Variant report

Variant	rs230967
Chromosome Location	chr17:15209659-15209660
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 17 )
Associated
traits (count: 6 )

rSNPs within LD-proxies of this variant (count:10)

rs_ID	r²[population]
rs2159289	0.92[CEU][hapmap]
rs230894	0.96[CEU][hapmap];0.98[GIH][hapmap];0.95[TSI][hapmap];0.83[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs230895	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs230896	0.98[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs230897	0.96[CEU][hapmap];0.98[GIH][hapmap];0.95[TSI][hapmap];0.81[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs230898	0.84[ASW][hapmap];0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.84[LWK][hapmap];1.00[MEX][hapmap];0.90[MKK][hapmap];1.00[TSI][hapmap];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs230954	0.92[AMR][1000 genomes];0.99[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs230963	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs230964	0.83[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs230968	0.81[AMR][1000 genomes];0.98[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:7 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1066329	chr17:14983674-15294071	Weak transcription Enhancers Flanking Active TSS Genic enhancers Bivalent Enhancer Active TSS Strong transcription Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA	22 gene(s)	inside rSNPs	diseases
2	nsv543212	chr17:14983674-15294071	Active TSS Genic enhancers Enhancers Weak transcription Strong transcription Transcr. at gene 5' and 3' Flanking Active TSS Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA	22 gene(s)	inside rSNPs	diseases
3	nsv492304	chr17:15043353-15611753	Active TSS Enhancers Weak transcription Flanking Active TSS Bivalent/Poised TSS Strong transcription Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	58 gene(s)	inside rSNPs	diseases
4	nsv916652	chr17:15093600-15856310	Strong transcription Weak transcription Enhancers Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3' Genic enhancers Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	73 gene(s)	inside rSNPs	diseases
5	nsv427990	chr17:15154329-15434020	Flanking Active TSS Enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Strong transcription Active TSS Weak transcription Transcr. at gene 5' and 3' Genic enhancers Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	31 gene(s)	inside rSNPs	diseases
6	nsv907703	chr17:15199907-15370701	Enhancers Flanking Active TSS Weak transcription Active TSS Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats Genic enhancers Strong transcription Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	10 gene(s)	inside rSNPs	diseases
7	nsv949172	chr17:15206970-15416808	Active TSS Flanking Active TSS Enhancers Weak transcription Strong transcription Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	14 gene(s)	inside rSNPs	diseases

mRNA abundance (count:6)

SNP	Gene	Cis/trans	Tissue	Source
rs230967	RAI1	cis	cerebellum	SCAN
rs230967	CENPV	cis	parietal	SCAN
rs230967	TEKT3	cis	uninvolved skin	skin_eQTL
rs230967	TEKT3	cis	Adipose Subcutaneous	GTEx
rs230967	PIGL	cis	parietal	SCAN
rs230967	DMRTB1	trans	parietal	SCAN

Chromatin state (count:33 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr17:15205400-15213400	Enhancers	Fetal Stomach	stomach
2	chr17:15205600-15210000	Weak transcription	HSMMtube	muscle
3	chr17:15207400-15209800	Enhancers	Fetal Lung	lung
4	chr17:15207400-15211800	Weak transcription	Brain Germinal Matrix	brain
5	chr17:15207600-15210400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
6	chr17:15207600-15210400	Weak transcription	Fetal Brain Male	brain
7	chr17:15207800-15210000	Enhancers	Colon Smooth Muscle	Colon
8	chr17:15208200-15210800	Enhancers	Fetal Muscle Leg	muscle
9	chr17:15208200-15211600	Enhancers	Rectal Smooth Muscle	rectum
10	chr17:15208400-15209800	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
11	chr17:15208600-15210000	Weak transcription	Placenta	Placenta
12	chr17:15209000-15210200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
13	chr17:15209000-15210200	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
14	chr17:15209000-15210600	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
15	chr17:15209000-15211800	Weak transcription	Fetal Muscle Trunk	muscle
16	chr17:15209000-15213400	Weak transcription	Stomach Smooth Muscle	stomach
17	chr17:15209200-15210200	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
18	chr17:15209400-15209800	Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
19	chr17:15209400-15210000	Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
20	chr17:15209400-15210000	Active TSS	Ovary	ovary
21	chr17:15209400-15210400	Flanking Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
22	chr17:15209400-15210400	Enhancers	Cortex derived primary cultured neurospheres	brain
23	chr17:15209600-15209800	Enhancers	Duodenum Smooth Muscle	Duodenum
24	chr17:15209600-15210000	Enhancers	HSMM	muscle
25	chr17:15209600-15210000	Active TSS	NHLF	lung
26	chr17:15209600-15210200	Flanking Active TSS	Muscle Satellite Cultured Cells	--
27	chr17:15209600-15210200	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
28	chr17:15209600-15210200	Active TSS	Right Atrium	heart
29	chr17:15209600-15210200	Flanking Active TSS	NHDF-Ad	bronchial
30	chr17:15209600-15210400	Flanking Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
31	chr17:15209600-15210400	Active TSS	Adipose Nuclei	Adipose
32	chr17:15209600-15210400	Enhancers	NH-A	brain
33	chr17:15209600-15210400	Flanking Active TSS	Osteobl	bone

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