Variant report

Variant	rs8029902
Chromosome Location	chr15:93391486-93391487
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr15:93388979..93392872-chr15:93411165..93413494,3	MCF-7	breast:
2	chr15:93380616..93384575-chr15:93388777..93392228,3	MCF-7	breast:
3	chr15:93363804..93365342-chr15:93390332..93393307,2	MCF-7	breast:
4	chr15:93350402..93355574-chr15:93391373..93396356,7	K562	blood:
5	chr15:93385940..93388443-chr15:93390069..93391852,2	K562	blood:

Variant related genes	Relation type
ENSG00000258922	Chromatin interaction
ENSG00000185442	Chromatin interaction

Extended variants
information (count: 35 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:30)

rs_ID	r²[population]
rs11074108	0.91[AMR][1000 genomes];0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs11074109	0.89[AMR][1000 genomes];0.94[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs11074110	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs11074111	0.91[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs12591890	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12592319	0.95[CEU][hapmap];1.00[CHB][hapmap];0.92[JPT][hapmap];0.91[AMR][1000 genomes];0.96[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs28360722	0.91[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs28445686	0.91[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs28613292	0.84[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs28734059	0.83[AMR][1000 genomes];0.85[ASN][1000 genomes]
rs28880667	0.94[ASN][1000 genomes]
rs4408491	0.85[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs4628913	0.83[AMR][1000 genomes];0.94[ASN][1000 genomes]
rs4777740	0.95[CEU][hapmap];1.00[CHB][hapmap];0.92[JPT][hapmap];0.91[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4777741	0.91[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4777742	0.91[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4778045	0.87[AMR][1000 genomes];0.97[ASN][1000 genomes]
rs6496994	0.96[CEU][hapmap];0.92[CHB][hapmap];0.84[CHD][hapmap];1.00[GIH][hapmap];0.81[LWK][hapmap];1.00[MEX][hapmap];0.94[TSI][hapmap];0.95[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs66967198	0.88[AMR][1000 genomes]
rs7180599	0.82[AMR][1000 genomes];0.92[ASN][1000 genomes]
rs7181781	0.82[AMR][1000 genomes];0.97[ASN][1000 genomes]
rs7184028	0.90[CEU][hapmap];0.92[CHB][hapmap];0.85[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs8023522	0.91[CEU][hapmap];0.92[CHB][hapmap];0.81[CHD][hapmap];0.97[GIH][hapmap];0.95[MEX][hapmap];0.94[TSI][hapmap];0.88[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs8026478	0.88[AMR][1000 genomes];0.90[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs8027176	0.88[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs8027321	0.88[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs8028071	0.82[AMR][1000 genomes]
rs8030383	0.95[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs8031154	0.95[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs8031163	0.95[AMR][1000 genomes];0.84[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:5 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv904499	chr15:92914795-93472582	Bivalent Enhancer Flanking Active TSS Genic enhancers Strong transcription Active TSS Transcr. at gene 5' and 3' Weak transcription Enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA	163 gene(s)	inside rSNPs	diseases
2	nsv948738	chr15:93070742-93728147	Strong transcription Weak transcription Flanking Active TSS Enhancers Genic enhancers Active TSS Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	169 gene(s)	inside rSNPs	diseases
3	nsv1049490	chr15:93134405-93591660	Enhancers Genic enhancers Weak transcription Strong transcription Active TSS ZNF genes & repeats Flanking Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	151 gene(s)	inside rSNPs	diseases
4	nsv530846	chr15:93323949-94030462	Active TSS Strong transcription Flanking Active TSS Enhancers Weak transcription Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	153 gene(s)	inside rSNPs	diseases
5	nsv948881	chr15:93383740-93603608	Genic enhancers Strong transcription Weak transcription Transcr. at gene 5' and 3' Enhancers Flanking Active TSS Active TSS ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	91 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs8029902	FAM174B	cis	cerebellum	SCAN
rs8029902	C15orf58	cis	cerebellum	SCAN
rs8029902	MRPS11	cis	parietal	SCAN

Chromatin state (count:48 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:93383800-93396600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
2	chr15:93384000-93394600	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
3	chr15:93384800-93391800	Weak transcription	Placenta	Placenta
4	chr15:93386800-93393800	Enhancers	Primary B cells from peripheral blood	blood
5	chr15:93387400-93391600	Weak transcription	Spleen	Spleen
6	chr15:93388000-93393000	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
7	chr15:93388200-93392600	Enhancers	NHDF-Ad	bronchial
8	chr15:93388600-93392200	Enhancers	Primary T cells fromperipheralblood	blood
9	chr15:93388600-93393200	Enhancers	Primary neutrophils fromperipheralblood	blood
10	chr15:93388600-93393600	Enhancers	Primary T helper naive cells from peripheral blood	blood
11	chr15:93388600-93393600	Enhancers	Primary T helper cells fromperipheralblood	blood
12	chr15:93388800-93392200	Enhancers	Primary T helper naive cells fromperipheralblood	blood
13	chr15:93388800-93393600	Enhancers	Primary B cells from cord blood	blood
14	chr15:93388800-93393600	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
15	chr15:93388800-93393600	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
16	chr15:93389000-93391800	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
17	chr15:93389000-93392400	Enhancers	Primary T cells from cord blood	blood
18	chr15:93389000-93393600	Enhancers	Primary T helper cells PMA-I stimulated	--
19	chr15:93389400-93391600	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
20	chr15:93389400-93391800	Weak transcription	Lung	lung
21	chr15:93389400-93392000	Weak transcription	Primary hematopoietic stem cells short term culture	blood
22	chr15:93389400-93392200	Weak transcription	Thymus	Thymus
23	chr15:93389600-93391600	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
24	chr15:93389600-93391600	Weak transcription	Sigmoid Colon	Sigmoid Colon
25	chr15:93389600-93391800	Weak transcription	Primary hematopoietic stem cells	blood
26	chr15:93389600-93392800	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
27	chr15:93389800-93391600	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
28	chr15:93389800-93391600	Weak transcription	GM12878-XiMat	blood
29	chr15:93389800-93391800	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
30	chr15:93389800-93391800	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
31	chr15:93390000-93392000	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
32	chr15:93390400-93391600	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
33	chr15:93390400-93391600	Weak transcription	Osteobl	bone
34	chr15:93390400-93392000	Weak transcription	Rectal Mucosa Donor 29	rectum
35	chr15:93390400-93392400	Enhancers	NHLF	lung
36	chr15:93390600-93391800	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
37	chr15:93390600-93392000	Weak transcription	HepG2	liver
38	chr15:93390600-93399000	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
39	chr15:93390800-93393600	Enhancers	K562	blood
40	chr15:93391000-93393000	Enhancers	Primary monocytes fromperipheralblood	blood
41	chr15:93391200-93391600	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
42	chr15:93391200-93392200	Enhancers	HSMM	muscle
43	chr15:93391200-93392800	Enhancers	NH-A	brain
44	chr15:93391400-93391600	Enhancers	Monocytes-CD14+_RO01746	blood
45	chr15:93391400-93393400	Enhancers	Primary mononuclear cells fromperipheralblood	Blood
46	chr15:93391400-93393600	Enhancers	Primary T killer naive cells fromperipheralblood	blood
47	chr15:93391400-93393600	Enhancers	Primary T killer memory cells from peripheral blood	blood
48	chr15:93391400-93393600	Enhancers	Fetal Thymus	thymus

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