LWK][hapmap];0.83[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs6761276	0.91[CHB][hapmap];0.81[CHD][hapmap];0.87[LWK][hapmap];0.82[AFR][1000 genomes];0.92[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:5 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv532471	chr2:113682449-113862981	ZNF genes & repeats Enhancers Weak transcription Bivalent Enhancer Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	15 gene(s)	inside rSNPs	diseases
2	nsv997348	chr2:113688093-113986508	Weak transcription Enhancers Flanking Active TSS Strong transcription Genic enhancers Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	24 gene(s)	inside rSNPs	diseases
3	nsv1007254	chr2:113726982-113887782	Enhancers Flanking Active TSS Weak transcription Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer Strong transcription ZNF genes & repeats Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	12 gene(s)	inside rSNPs	diseases
4	nsv535894	chr2:113726982-113887782	Enhancers Weak transcription Flanking Active TSS ZNF genes & repeats Bivalent Enhancer Strong transcription Active TSS Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	12 gene(s)	inside rSNPs	diseases
5	nsv2881	chr2:113800805-113846597	Weak transcription Enhancers ZNF genes & repeats Bivalent/Poised TSS Flanking Active TSS Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	7 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs10181720	PSD4	cis	cerebellum	SCAN
rs10181720	PAX8	cis	cerebellum	SCAN
rs10181720	ZC3H6	cis	cerebellum	SCAN

Chromatin state (count:9 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:113825800-113839600	Enhancers	HMEC	breast
2	chr2:113834600-113840000	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
3	chr2:113835600-113838800	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
4	chr2:113837600-113838800	Enhancers	HepG2	liver
5	chr2:113838000-113839400	Enhancers	Esophagus	oesophagus
6	chr2:113838200-113842200	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
7	chr2:113838200-113842200	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
8	chr2:113838200-113842200	Weak transcription	Stomach Mucosa	stomach
9	chr2:113838600-113842000	Weak transcription	NHEK	skin

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