Variant report

Variant	rs16829413
Chromosome Location	chr3:118904916-118904917
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	MAX	chr3:118903564-118905008	A549	lung:	n/a	n/a
2	SP1	chr3:118903422-118904951	A549	lung:	n/a	n/a
3	MAX	chr3:118903555-118905093	A549	lung:	n/a	n/a
4	E2F6	chr3:118903934-118904952	A549	lung:	n/a	chr3:118904395-118904407 chr3:118904730-118904741

No.	Distal block	Cell Line	Cell type
1	chr3:118903933..118906787-chr3:118956775..118959458,2	MCF-7	breast:
2	chr3:118902403..118905431-chr3:118923096..118925754,3	MCF-7	breast:
3	chr3:118898555..118900454-chr3:118903177..118905201,3	K562	blood:
4	chr3:118894224..118896786-chr3:118901014..118905072,3	MCF-7	breast:

Variant related genes	Relation type
UPK1B	TF binding region
ENSG00000121578	Chromatin interaction

Extended variants
information (count: 20 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:16)

rs_ID	r²[population]
rs10934486	1.00[CEU][hapmap]
rs12487052	0.87[CEU][hapmap];0.90[CHB][hapmap];0.85[JPT][hapmap];0.87[ASN][1000 genomes]
rs12492305	0.83[ASN][1000 genomes]
rs13315549	1.00[ASW][hapmap];0.87[CEU][hapmap];1.00[CHB][hapmap];0.94[CHD][hapmap];0.86[GIH][hapmap];1.00[JPT][hapmap];0.91[LWK][hapmap];0.86[MEX][hapmap];0.90[MKK][hapmap];1.00[YRI][hapmap];0.92[AFR][1000 genomes];0.88[AMR][1000 genomes];0.96[ASN][1000 genomes]
rs13320556	0.87[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.92[AFR][1000 genomes];0.92[AMR][1000 genomes];0.83[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs13324867	0.87[CEU][hapmap]
rs2594731	0.87[CEU][hapmap];0.90[CHB][hapmap];0.88[CHD][hapmap];0.85[JPT][hapmap];0.86[MEX][hapmap]
rs28428903	0.87[ASN][1000 genomes]
rs4234656	0.87[CEU][hapmap];0.90[CHB][hapmap];0.94[CHD][hapmap];0.85[JPT][hapmap];0.87[ASN][1000 genomes]
rs4450805	1.00[CEU][hapmap]
rs56193405	0.89[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs67108505	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6766503	0.87[CEU][hapmap];1.00[CHB][hapmap];0.94[CHD][hapmap];0.85[JPT][hapmap];0.86[MEX][hapmap];0.89[ASN][1000 genomes]
rs6774	0.87[CEU][hapmap];1.00[CHB][hapmap];0.94[CHD][hapmap];0.85[JPT][hapmap];0.91[ASN][1000 genomes]
rs6805930	0.87[CEU][hapmap];0.90[CHB][hapmap];0.94[CHD][hapmap];0.85[JPT][hapmap];0.86[MEX][hapmap];0.83[ASN][1000 genomes]
rs9844248	0.87[AFR][1000 genomes];0.87[ASN][1000 genomes]

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	esv3487859	chr3:118570588-119419623	Weak transcription Active TSS Strong transcription Enhancers Flanking Active TSS ZNF genes & repeats Genic enhancers Bivalent Enhancer 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	61 gene(s)	inside rSNPs	diseases
2	esv3487860	chr3:118570588-119419623	Strong transcription Enhancers Active TSS Weak transcription ZNF genes & repeats Flanking 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	61 gene(s)	inside rSNPs	diseases
3	esv18354	chr3:118855337-119000251	Enhancers Genic enhancers Strong transcription Flanking Active TSS Weak transcription Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	15 gene(s)	inside rSNPs	diseases
4	nsv591361	chr3:118901832-118909987	Weak transcription Enhancers Flanking Active TSS Strong transcription Genic enhancers ZNF genes & repeats Active TSS	TF binding region CpG island Chromatin interactive region	2 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs16829413	PTPLB	cis	cerebellum	SCAN
rs16829413	GOLGB1	cis	parietal	SCAN
rs16829413	C3orf30	cis	parietal	SCAN

Chromatin state (count:22 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:118884000-118914200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
2	chr3:118899000-118905000	Enhancers	Stomach Mucosa	stomach
3	chr3:118899600-118905200	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
4	chr3:118900600-118908400	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
5	chr3:118901000-118905400	Enhancers	Fetal Intestine Small	intestine
6	chr3:118901000-118924200	Weak transcription	Pancreas	Pancrea
7	chr3:118902200-118905000	Enhancers	Placenta	Placenta
8	chr3:118903400-118924200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
9	chr3:118903800-118905000	Enhancers	Fetal Intestine Large	intestine
10	chr3:118903800-118905200	Flanking Active TSS	A549	lung
11	chr3:118903800-118908600	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
12	chr3:118904000-118905400	Enhancers	NHDF-Ad	bronchial
13	chr3:118904400-118910600	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
14	chr3:118904400-118912800	Weak transcription	NH-A	brain
15	chr3:118904400-118913000	Weak transcription	Muscle Satellite Cultured Cells	--
16	chr3:118904600-118906000	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
17	chr3:118904600-118936400	Weak transcription	Gastric	stomach
18	chr3:118904800-118906000	Weak transcription	Osteobl	bone
19	chr3:118904800-118906600	Weak transcription	Placenta Amnion	Placenta Amnion
20	chr3:118904800-118910400	Weak transcription	HMEC	breast
21	chr3:118904800-118913000	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
22	chr3:118904800-118914400	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin

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