Variant report

Variant	rs936308
Chromosome Location	chr15:51581074-51581075
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr15:51580287..51582308-chr15:51658111..51659816,2	MCF-7	breast:
2	chr15:51577243..51581816-chr15:51658096..51661289,5	MCF-7	breast:
3	chr15:51578343..51581420-chr15:51671893..51675869,118	MCF-7	breast:

Variant related genes	Relation type
ENSG00000259194	Chromatin interaction

Extended variants
information (count: 29 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:21)

rs_ID	r²[population]
rs10519302	1.00[CHB][hapmap];0.94[CHD][hapmap];0.95[JPT][hapmap];0.94[ASN][1000 genomes]
rs16964254	0.94[ASN][1000 genomes]
rs16964258	1.00[CHB][hapmap];0.91[CHD][hapmap];0.95[JPT][hapmap];0.93[ASN][1000 genomes]
rs17647719	0.83[CHD][hapmap]
rs1902586	0.94[CHB][hapmap];0.94[CHD][hapmap];0.85[ASN][1000 genomes]
rs2008691	0.88[CEU][hapmap];0.82[JPT][hapmap];0.82[TSI][hapmap]
rs2305706	0.90[AMR][1000 genomes];0.94[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2305707	0.94[CEU][hapmap];0.94[CHB][hapmap];0.97[CHD][hapmap];0.82[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs2445752	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2470176	1.00[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.92[MKK][hapmap];1.00[TSI][hapmap];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2470178	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28559787	0.93[ASN][1000 genomes]
rs28566535	0.94[ASN][1000 genomes]
rs28723025	0.93[ASN][1000 genomes]
rs28757131	0.90[AMR][1000 genomes];0.96[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs36066823	0.91[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4614671	0.94[CEU][hapmap]
rs730154	0.88[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];0.87[LWK][hapmap];1.00[MEX][hapmap];0.98[MKK][hapmap];1.00[TSI][hapmap];0.91[YRI][hapmap];0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs8031463	1.00[CHB][hapmap];0.94[CHD][hapmap];0.95[JPT][hapmap];0.94[ASN][1000 genomes]
rs936306	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[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]
rs936309	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:8 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1047443	chr15:50744781-51647023	Strong transcription Active TSS Weak transcription Genic enhancers Enhancers Flanking Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	82 gene(s)	inside rSNPs	diseases
2	nsv569400	chr15:50874964-51767265	ZNF genes & repeats Weak transcription Strong transcription Active TSS Flanking Active TSS Bivalent/Poised TSS Bivalent Enhancer Enhancers Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	80 gene(s)	inside rSNPs	diseases
3	esv34532	chr15:51276128-51752856	Flanking Active TSS Weak transcription Strong transcription Enhancers Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	21 gene(s)	inside rSNPs	diseases
4	esv2758382	chr15:51282257-51830339	Enhancers Bivalent/Poised TSS Weak transcription Bivalent Enhancer Strong transcription Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	22 gene(s)	inside rSNPs	diseases
5	esv2760031	chr15:51282257-51830339	Weak transcription Enhancers Strong transcription Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh Flanking Active TSS Active TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	22 gene(s)	inside rSNPs	diseases
6	nsv471243	chr15:51345485-52018096	Weak transcription Enhancers Active TSS Flanking Active TSS Genic enhancers Strong transcription Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	39 gene(s)	inside rSNPs	diseases
7	esv2757600	chr15:51352249-51783981	Weak transcription Bivalent Enhancer Enhancers Strong transcription Active TSS Flanking Bivalent TSS/Enh Flanking Active TSS Genic enhancers Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	21 gene(s)	inside rSNPs	diseases
8	nsv904215	chr15:51542193-51673125	Active TSS Enhancers Bivalent Enhancer Flanking Active TSS Weak transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS Strong transcription Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA	11 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs936308	TNFAIP8L3	cis	parietal	SCAN
rs936308	TMOD2	cis	parietal	SCAN

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:51578400-51583400	Genic enhancers	Placenta	Placenta
2	chr15:51578600-51582400	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
3	chr15:51578600-51582400	Enhancers	HepG2	liver
4	chr15:51578800-51581800	Enhancers	Fetal Intestine Large	intestine
5	chr15:51578800-51582000	Enhancers	Fetal Intestine Small	intestine
6	chr15:51579400-51582000	Enhancers	Stomach Mucosa	stomach
7	chr15:51579600-51581200	Enhancers	iPS DF 19.11 Cell Line	embryonic stem cell
8	chr15:51579600-51590800	Weak transcription	Stomach Smooth Muscle	stomach
9	chr15:51579800-51581800	Weak transcription	Brain Substantia Nigra	brain
10	chr15:51580200-51581800	Enhancers	Osteobl	bone
11	chr15:51580400-51581200	Bivalent Enhancer	Foreskin Fibroblast Primary Cells skin01	Skin
12	chr15:51580400-51581200	Enhancers	Duodenum Mucosa	Duodenum
13	chr15:51580400-51581200	Enhancers	Lung	lung
14	chr15:51580400-51581200	Enhancers	Sigmoid Colon	Sigmoid Colon
15	chr15:51580400-51581400	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
16	chr15:51580400-51581400	Enhancers	HSMMtube	muscle
17	chr15:51580600-51581200	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
18	chr15:51580600-51581200	Enhancers	Fetal Lung	lung
19	chr15:51580600-51581200	Enhancers	Spleen	Spleen
20	chr15:51580600-51581400	Enhancers	Muscle Satellite Cultured Cells	--
21	chr15:51580600-51581600	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
22	chr15:51580800-51581200	Enhancers	Gastric	stomach
23	chr15:51580800-51581600	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell

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