Variant report

Variant	rs1017967
Chromosome Location	chr3:99905803-99905804
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 24 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:21)

rs_ID	r²[population]
rs16841874	0.84[CEU][hapmap];0.82[GIH][hapmap];0.81[TSI][hapmap]
rs2130369	0.81[CEU][hapmap];0.82[TSI][hapmap]
rs2316263	1.00[ASW][hapmap];0.96[CEU][hapmap];1.00[GIH][hapmap];0.95[LWK][hapmap];0.95[MEX][hapmap];0.89[MKK][hapmap];1.00[TSI][hapmap];0.86[YRI][hapmap];0.93[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs35170554	0.84[ASN][1000 genomes]
rs3850726	0.95[CHB][hapmap];0.91[CHD][hapmap];0.84[ASN][1000 genomes]
rs6767441	0.82[TSI][hapmap]
rs6776886	0.89[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6810262	0.87[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7620267	0.81[AMR][1000 genomes]
rs7623587	0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7631174	0.93[AMR][1000 genomes];0.92[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs7632678	0.81[ASN][1000 genomes]
rs7653276	0.92[AMR][1000 genomes];0.91[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs9290003	0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs9837131	0.80[MKK][hapmap];0.82[TSI][hapmap]
rs9847283	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.95[MEX][hapmap];0.98[TSI][hapmap];0.83[YRI][hapmap];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs9849977	0.90[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs9850382	0.86[AMR][1000 genomes];0.84[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs9860514	0.85[ASN][1000 genomes]
rs9860561	0.85[ASN][1000 genomes]
rs9868170	0.93[AMR][1000 genomes];0.92[EUR][1000 genomes];0.87[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	nsv817478	chr3:99474086-99955548	Flanking Active TSS Weak transcription Enhancers Bivalent Enhancer Active TSS ZNF genes & repeats Genic enhancers Strong transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	21 gene(s)	inside rSNPs	diseases
2	nsv916476	chr3:99478229-100124625	Active TSS Weak transcription Flanking Active TSS Strong transcription Enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3' Genic enhancers Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	46 gene(s)	inside rSNPs	diseases
3	nsv591148	chr3:99774720-99905803	Weak transcription Enhancers Active TSS Strong transcription Flanking Active TSS ZNF genes & repeats Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs1017967	TMEM45A	cis	parietal	SCAN
rs1017967	C3orf26	Cis_1M	lymphoblastoid	RTeQTL
rs1017967	SENP7	cis	parietal	SCAN

Chromatin state (count:13 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:99899000-99907800	Weak transcription	Psoas Muscle	Psoas
2	chr3:99899000-99911000	Weak transcription	Aorta	Aorta
3	chr3:99903800-99906000	Enhancers	Fetal Adrenal Gland	Adrenal Gland
4	chr3:99905000-99906800	Weak transcription	Fetal Stomach	stomach
5	chr3:99905000-99907400	Weak transcription	Skeletal Muscle Female	skeletal muscle
6	chr3:99905000-99907800	Weak transcription	Left Ventricle	heart
7	chr3:99905400-99908600	Weak transcription	Placenta	Placenta
8	chr3:99905600-99906800	Weak transcription	HepG2	liver
9	chr3:99905600-99908000	Weak transcription	Skeletal Muscle Male	skeletal muscle
10	chr3:99905600-99910400	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
11	chr3:99905600-99910400	Weak transcription	Fetal Muscle Leg	muscle
12	chr3:99905800-99907800	Weak transcription	K562	blood
13	chr3:99905800-99910600	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin

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