Variant report

Variant	rs17820515
Chromosome Location	chr15:57879310-57879311
allele	C/T
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	FOS	chr15:57879237-57879627	HUVEC	blood vessel:	n/a	n/a
2	BATF	chr15:57879213-57879483	GM12878	blood:	n/a	chr15:57879236-57879245
3	BHLHE40	chr15:57879191-57879484	GM12878	blood:	n/a	n/a

Variant related genes	Relation type
GCOM1	TF binding region
MYZAP	TF binding region
POLR2M	TF binding region

Extended variants
information (count: 45 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:42)

rs_ID	r²[population]
rs1009319	1.00[CHB][hapmap];1.00[ASN][1000 genomes]
rs10152310	1.00[CHB][hapmap];1.00[ASN][1000 genomes]
rs10152878	0.86[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10851618	0.98[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10851619	0.98[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11071335	0.84[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.89[MEX][hapmap];0.95[TSI][hapmap];0.87[AMR][1000 genomes];0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11852838	1.00[ASN][1000 genomes]
rs11853270	1.00[CHB][hapmap];1.00[ASN][1000 genomes]
rs11856824	1.00[CHB][hapmap];1.00[ASN][1000 genomes]
rs12323998	0.92[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12324010	1.00[ASN][1000 genomes]
rs12324289	0.91[CEU][hapmap];0.91[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12324526	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.89[MEX][hapmap];1.00[ASN][1000 genomes]
rs12442978	1.00[CHB][hapmap];1.00[ASN][1000 genomes]
rs12442987	1.00[CHB][hapmap];1.00[CHD][hapmap];0.86[GIH][hapmap];0.89[MEX][hapmap];1.00[ASN][1000 genomes]
rs12443389	0.98[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12443485	0.98[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13380406	1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13380418	1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1346125	1.00[ASN][1000 genomes]
rs16977452	1.00[CHB][hapmap]
rs16977630	1.00[CHB][hapmap]
rs17239937	0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2172608	0.88[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28557258	0.87[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs4774273	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.94[MEX][hapmap];0.95[TSI][hapmap];0.98[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4774274	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[GIH][hapmap];0.94[MEX][hapmap];0.95[TSI][hapmap];0.98[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4774281	1.00[CHB][hapmap];1.00[ASN][1000 genomes]
rs4774282	1.00[ASN][1000 genomes]
rs4774971	0.88[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4774974	0.87[AMR][1000 genomes];0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs57589057	1.00[ASN][1000 genomes]
rs58017146	0.84[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs58919063	0.87[AMR][1000 genomes];0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs61600143	0.84[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7178159	0.84[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.86[GIH][hapmap];0.89[MEX][hapmap];0.86[TSI][hapmap];0.93[AMR][1000 genomes];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72743512	0.94[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72743516	0.96[AMR][1000 genomes];0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72745565	1.00[ASN][1000 genomes]
rs7359330	1.00[CHB][hapmap];1.00[ASN][1000 genomes]
rs74016366	1.00[ASN][1000 genomes]
rs9796502	0.91[CEU][hapmap];0.94[AMR][1000 genomes];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1045611	chr15:57350965-58070807	Weak transcription Enhancers Strong transcription Genic enhancers Flanking Active TSS Active TSS ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	49 gene(s)	inside rSNPs	diseases
2	nsv1054547	chr15:57600488-57977659	Active TSS Weak transcription Enhancers Strong transcription Flanking Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	19 gene(s)	inside rSNPs	diseases
3	nsv904255	chr15:57790436-57907574	Weak transcription Enhancers Flanking Active TSS Strong transcription Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3' Active TSS Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	10 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs17820515	PAPD7	trans	cerebellum	SCAN

Chromatin state (count:34 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:57874600-57882000	Weak transcription	Pancreas	Pancrea
2	chr15:57875600-57879400	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
3	chr15:57877400-57883600	Enhancers	Primary B cells from peripheral blood	blood
4	chr15:57877600-57882400	Enhancers	Primary B cells from cord blood	blood
5	chr15:57877800-57880000	Weak transcription	Right Atrium	heart
6	chr15:57878000-57880200	Weak transcription	Left Ventricle	heart
7	chr15:57878000-57880600	Weak transcription	Fetal Heart	heart
8	chr15:57878000-57881800	Enhancers	Primary T helper naive cells fromperipheralblood	blood
9	chr15:57878200-57881000	Enhancers	Primary T helper cells fromperipheralblood	blood
10	chr15:57878400-57879400	Enhancers	Stomach Mucosa	stomach
11	chr15:57878400-57881000	Enhancers	Primary T cells from cord blood	blood
12	chr15:57878400-57881000	Enhancers	Primary T helper naive cells from peripheral blood	blood
13	chr15:57878400-57881200	Enhancers	Primary T killer memory cells from peripheral blood	blood
14	chr15:57878400-57883600	Enhancers	Primary T helper cells PMA-I stimulated	--
15	chr15:57878600-57880000	Enhancers	Primary monocytes fromperipheralblood	blood
16	chr15:57878600-57880400	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
17	chr15:57878600-57880800	Enhancers	Primary T cells fromperipheralblood	blood
18	chr15:57878600-57880800	Enhancers	Primary T regulatory cells fromperipheralblood	blood
19	chr15:57878600-57881600	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
20	chr15:57878600-57883400	Enhancers	Adipose Nuclei	Adipose
21	chr15:57878800-57879800	Weak transcription	Right Ventricle	heart
22	chr15:57878800-57880000	Enhancers	HUVEC	blood vessel
23	chr15:57878800-57881000	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
24	chr15:57878800-57881600	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
25	chr15:57878800-57882200	Weak transcription	Gastric	stomach
26	chr15:57878800-57883400	Enhancers	Rectal Mucosa Donor 31	rectum
27	chr15:57879000-57879600	Weak transcription	Lung	lung
28	chr15:57879000-57880000	Weak transcription	Duodenum Mucosa	Duodenum
29	chr15:57879000-57880000	Weak transcription	Psoas Muscle	Psoas
30	chr15:57879000-57880200	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
31	chr15:57879000-57881800	Weak transcription	Fetal Intestine Small	intestine
32	chr15:57879000-57882200	Enhancers	NHEK	skin
33	chr15:57879200-57880000	Enhancers	Primary T helper 17 cells PMA-I stimulated	--
34	chr15:57879200-57880000	Enhancers	Monocytes-CD14+_RO01746	blood

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