Variant report

Variant	rs230894
Chromosome Location	chr17:15211652-15211653
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 18 )
Associated
traits (count: 6 )

rSNPs within LD-proxies of this variant (count:11)

rs_ID	r²[population]
rs2159289	0.96[CEU][hapmap]
rs230895	1.00[CEU][hapmap];0.82[AFR][1000 genomes];0.89[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs230896	0.82[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs230897	0.89[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.95[LWK][hapmap];0.91[MEX][hapmap];0.97[MKK][hapmap];1.00[TSI][hapmap];0.90[YRI][hapmap];0.94[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs230898	1.00[CEU][hapmap];0.98[GIH][hapmap];0.95[TSI][hapmap];0.82[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs230954	0.97[EUR][1000 genomes]
rs230963	0.83[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs230964	0.83[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs230967	0.96[CEU][hapmap];0.98[GIH][hapmap];0.95[TSI][hapmap];0.83[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs230968	0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7209263	0.83[YRI][hapmap]

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
rs230894	CENPV	cis	parietal	SCAN
rs230894	DMRTB1	trans	parietal	SCAN
rs230894	TEKT3	cis	uninvolved skin	skin_eQTL
rs230894	TEKT3	cis	Adipose Subcutaneous	GTEx
rs230894	PIGL	cis	parietal	SCAN
rs230894	RAI1	cis	cerebellum	SCAN

Chromatin state (count:21 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr17:15205400-15213400	Enhancers	Fetal Stomach	stomach
2	chr17:15207400-15211800	Weak transcription	Brain Germinal Matrix	brain
3	chr17:15209000-15211800	Weak transcription	Fetal Muscle Trunk	muscle
4	chr17:15209000-15213400	Weak transcription	Stomach Smooth Muscle	stomach
5	chr17:15209800-15213800	Enhancers	Skeletal Muscle Female	skeletal muscle
6	chr17:15210200-15212000	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
7	chr17:15210200-15212000	Enhancers	Duodenum Smooth Muscle	Duodenum
8	chr17:15210200-15213800	Enhancers	Skeletal Muscle Male	skeletal muscle
9	chr17:15210400-15211800	Active TSS	Fetal Brain Male	brain
10	chr17:15210400-15215400	Weak transcription	Breast Myoepithelial Primary Cells	Breast
11	chr17:15210400-15215600	Weak transcription	Cortex derived primary cultured neurospheres	brain
12	chr17:15210400-15216800	Weak transcription	Ovary	ovary
13	chr17:15210600-15212000	Weak transcription	Spleen	Spleen
14	chr17:15210600-15215800	Weak transcription	Fetal Intestine Small	intestine
15	chr17:15210800-15212200	Weak transcription	Fetal Muscle Leg	muscle
16	chr17:15211000-15213800	Enhancers	Colon Smooth Muscle	Colon
17	chr17:15211200-15212200	Weak transcription	Placenta	Placenta
18	chr17:15211200-15213000	Weak transcription	Fetal Kidney	kidney
19	chr17:15211400-15211800	Flanking Active TSS	Fetal Lung	lung
20	chr17:15211400-15211800	Weak transcription	Psoas Muscle	Psoas
21	chr17:15211600-15213200	Weak transcription	Rectal Smooth Muscle	rectum

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