Variant report

Variant	rs2172608
Chromosome Location	chr15:57874473-57874474
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr15:57862794..57866140-chr15:57871605..57875342,4	K562	blood:

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	0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10851618	0.86[AMR][1000 genomes];0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10851619	0.86[AMR][1000 genomes];0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11071335	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.94[MEX][hapmap];0.95[TSI][hapmap];0.93[AMR][1000 genomes];0.93[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	0.81[AMR][1000 genomes];0.84[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12324010	1.00[ASN][1000 genomes]
rs12324289	0.84[CEU][hapmap];0.84[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12324526	0.85[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.84[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];0.84[MEX][hapmap];1.00[ASN][1000 genomes]
rs12443389	0.86[AMR][1000 genomes];0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12443485	0.86[AMR][1000 genomes];0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13380406	0.88[AMR][1000 genomes];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13380418	0.88[AMR][1000 genomes];0.89[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	0.89[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17820515	0.84[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.94[MEX][hapmap];1.00[TSI][hapmap];0.88[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28557258	1.00[ASN][1000 genomes]
rs4774273	0.85[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.89[MEX][hapmap];0.95[TSI][hapmap];0.86[AMR][1000 genomes];0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4774274	0.85[CEU][hapmap];1.00[CHB][hapmap];0.89[MEX][hapmap];0.95[TSI][hapmap];0.86[AMR][1000 genomes];0.88[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	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4774974	1.00[ASN][1000 genomes]
rs57589057	1.00[ASN][1000 genomes]
rs58017146	0.86[AMR][1000 genomes];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs58919063	0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs61600143	0.86[AMR][1000 genomes];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7178159	1.00[CHB][hapmap];1.00[CHD][hapmap];0.84[MEX][hapmap];0.86[TSI][hapmap];0.84[AMR][1000 genomes];0.82[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72743512	0.83[AMR][1000 genomes];0.83[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72743516	0.84[AMR][1000 genomes];0.81[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	0.83[AMR][1000 genomes];0.82[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
rs2172608	PAPD7	trans	cerebellum	SCAN

Chromatin state (count:11 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:57869800-57875000	Enhancers	Fetal Intestine Small	intestine
2	chr15:57869800-57875000	Enhancers	Sigmoid Colon	Sigmoid Colon
3	chr15:57869800-57875200	Enhancers	Fetal Intestine Large	intestine
4	chr15:57870800-57874800	Enhancers	Small Intestine	intestine
5	chr15:57872200-57874600	Enhancers	Stomach Mucosa	stomach
6	chr15:57872400-57875000	Enhancers	Rectal Mucosa Donor 31	rectum
7	chr15:57872600-57874600	Enhancers	Pancreas	Pancrea
8	chr15:57872600-57875000	Enhancers	Colonic Mucosa	Colon
9	chr15:57872600-57875000	Enhancers	Rectal Mucosa Donor 29	rectum
10	chr15:57872800-57875400	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
11	chr15:57874400-57875000	Enhancers	Duodenum Mucosa	Duodenum

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