Variant report

Variant	rs7574787
Chromosome Location	chr2:113837416-113837417
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:0)
CpG islands
(count:0)
Chromatin interactive
region (count:14)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

(count:14 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr2:113836939..113839548-chr2:113991525..113994507,2	MCF-7	breast:
2	chr2:113837374..113838246-chr2:113894254..113895056,3	MCF-7	breast:
3	chr2:113837374..113837912-chr2:114127892..114128718,2	K562	blood:
4	chr2:113835964..113840226-chr2:113955452..113959687,5	MCF-7	breast:
5	chr2:113836433..113838367-chr2:113961484..113963853,2	MCF-7	breast:
6	chr2:113837351..113838104-chr2:114147540..114148341,3	K562	blood:
7	chr2:113835706..113838400-chr2:113880453..113883939,3	MCF-7	breast:
8	chr2:113799300..113800125-chr2:113836934..113837726,3	MCF-7	breast:
9	chr2:113837298..113838414-chr2:113957612..113958528,4	MCF-7	breast:
10	chr2:113836933..113837467-chr2:113934054..113934934,2	MCF-7	breast:
11	chr2:113837325..113838487-chr2:113894163..113895181,5	K562	blood:
12	chr2:113835663..113838530-chr2:113914513..113916116,2	MCF-7	breast:
13	chr2:113837234..113838476-chr2:113956411..113957308,6	MCF-7	breast:
14	chr2:113718593..113720289-chr2:113834611..113837557,2	MCF-7	breast:

No data

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

Extended variants
information (count: 25 )
Associated
traits (count: 2 )

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

rs_ID	r²[population]
rs10199363	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.87[MKK][hapmap];1.00[TSI][hapmap];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11123160	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs11693683	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1618889	0.86[AMR][1000 genomes];0.93[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs1665186	0.91[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1665188	0.91[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1688072	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.84[MKK][hapmap];0.96[TSI][hapmap];0.81[AMR][1000 genomes];0.88[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs1688077	0.86[AMR][1000 genomes];0.93[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2121326	0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28928273	1.00[YRI][hapmap]
rs28928279	0.85[YRI][hapmap]
rs315920	0.80[CEU][hapmap];0.86[MEX][hapmap];0.90[TSI][hapmap]
rs315921	0.93[CEU][hapmap];1.00[GIH][hapmap];1.00[MEX][hapmap];0.93[TSI][hapmap];0.81[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs315922	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.83[AMR][1000 genomes];0.90[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs315923	0.90[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs315924	0.81[AMR][1000 genomes];0.91[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs315928	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[AMR][1000 genomes];0.89[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs4358126	0.81[EUR][1000 genomes]
rs67213447	0.86[AMR][1000 genomes];0.93[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs7578112	0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[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:2)

SNP	Gene	Cis/trans	Tissue	Source
rs7574787	IL1F8	cis	parietal	SCAN
rs7574787	PSD4	cis	cerebellum	SCAN

Chromatin state (count:15 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:113825800-113839600	Enhancers	HMEC	breast
2	chr2:113834000-113838200	Enhancers	Stomach Mucosa	stomach
3	chr2:113834600-113837800	Enhancers	Duodenum Mucosa	Duodenum
4	chr2:113834600-113838200	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
5	chr2:113834600-113840000	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
6	chr2:113835600-113838800	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
7	chr2:113835800-113838200	Enhancers	Liver	Liver
8	chr2:113835800-113838200	Enhancers	HSMMtube	muscle
9	chr2:113836000-113838000	Weak transcription	Esophagus	oesophagus
10	chr2:113836600-113837600	Enhancers	iPS-20b Cell Line	embryonic stem cell
11	chr2:113836800-113837600	Weak transcription	ES-I3 Cell Line	embryonic stem cell
12	chr2:113836800-113838600	Enhancers	NHEK	skin
13	chr2:113837000-113838200	Enhancers	iPS DF 6.9 Cell Line	embryonic stem cell
14	chr2:113837200-113838200	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
15	chr2:113837400-113838000	Weak transcription	Gastric	stomach

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