Variant report

Variant	rs10828679
Chromosome Location	chr10:18711288-18711289
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 51 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:49)

rs_ID	r²[population]
rs10734052	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs10734054	0.86[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs10734056	0.86[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs10741057	0.98[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs10741058	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHD][hapmap];0.82[GIH][hapmap];1.00[JPT][hapmap];0.95[MEX][hapmap];1.00[TSI][hapmap];0.87[YRI][hapmap];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs10741059	0.86[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs10741060	0.86[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs10741061	0.92[CEU][hapmap];0.88[CHD][hapmap];0.82[GIH][hapmap];1.00[JPT][hapmap];0.95[MEX][hapmap];1.00[TSI][hapmap];0.86[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs10764483	1.00[CEU][hapmap];0.88[CHD][hapmap];0.82[GIH][hapmap];1.00[JPT][hapmap];0.95[MEX][hapmap];1.00[TSI][hapmap];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs10764493	0.82[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs10828623	1.00[JPT][hapmap]
rs10828653	0.83[AMR][1000 genomes]
rs11014125	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs11014185	0.91[AFR][1000 genomes];0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs11014186	0.91[AFR][1000 genomes];0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs11014196	1.00[CHB][hapmap];1.00[JPT][hapmap];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs12777508	0.90[CEU][hapmap]
rs1575835	1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[ASN][1000 genomes]
rs1575836	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.82[GIH][hapmap];1.00[JPT][hapmap];0.95[MEX][hapmap];1.00[TSI][hapmap];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs17690724	1.00[CEU][hapmap];0.92[EUR][1000 genomes]
rs1926026	1.00[CHB][hapmap];0.88[CHD][hapmap];0.91[GIH][hapmap];1.00[JPT][hapmap];0.95[MEX][hapmap];0.93[TSI][hapmap];0.87[AMR][1000 genomes];0.85[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs1998820	1.00[CHB][hapmap];0.94[TSI][hapmap]
rs2148184	0.92[CEU][hapmap]
rs2209587	0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2209588	0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs2209589	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2209590	0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs4748464	0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs4748465	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs4748468	1.00[CHB][hapmap]
rs6415973	1.00[CEU][hapmap];1.00[JPT][hapmap];0.82[YRI][hapmap];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs6415974	0.98[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs6482397	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[AMR][1000 genomes];0.93[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs6482406	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6482408	0.98[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs6482409	1.00[CEU][hapmap];1.00[JPT][hapmap];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs6482410	0.98[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs6482412	0.90[AMR][1000 genomes];0.92[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs6482437	0.87[AMR][1000 genomes]
rs7071123	0.86[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs7077248	0.92[CEU][hapmap];1.00[CHB][hapmap];0.88[CHD][hapmap];1.00[JPT][hapmap];0.90[MEX][hapmap];1.00[TSI][hapmap];0.86[AMR][1000 genomes];0.89[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs7084123	0.83[AMR][1000 genomes]
rs7095057	0.87[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs7893279	1.00[CHB][hapmap];0.94[TSI][hapmap]
rs7912753	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs7923938	1.00[CHB][hapmap];0.94[TSI][hapmap]
rs982003	1.00[CHB][hapmap];0.88[CHD][hapmap];1.00[JPT][hapmap];0.80[MEX][hapmap];0.97[ASN][1000 genomes]
rs983048	0.91[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs997264	1.00[CEU][hapmap];1.00[CHB][hapmap];0.88[CHD][hapmap];0.82[GIH][hapmap];1.00[JPT][hapmap];0.90[MEX][hapmap];1.00[TSI][hapmap];0.92[AMR][1000 genomes];0.98[EUR][1000 genomes];0.93[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:2 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv550042	chr10:18683267-18994583	ZNF genes & repeats Weak transcription Flanking Active TSS Enhancers Strong transcription Active TSS Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	16 gene(s)	inside rSNPs	diseases
2	nsv1053675	chr10:18703895-18722912	Enhancers Weak transcription Flanking Active TSS Strong transcription	Chromatin interactive region	n/a	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs10828679	ARL5B	Cis_1M	lymphoblastoid	RTeQTL
rs10828679	STAM	cis	parietal	SCAN

Chromatin state (count:12 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr10:18690200-18713000	Weak transcription	Ovary	ovary
2	chr10:18692000-18712600	Weak transcription	Cortex derived primary cultured neurospheres	brain
3	chr10:18703600-18732000	Weak transcription	Pancreas	Pancrea
4	chr10:18707800-18713000	Weak transcription	H9 Cell Line	embryonic stem cell
5	chr10:18707800-18713000	Weak transcription	Left Ventricle	heart
6	chr10:18708000-18713000	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
7	chr10:18708000-18713200	Weak transcription	HUES64 Cell Line	embryonic stem cell
8	chr10:18708200-18712200	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
9	chr10:18710400-18711600	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
10	chr10:18710800-18715200	Enhancers	Fetal Heart	heart
11	chr10:18711200-18711400	Enhancers	Stomach Smooth Muscle	stomach
12	chr10:18711200-18713000	Weak transcription	Pancreatic Islets	Pancreatic Islet

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