Variant report

Variant	rs12898704
Chromosome Location	chr15:74260983-74260984
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 36 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:32)

rs_ID	r²[population]
rs10152126	0.89[AFR][1000 genomes];0.93[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs10152898	0.86[AMR][1000 genomes];0.97[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs10152975	0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs1078555	1.00[CHB][hapmap];1.00[JPT][hapmap];0.83[ASN][1000 genomes]
rs11072453	0.90[CEU][hapmap];0.90[CHB][hapmap];1.00[YRI][hapmap];0.93[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs11072455	0.86[AFR][1000 genomes];0.89[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs11072456	1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs11072457	0.81[AMR][1000 genomes];0.94[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs11072468	0.83[CHB][hapmap]
rs11630778	0.89[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs11636435	1.00[CEU][hapmap];0.90[CHB][hapmap];0.83[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs11637420	0.88[ASN][1000 genomes]
rs11854876	0.90[CEU][hapmap];0.90[CHB][hapmap];1.00[GIH][hapmap];1.00[LWK][hapmap];0.88[MEX][hapmap];0.80[MKK][hapmap];0.93[TSI][hapmap];1.00[YRI][hapmap];0.89[AFR][1000 genomes];0.93[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs11858082	0.90[CEU][hapmap];0.90[CHB][hapmap];0.86[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs11858669	0.81[ASN][1000 genomes]
rs12050565	0.94[EUR][1000 genomes]
rs12102019	0.90[CEU][hapmap];0.90[CHB][hapmap];0.95[EUR][1000 genomes]
rs12438442	0.85[YRI][hapmap]
rs12901885	0.88[ASN][1000 genomes]
rs12906079	0.95[AFR][1000 genomes];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs12907105	0.90[CEU][hapmap];0.90[CHB][hapmap];0.83[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs12907194	1.00[AFR][1000 genomes];0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs12907609	1.00[AFR][1000 genomes];0.80[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12913399	0.90[CHB][hapmap];1.00[YRI][hapmap]
rs12917449	0.90[CHB][hapmap];0.93[GIH][hapmap];1.00[JPT][hapmap];0.81[ASN][1000 genomes]
rs1550434	1.00[CHB][hapmap];1.00[JPT][hapmap];0.83[ASN][1000 genomes]
rs28405144	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28642047	0.86[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs34080912	0.92[AFR][1000 genomes];0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs3816197	0.83[CHB][hapmap]
rs7171694	0.83[CHB][hapmap]
rs9630437	0.97[AFR][1000 genomes];0.86[AMR][1000 genomes];0.94[EUR][1000 genomes];0.93[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv2758387	chr15:74215114-74464916	Enhancers Flanking Active TSS Bivalent/Poised TSS Weak transcription Strong transcription Active TSS Flanking Bivalent TSS/Enh Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	32 gene(s)	inside rSNPs	diseases
2	esv2760040	chr15:74215114-74464916	Weak transcription Enhancers Strong transcription Flanking Bivalent TSS/Enh Active TSS Flanking Active TSS Bivalent Enhancer Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	32 gene(s)	inside rSNPs	diseases
3	nsv428308	chr15:74215114-74464916	Transcr. at gene 5' and 3' Enhancers Weak transcription Bivalent Enhancer Bivalent/Poised TSS Strong transcription Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	32 gene(s)	inside rSNPs	diseases
4	nsv833052	chr15:74250378-74377150	Genic enhancers Enhancers Transcr. at gene 5' and 3' Strong transcription Weak transcription Flanking Active TSS Bivalent Enhancer Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	14 gene(s)	inside rSNPs	diseases

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs12898704	CYP11A1	cis	cerebellum	SCAN
rs12898704	UBL7	cis	cerebellum	SCAN
rs12898704	PML	cis	parietal	SCAN
rs12898704	STOML1	cis	cerebellum	SCAN

Chromatin state (count:44 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:74257800-74264400	Weak transcription	Placenta	Placenta
2	chr15:74257800-74265200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
3	chr15:74257800-74265200	Weak transcription	Gastric	stomach
4	chr15:74257800-74265200	Weak transcription	Right Atrium	heart
5	chr15:74258000-74265200	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
6	chr15:74258400-74261800	Weak transcription	Hela-S3	cervix
7	chr15:74258400-74265000	Weak transcription	Fetal Stomach	stomach
8	chr15:74258600-74261000	Weak transcription	H1 Cell Line	embryonic stem cell
9	chr15:74258600-74261800	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
10	chr15:74258600-74264800	Weak transcription	iPS-15b Cell Line	embryonic stem cell
11	chr15:74258600-74265000	Weak transcription	A549	lung
12	chr15:74259000-74265200	Weak transcription	HUES64 Cell Line	embryonic stem cell
13	chr15:74259200-74261000	Weak transcription	iPS-20b Cell Line	embryonic stem cell
14	chr15:74259200-74261600	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
15	chr15:74259200-74265000	Weak transcription	HUES48 Cell Line	embryonic stem cell
16	chr15:74259200-74265000	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
17	chr15:74259200-74265000	Weak transcription	Muscle Satellite Cultured Cells	--
18	chr15:74259200-74265200	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
19	chr15:74259400-74261600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
20	chr15:74259400-74261800	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
21	chr15:74259400-74261800	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
22	chr15:74259400-74264400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
23	chr15:74259400-74264800	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
24	chr15:74259400-74264800	Weak transcription	HMEC	breast
25	chr15:74259400-74265000	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
26	chr15:74259400-74265000	Weak transcription	NHEK	skin
27	chr15:74259400-74265200	Weak transcription	Primary hematopoietic stem cells short term culture	blood
28	chr15:74259600-74265000	Weak transcription	Primary T helper cells PMA-I stimulated	--
29	chr15:74259600-74265000	Weak transcription	Primary T killer memory cells from peripheral blood	blood
30	chr15:74259600-74265200	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
31	chr15:74259600-74265400	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
32	chr15:74259800-74261000	Weak transcription	Thymus	Thymus
33	chr15:74259800-74265000	Weak transcription	Primary T helper naive cells from peripheral blood	blood
34	chr15:74259800-74265000	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
35	chr15:74259800-74265200	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
36	chr15:74260000-74265200	Weak transcription	GM12878-XiMat	blood
37	chr15:74260600-74261000	Weak transcription	H9 Cell Line	embryonic stem cell
38	chr15:74260600-74261000	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
39	chr15:74260600-74261200	Enhancers	iPS-18 Cell Line	embryonic stem cell
40	chr15:74260600-74261400	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
41	chr15:74260600-74262800	Enhancers	HUVEC	blood vessel
42	chr15:74260600-74265200	Weak transcription	Dnd41	blood
43	chr15:74260800-74261400	Enhancers	ES-I3 Cell Line	embryonic stem cell
44	chr15:74260800-74261600	Weak transcription	Fetal Thymus	thymus

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