Variant report

Variant	rs8028089
Chromosome Location	chr15:73913238-73913239
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr15:73910087..73912368-chr15:73912396..73915641,4	MCF-7	breast:
2	chr15:73893850..73896268-chr15:73911342..73914138,2	MCF-7	breast:
3	chr15:73912420..73913927-chr15:73920373..73922798,2	K562	blood:
4	chr15:73910690..73914006-chr15:73922937..73927508,5	K562	blood:
5	chr15:73910665..73914600-chr15:73924026..73926567,6	MCF-7	breast:
6	chr15:73903840..73905741-chr15:73912777..73915445,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000156642	Chromatin interaction

Extended variants
information (count: 27 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:26)

rs_ID	r²[population]
rs10851863	0.89[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs11072428	0.91[CEU][hapmap];1.00[CHB][hapmap];0.93[CHD][hapmap];0.91[GIH][hapmap];1.00[JPT][hapmap];0.92[MEX][hapmap];0.93[TSI][hapmap];0.89[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs11072429	0.88[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs11072430	0.80[JPT][hapmap]
rs11072431	0.80[JPT][hapmap]
rs12148532	0.86[CEU][hapmap];0.87[CHB][hapmap];0.84[CHD][hapmap];0.91[GIH][hapmap];0.81[JPT][hapmap];0.88[MEX][hapmap];0.91[TSI][hapmap];0.83[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs12148719	0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs12185108	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.93[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.80[YRI][hapmap];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12442903	0.88[AFR][1000 genomes];0.91[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs12593246	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1383616	0.87[CEU][hapmap];0.95[CHB][hapmap];0.98[CHD][hapmap];0.91[GIH][hapmap];1.00[JPT][hapmap];0.88[MEX][hapmap];0.98[TSI][hapmap];0.82[AMR][1000 genomes];0.90[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1481088	0.82[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs1481089	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs16958079	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs3743500	0.82[AMR][1000 genomes];0.83[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs4470111	0.90[AFR][1000 genomes];0.91[AMR][1000 genomes];0.92[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs4558379	0.87[AFR][1000 genomes];0.84[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs6495069	0.94[ASW][hapmap];1.00[CEU][hapmap];0.95[CHB][hapmap];0.98[CHD][hapmap];0.93[GIH][hapmap];1.00[JPT][hapmap];0.90[LWK][hapmap];1.00[MEX][hapmap];0.81[MKK][hapmap];0.98[TSI][hapmap];0.90[YRI][hapmap];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs6495075	0.80[JPT][hapmap]
rs6495076	0.82[JPT][hapmap]
rs7169374	0.82[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs7176637	0.83[AMR][1000 genomes]
rs8023823	0.87[CEU][hapmap];0.87[CHB][hapmap];0.85[JPT][hapmap];0.83[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs8037836	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	0.86[ASN][1000 genomes]
rs9920359	0.96[CEU][hapmap];0.86[CHB][hapmap];0.88[CHD][hapmap];0.93[GIH][hapmap];0.95[JPT][hapmap];1.00[MEX][hapmap];0.95[TSI][hapmap];0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];0.85[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:1 , 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

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs8028089	FEZ1	trans	lymphoblastoid	seeQTL
rs8028089	ARIH1	cis	cerebellum	SCAN
rs8028089	LMAN1L	cis	parietal	SCAN

Chromatin state (count:102 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:73895000-73924400	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
2	chr15:73895200-73921400	Weak transcription	Fetal Thymus	thymus
3	chr15:73895200-73924200	Weak transcription	Esophagus	oesophagus
4	chr15:73895400-73922400	Weak transcription	Colonic Mucosa	Colon
5	chr15:73895800-73913600	Weak transcription	A549	lung
6	chr15:73895800-73923600	Weak transcription	Placenta Amnion	Placenta Amnion
7	chr15:73895800-73924200	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
8	chr15:73896400-73920400	Weak transcription	Primary T cells from cord blood	blood
9	chr15:73899600-73924200	Weak transcription	Gastric	stomach
10	chr15:73900400-73921800	Weak transcription	Primary B cells from cord blood	blood
11	chr15:73900400-73924000	Weak transcription	Fetal Muscle Leg	muscle
12	chr15:73901200-73915200	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
13	chr15:73901400-73916400	Weak transcription	Fetal Kidney	kidney
14	chr15:73901400-73916800	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
15	chr15:73901400-73920600	Weak transcription	Primary monocytes fromperipheralblood	blood
16	chr15:73901600-73919800	Weak transcription	Adipose Nuclei	Adipose
17	chr15:73901800-73916600	Weak transcription	Right Ventricle	heart
18	chr15:73901800-73922400	Weak transcription	Right Atrium	heart
19	chr15:73902000-73920600	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
20	chr15:73902800-73916800	Weak transcription	Ovary	ovary
21	chr15:73902800-73924400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
22	chr15:73903400-73924000	Weak transcription	Thymus	Thymus
23	chr15:73904000-73916200	Weak transcription	Fetal Stomach	stomach
24	chr15:73904200-73913800	Weak transcription	Primary T helper naive cells from peripheral blood	blood
25	chr15:73904800-73919200	Weak transcription	Pancreas	Pancrea
26	chr15:73904800-73921400	Weak transcription	K562	blood
27	chr15:73904800-73924200	Weak transcription	Lung	lung
28	chr15:73906000-73917000	Weak transcription	Monocytes-CD14+_RO01746	blood
29	chr15:73908200-73916200	Weak transcription	Brain Anterior Caudate	brain
30	chr15:73909000-73917800	Enhancers	HUES48 Cell Line	embryonic stem cell
31	chr15:73909600-73919600	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
32	chr15:73909800-73917000	Weak transcription	Muscle Satellite Cultured Cells	--
33	chr15:73910200-73918600	Weak transcription	Hela-S3	cervix
34	chr15:73910200-73922400	Weak transcription	Aorta	Aorta
35	chr15:73910400-73916000	Weak transcription	Stomach Smooth Muscle	stomach
36	chr15:73910400-73916200	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
37	chr15:73910400-73916200	Weak transcription	HMEC	breast
38	chr15:73910400-73921200	Weak transcription	NH-A	brain
39	chr15:73910400-73922200	Weak transcription	HSMM	muscle
40	chr15:73910400-73924200	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
41	chr15:73910600-73915600	Weak transcription	NHEK	skin
42	chr15:73910600-73916800	Weak transcription	NHDF-Ad	bronchial
43	chr15:73910600-73917000	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
44	chr15:73910600-73920600	Weak transcription	Osteobl	bone
45	chr15:73910600-73921200	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
46	chr15:73911000-73921600	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
47	chr15:73911400-73917000	Weak transcription	Left Ventricle	heart
48	chr15:73911400-73920800	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
49	chr15:73911800-73913600	Enhancers	Fetal Intestine Large	intestine
50	chr15:73911800-73914000	Enhancers	Pancreatic Islets	Pancreatic Islet

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