Variant report

Variant	rs10508654
Chromosome Location	chr10:23104639-23104640
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr10:23001422..23003561-chr10:23104622..23106652,2	K562	blood:
2	chr10:23103158..23106579-chr10:23341900..23344132,3	K562	blood:
3	chr10:23104132..23107506-chr10:23342632..23345950,5	K562	blood:

Variant related genes	Relation type
ENSG00000150867	Chromatin interaction

Extended variants
information (count: 56 )
Associated
traits (count: 5 )

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

rs_ID	r²[population]
rs11013153	0.94[EUR][1000 genomes]
rs11593600	1.00[CHB][hapmap];0.94[JPT][hapmap];0.89[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];0.95[ASN][1000 genomes]
rs12571540	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12571972	0.94[EUR][1000 genomes]
rs12572450	0.90[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs12572705	0.90[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs12573183	0.93[ASN][1000 genomes]
rs16922710	0.90[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs16922713	0.90[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs16922725	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]
rs16922729	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[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];0.87[ASN][1000 genomes]
rs66625374	0.90[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs67161290	0.94[ASN][1000 genomes]
rs68141405	0.90[ASN][1000 genomes]
rs7078306	0.95[CHB][hapmap];0.94[JPT][hapmap];0.90[AMR][1000 genomes];0.94[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs7078414	0.83[EUR][1000 genomes]
rs7082819	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7083521	0.82[CHB][hapmap]
rs7085241	0.83[AFR][1000 genomes];0.93[AMR][1000 genomes];0.84[ASN][1000 genomes]
rs7090785	0.91[ASN][1000 genomes]
rs7091463	0.89[ASN][1000 genomes]
rs7094800	0.92[ASN][1000 genomes]
rs7094886	0.88[AFR][1000 genomes];0.93[AMR][1000 genomes];0.94[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs7094895	0.84[AMR][1000 genomes];0.94[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs72648289	0.85[AFR][1000 genomes];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	0.92[AFR][1000 genomes];0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs72648292	0.88[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs72648293	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs72648294	0.86[AMR][1000 genomes];0.94[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs72648295	0.89[EUR][1000 genomes]
rs73600523	0.90[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7476242	0.89[EUR][1000 genomes]
rs7903799	0.90[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7903834	0.86[AMR][1000 genomes];0.83[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs7908933	0.84[ASN][1000 genomes]
rs7912540	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7913025	1.00[EUR][1000 genomes]
rs7913783	0.91[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:9 , 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

mRNA abundance (count:5)

SNP	Gene	Cis/trans	Tissue	Source
rs10508654	GPR88	trans	brain	seeQTL
rs10508654	PENK	trans	brain	seeQTL
rs10508654	CCDC88C	trans	brain	seeQTL
rs10508654	COL5A2	trans	lymphoblastoid	seeQTL
rs10508654	DTNBP1	trans	brain	seeQTL

Chromatin state (count:19 , 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	chr10:23094800-23105200	Weak transcription	Osteobl	bone
3	chr10:23100000-23105200	Weak transcription	NHLF	lung
4	chr10:23100200-23105200	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
5	chr10:23100200-23105200	Weak transcription	Hela-S3	cervix
6	chr10:23100200-23105600	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
7	chr10:23100200-23105600	Weak transcription	HSMM	muscle
8	chr10:23100200-23114400	Weak transcription	ES-I3 Cell Line	embryonic stem cell
9	chr10:23100400-23104800	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
10	chr10:23100400-23105200	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
11	chr10:23100400-23105200	Weak transcription	NHDF-Ad	bronchial
12	chr10:23101200-23105200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
13	chr10:23103800-23104800	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
14	chr10:23104000-23105200	Enhancers	Muscle Satellite Cultured Cells	--
15	chr10:23104400-23106600	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
16	chr10:23104400-23106600	Enhancers	NH-A	brain
17	chr10:23104600-23104800	Enhancers	HSMMtube	muscle
18	chr10:23104600-23105200	Enhancers	Fetal Intestine Large	intestine
19	chr10:23104600-23105200	Enhancers	Fetal Intestine Small	intestine

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