Variant report

Variant	rs8037836
Chromosome Location	chr15:73859855-73859856
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	NR2F2	chr15:73859579-73859964	MCF-7	breast:	n/a	chr15:73859739-73859754
2	GATA3	chr15:73859432-73860104	MCF-7	breast:	n/a	chr15:73859723-73859730
3	GATA3	chr15:73859557-73859868	MCF-7	breast:	n/a	chr15:73859723-73859730
4	GATA3	chr15:73859510-73860000	MCF-7	breast:	n/a	chr15:73859723-73859730
5	NR2F2	chr15:73859496-73860010	MCF-7	breast:	n/a	chr15:73859739-73859754

No.	Distal block	Cell Line	Cell type
1	chr15:73856862..73860263-chr15:73923862..73927782,5	MCF-7	breast:
2	chr15:73858288..73861135-chr15:73861211..73863696,2	MCF-7	breast:
3	chr15:73859098..73862210-chr15:73922797..73926936,5	MCF-7	breast:

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-C15orf59-5	chr15:73859279-73861884	NONHSAT047148

Variant related genes	Relation type
NPTN	TF binding region
ENSG00000156642	Chromatin interaction

Extended variants
information (count: 25 )
Associated
traits (count: 3 )

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

rs_ID	r²[population]
rs10851863	0.87[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs11072428	0.91[CEU][hapmap];0.95[CHB][hapmap];0.93[CHD][hapmap];0.88[GIH][hapmap];1.00[JPT][hapmap];0.92[MEX][hapmap];0.91[TSI][hapmap];0.85[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs11072429	0.83[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs12148532	0.86[CEU][hapmap];0.83[CHB][hapmap];0.84[CHD][hapmap];0.88[GIH][hapmap];0.80[JPT][hapmap];0.88[MEX][hapmap];0.89[TSI][hapmap]
rs12148719	0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs12185108	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.98[TSI][hapmap];0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs12442903	0.84[AFR][1000 genomes];0.93[AMR][1000 genomes];0.85[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs12593246	0.86[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs1383616	0.87[CEU][hapmap];0.91[CHB][hapmap];0.98[CHD][hapmap];0.89[GIH][hapmap];1.00[JPT][hapmap];0.88[MEX][hapmap];0.95[TSI][hapmap];0.80[AMR][1000 genomes];0.86[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs1481088	0.82[AMR][1000 genomes];0.83[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs1481089	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.91[AMR][1000 genomes];0.97[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs16958079	1.00[CEU][hapmap];0.90[CHB][hapmap];1.00[JPT][hapmap];0.95[AMR][1000 genomes];0.95[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs17185294	0.81[TSI][hapmap]
rs4470111	0.91[AFR][1000 genomes];0.93[AMR][1000 genomes];0.93[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs4558379	0.83[AFR][1000 genomes];0.86[AMR][1000 genomes];0.82[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs55816897	0.82[AMR][1000 genomes]
rs6495069	0.88[ASW][hapmap];1.00[CEU][hapmap];0.90[CHB][hapmap];0.98[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.88[LWK][hapmap];1.00[MEX][hapmap];0.81[MKK][hapmap];1.00[TSI][hapmap];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs6495076	0.81[JPT][hapmap]
rs7176637	0.85[AMR][1000 genomes];0.80[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs8023823	0.87[CEU][hapmap];0.83[CHB][hapmap];0.85[JPT][hapmap]
rs8028089	0.94[ASW][hapmap];1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[CHD][hapmap];0.93[GIH][hapmap];1.00[JPT][hapmap];0.97[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];0.98[TSI][hapmap];0.86[YRI][hapmap];0.86[AFR][1000 genomes];0.98[AMR][1000 genomes];0.95[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs922687	0.94[ASN][1000 genomes]
rs9920359	0.96[CEU][hapmap];0.90[CHB][hapmap];0.88[CHD][hapmap];1.00[GIH][hapmap];0.95[JPT][hapmap];1.00[MEX][hapmap];0.98[TSI][hapmap];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:2 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1037540	chr15:73712637-73982420	Weak transcription Bivalent Enhancer Enhancers Strong transcription Flanking Active TSS Genic enhancers Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	34 gene(s)	inside rSNPs	diseases
2	nsv904344	chr15:73800519-73864831	Strong transcription Enhancers Weak transcription Genic enhancers Active TSS Flanking Active TSS Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	4 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs8037836	FEZ1	trans	lymphoblastoid	seeQTL
rs8037836	LMAN1L	cis	parietal	SCAN
rs8037836	ARIH1	cis	cerebellum	SCAN

Chromatin state (count:126 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:73837000-73860000	Weak transcription	Gastric	stomach
2	chr15:73844200-73863800	Weak transcription	Pancreatic Islets	Pancreatic Islet
3	chr15:73844800-73865200	Weak transcription	Stomach Mucosa	stomach
4	chr15:73846200-73863800	Strong transcription	Duodenum Mucosa	Duodenum
5	chr15:73846400-73863200	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
6	chr15:73847400-73862000	Strong transcription	Fetal Intestine Large	intestine
7	chr15:73847400-73866000	Strong transcription	Adipose Nuclei	Adipose
8	chr15:73847400-73893200	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
9	chr15:73847600-73865000	Strong transcription	Rectal Mucosa Donor 29	rectum
10	chr15:73847600-73865400	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
11	chr15:73847600-73865800	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
12	chr15:73847600-73866200	Strong transcription	Liver	Liver
13	chr15:73847600-73882400	Strong transcription	Placenta	Placenta
14	chr15:73848000-73860000	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
15	chr15:73848000-73860600	Weak transcription	iPS-15b Cell Line	embryonic stem cell
16	chr15:73848600-73860600	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
17	chr15:73848600-73868600	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
18	chr15:73848600-73868600	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
19	chr15:73848800-73861000	Weak transcription	Small Intestine	intestine
20	chr15:73848800-73884800	Strong transcription	Primary T helper cells fromperipheralblood	blood
21	chr15:73848800-73885000	Strong transcription	Primary B cells from cord blood	blood
22	chr15:73849400-73860400	Weak transcription	Pancreas	Pancrea
23	chr15:73850000-73868600	Strong transcription	iPS-18 Cell Line	embryonic stem cell
24	chr15:73850200-73861600	Weak transcription	Primary T killer memory cells from peripheral blood	blood
25	chr15:73850200-73884400	Strong transcription	iPS-20b Cell Line	embryonic stem cell
26	chr15:73850400-73866200	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
27	chr15:73850400-73870800	Strong transcription	Primary T cells fromperipheralblood	blood
28	chr15:73851200-73861000	Strong transcription	Fetal Muscle Trunk	muscle
29	chr15:73852200-73861200	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
30	chr15:73852200-73861600	Weak transcription	Fetal Brain Male	brain
31	chr15:73852200-73874600	Weak transcription	Fetal Heart	heart
32	chr15:73853400-73864200	Strong transcription	Primary T helper 17 cells PMA-I stimulated	--
33	chr15:73853400-73869000	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
34	chr15:73853800-73860800	Weak transcription	Fetal Kidney	kidney
35	chr15:73853800-73868600	Strong transcription	Primary T cells from cord blood	blood
36	chr15:73854000-73860000	Weak transcription	Aorta	Aorta
37	chr15:73855200-73867000	Strong transcription	GM12878-XiMat	blood
38	chr15:73855400-73869200	Strong transcription	Primary T helper naive cells fromperipheralblood	blood
39	chr15:73855800-73860200	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
40	chr15:73855800-73865000	Strong transcription	Spleen	Spleen
41	chr15:73855800-73868200	Weak transcription	Psoas Muscle	Psoas
42	chr15:73855800-73872400	Strong transcription	Fetal Stomach	stomach
43	chr15:73856200-73861600	Weak transcription	Primary T helper naive cells from peripheral blood	blood
44	chr15:73856200-73863000	Strong transcription	Fetal Intestine Small	intestine
45	chr15:73856400-73860000	Weak transcription	H9 Cell Line	embryonic stem cell
46	chr15:73856400-73860000	Weak transcription	Dnd41	blood
47	chr15:73856400-73860200	Weak transcription	Ovary	ovary
48	chr15:73856400-73878000	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
49	chr15:73856600-73860200	Weak transcription	Fetal Thymus	thymus
50	chr15:73856600-73860600	Weak transcription	Brain Germinal Matrix	brain

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