Variant report

Variant	rs936306
Chromosome Location	chr15:51579598-51579599
allele	C/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:13)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

(count:13 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr15:51578878..51579655-chr15:51590376..51591161,2	MCF-7	breast:
2	chr15:51578136..51580943-chr15:51585149..51588090,2	MCF-7	breast:
3	chr15:51577515..51580026-chr15:51665371..51667352,2	MCF-7	breast:
4	chr15:51578814..51579731-chr15:51659110..51659788,4	MCF-7	breast:
5	chr15:51577066..51580410-chr15:51672799..51675704,3	MCF-7	breast:
6	chr15:51578411..51580276-chr15:51657796..51660654,2	MCF-7	breast:
7	chr15:51578798..51579654-chr15:51695165..51696058,4	MCF-7	breast:
8	chr15:51579282..51579915-chr15:51633506..51634068,2	MCF-7	breast:
9	chr15:51577243..51581816-chr15:51658096..51661289,5	MCF-7	breast:
10	chr15:51578501..51580863-chr15:51587732..51590642,2	MCF-7	breast:
11	chr15:51578756..51579683-chr15:51627850..51628798,2	MCF-7	breast:
12	chr15:51578027..51580996-chr15:51672826..51674102,51	MCF-7	breast:
13	chr15:51578343..51581420-chr15:51671893..51675869,118	MCF-7	breast:

No data

Variant related genes	Relation type
ENSG00000259194	Chromatin interaction
ENSG00000186417	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];0.97[CHD][hapmap];0.95[JPT][hapmap];0.94[ASN][1000 genomes]
rs16964254	0.94[ASN][1000 genomes]
rs16964258	1.00[CHB][hapmap];0.94[CHD][hapmap];0.95[JPT][hapmap];0.93[ASN][1000 genomes]
rs17647719	0.81[CHD][hapmap]
rs1902586	0.94[CHB][hapmap];0.91[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];0.94[CHD][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];1.00[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];1.00[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];0.97[CHD][hapmap];0.95[JPT][hapmap];0.94[ASN][1000 genomes]
rs936308	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
rs936306	TNFAIP8L3	cis	parietal	SCAN
rs936306	TMOD2	cis	parietal	SCAN

Chromatin state (count:17 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:51575000-51580400	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
2	chr15:51575000-51580400	Weak transcription	Rectal Mucosa Donor 31	rectum
3	chr15:51575000-51580400	Weak transcription	Sigmoid Colon	Sigmoid Colon
4	chr15:51575000-51580400	Weak transcription	NHDF-Ad	bronchial
5	chr15:51575200-51580600	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
6	chr15:51575200-51580600	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
7	chr15:51575400-51579600	Weak transcription	Brain Substantia Nigra	brain
8	chr15:51575800-51580800	Weak transcription	Adipose Nuclei	Adipose
9	chr15:51576000-51580400	Weak transcription	Rectal Mucosa Donor 29	rectum
10	chr15:51578400-51583400	Genic enhancers	Placenta	Placenta
11	chr15:51578600-51582400	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
12	chr15:51578600-51582400	Enhancers	HepG2	liver
13	chr15:51578800-51581800	Enhancers	Fetal Intestine Large	intestine
14	chr15:51578800-51582000	Enhancers	Fetal Intestine Small	intestine
15	chr15:51579400-51579600	Enhancers	Stomach Smooth Muscle	stomach
16	chr15:51579400-51579800	Enhancers	Left Ventricle	heart
17	chr15:51579400-51582000	Enhancers	Stomach Mucosa	stomach

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