Variant report

Variant	rs16922725
Chromosome Location	chr10:23100287-23100288
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr10:23098595..23101084-chr2:58865453..58867756,2	MCF-7	breast:
2	chr10:23001483..23003855-chr10:23099770..23102739,2	K562	blood:

Variant related genes	Relation type
ENSG00000150867	Chromatin interaction

Extended variants
information (count: 57 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:47)

rs_ID	r²[population]
rs10508654	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];0.84[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.91[MKK][hapmap];1.00[TSI][hapmap];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs11013153	0.94[EUR][1000 genomes]
rs11593600	1.00[CHB][hapmap];0.94[JPT][hapmap];0.90[ASN][1000 genomes]
rs12266797	0.89[EUR][1000 genomes]
rs12267652	0.89[EUR][1000 genomes]
rs12571255	0.90[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12571540	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12571972	0.94[EUR][1000 genomes]
rs12572450	0.90[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12572705	0.90[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12573183	0.94[ASN][1000 genomes]
rs16922710	0.90[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs16922713	0.90[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs16922729	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs16922749	0.94[EUR][1000 genomes]
rs16922762	0.89[EUR][1000 genomes]
rs16922768	0.89[EUR][1000 genomes]
rs1934779	0.89[EUR][1000 genomes]
rs34490324	0.86[AMR][1000 genomes];0.88[ASN][1000 genomes]
rs66625374	0.90[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs67161290	0.94[ASN][1000 genomes]
rs68141405	0.91[ASN][1000 genomes]
rs7078306	0.95[CHB][hapmap];0.94[JPT][hapmap];0.90[AMR][1000 genomes];0.94[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs7078414	0.83[EUR][1000 genomes]
rs7082819	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7083521	0.82[CHB][hapmap]
rs7085241	0.93[AMR][1000 genomes];0.83[ASN][1000 genomes]
rs7090785	0.92[ASN][1000 genomes]
rs7091463	0.88[ASN][1000 genomes]
rs7094800	0.93[ASN][1000 genomes]
rs7094886	0.93[AMR][1000 genomes];0.94[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7094895	0.84[AFR][1000 genomes];0.84[AMR][1000 genomes];0.94[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs72648289	0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs72648290	0.89[AMR][1000 genomes];0.94[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs72648291	0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs72648292	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs72648293	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72648294	0.86[AMR][1000 genomes];0.94[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs72648295	0.89[EUR][1000 genomes]
rs73600523	0.90[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7476242	0.89[EUR][1000 genomes]
rs7903799	0.90[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7903834	0.86[AMR][1000 genomes];0.83[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs7908933	0.85[ASN][1000 genomes]
rs7912540	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7913025	1.00[EUR][1000 genomes]
rs7913783	0.92[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:10 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv894960	chr10:23049139-23113841	Enhancers Weak transcription Flanking Active TSS Bivalent Enhancer Active TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region	2 gene(s)	inside rSNPs	diseases
2	nsv894961	chr10:23049139-23128475	Weak transcription Enhancers Flanking Active TSS Active TSS Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region	2 gene(s)	inside rSNPs	diseases
3	nsv466833	chr10:23050683-23110797	Weak transcription Enhancers Flanking Active TSS Active TSS Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region	2 gene(s)	inside rSNPs	diseases
4	nsv894962	chr10:23050683-23113841	Enhancers Weak transcription Flanking Active TSS Active TSS Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region	2 gene(s)	inside rSNPs	diseases
5	nsv894963	chr10:23050683-23121820	Enhancers Flanking Active TSS Weak transcription Active TSS Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region	2 gene(s)	inside rSNPs	diseases
6	nsv894964	chr10:23050683-23128475	Weak transcription Enhancers Flanking Active TSS Active TSS Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region	2 gene(s)	inside rSNPs	diseases
7	nsv894965	chr10:23071128-23113841	Enhancers Weak transcription Flanking Active TSS Bivalent Enhancer Active TSS	TF binding region CpG island Chromatin interactive region	2 gene(s)	inside rSNPs	diseases
8	esv2764013	chr10:23087298-23239345	Enhancers Weak transcription Active TSS Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region	3 gene(s)	inside rSNPs	diseases
9	nsv894966	chr10:23090535-23202522	Enhancers Weak transcription Flanking Active TSS Active TSS ZNF genes & repeats Bivalent Enhancer	Chromatin interactive region	2 gene(s)	inside rSNPs	diseases
10	esv275133	chr10:23098092-23100287	Weak transcription Enhancers Bivalent Enhancer Flanking Active TSS Active TSS	Chromatin interactive region	1 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs16922725	PENK	trans	brain	seeQTL
rs16922725	GPR88	trans	brain	seeQTL
rs16922725	COL5A2	trans	lymphoblastoid	seeQTL

Chromatin state (count:23 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr10:23093000-23105200	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
2	chr10:23094800-23104400	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
3	chr10:23094800-23105200	Weak transcription	Osteobl	bone
4	chr10:23099400-23100400	Enhancers	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
5	chr10:23099400-23100400	Enhancers	HUES48 Cell Line	embryonic stem cell
6	chr10:23099400-23100400	Enhancers	HUES64 Cell Line	embryonic stem cell
7	chr10:23099400-23100400	Enhancers	iPS-15b Cell Line	embryonic stem cell
8	chr10:23099600-23100400	Enhancers	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
9	chr10:23099600-23100400	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
10	chr10:23099600-23100400	Bivalent Enhancer	ES-UCSF4 Cell Line	embryonic stem cell
11	chr10:23099600-23100400	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
12	chr10:23099600-23100400	Enhancers	NHDF-Ad	bronchial
13	chr10:23099800-23100400	Enhancers	H1 Cell Line	embryonic stem cell
14	chr10:23099800-23100400	Enhancers	H9 Cell Line	embryonic stem cell
15	chr10:23100000-23100400	Enhancers	iPS-18 Cell Line	embryonic stem cell
16	chr10:23100000-23105200	Weak transcription	NHLF	lung
17	chr10:23100200-23100400	Enhancers	iPS-20b Cell Line	embryonic stem cell
18	chr10:23100200-23104400	Weak transcription	NH-A	brain
19	chr10:23100200-23105200	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
20	chr10:23100200-23105200	Weak transcription	Hela-S3	cervix
21	chr10:23100200-23105600	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
22	chr10:23100200-23105600	Weak transcription	HSMM	muscle
23	chr10:23100200-23114400	Weak transcription	ES-I3 Cell Line	embryonic stem cell

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