Variant report

Variant	rs3849317
Chromosome Location	chr2:113373950-113373951
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	chr2:113373245..113375178-chr2:113378816..113381311,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000231747	Chromatin interaction

Extended variants
information (count: 27 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:23)

rs_ID	r²[population]
rs11680446	0.93[CEU][hapmap];0.87[EUR][1000 genomes]
rs11691929	0.83[JPT][hapmap]
rs3088301	0.98[ASN][1000 genomes]
rs35743012	0.98[ASN][1000 genomes]
rs3849316	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3980075	0.87[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4547533	0.81[ASN][1000 genomes]
rs4848284	1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[ASN][1000 genomes]
rs4849078	0.93[ASN][1000 genomes]
rs4849079	0.97[ASN][1000 genomes]
rs4849083	0.93[ASN][1000 genomes]
rs6542065	0.85[AFR][1000 genomes];0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs6542066	0.92[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6542067	0.86[AFR][1000 genomes];0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6542068	0.93[AFR][1000 genomes];0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs6740202	0.83[AFR][1000 genomes];0.93[AMR][1000 genomes];0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6748577	0.83[JPT][hapmap]
rs6757781	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.91[GIH][hapmap];1.00[JPT][hapmap];0.95[MEX][hapmap];0.95[TSI][hapmap]
rs6758898	0.93[ASN][1000 genomes]
rs7559385	0.90[AFR][1000 genomes];0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs7594007	0.83[JPT][hapmap]
rs934748	0.82[JPT][hapmap]
rs934749	0.83[JPT][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	nsv874877	chr2:113287964-113382054	Enhancers Strong transcription Genic enhancers Flanking Active TSS Active TSS Weak transcription Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	36 gene(s)	inside rSNPs	diseases
2	nsv458997	chr2:113313794-113431092	Flanking Active TSS Strong transcription Weak transcription Genic enhancers Enhancers Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	73 gene(s)	inside rSNPs	diseases
3	nsv582708	chr2:113313794-113431092	Strong transcription Weak transcription Enhancers Flanking Active TSS Genic enhancers Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	73 gene(s)	inside rSNPs	diseases
4	nsv470480	chr2:113373950-113429752	Flanking Active TSS Strong transcription Enhancers Weak transcription Genic enhancers Bivalent Enhancer Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	51 gene(s)	inside rSNPs	diseases

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs3849317	IL3	trans	cerebellum	SCAN
rs3849317	LRRC49	trans	cerebellum	SCAN
rs3849317	IL1F10	cis	parietal	SCAN
rs3849317	LOC654433	cis	parietal	SCAN

Chromatin state (count:23 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:113346800-113374600	Weak transcription	Ovary	ovary
2	chr2:113348600-113383600	Weak transcription	Brain Cingulate Gyrus	brain
3	chr2:113349000-113384000	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
4	chr2:113357800-113375200	Weak transcription	Stomach Smooth Muscle	stomach
5	chr2:113357800-113384200	Weak transcription	Pancreas	Pancrea
6	chr2:113358000-113384000	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
7	chr2:113370400-113383800	Weak transcription	Fetal Muscle Leg	muscle
8	chr2:113370600-113377800	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
9	chr2:113371600-113374000	Enhancers	HepG2	liver
10	chr2:113371600-113382000	Weak transcription	Spleen	Spleen
11	chr2:113372200-113379800	Weak transcription	Fetal Muscle Trunk	muscle
12	chr2:113372200-113384200	Weak transcription	Fetal Intestine Small	intestine
13	chr2:113372400-113384000	Weak transcription	Brain Anterior Caudate	brain
14	chr2:113372400-113388600	Weak transcription	Gastric	stomach
15	chr2:113372600-113379800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
16	chr2:113372800-113388000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
17	chr2:113373000-113379800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
18	chr2:113373000-113379800	Weak transcription	Skeletal Muscle Male	skeletal muscle
19	chr2:113373000-113383200	Weak transcription	Fetal Brain Female	brain
20	chr2:113373200-113374000	Weak transcription	Placenta	Placenta
21	chr2:113373200-113378400	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
22	chr2:113373200-113384000	Weak transcription	Brain Germinal Matrix	brain
23	chr2:113373800-113375400	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived

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