Variant report

Variant	rs230966
Chromosome Location	chr17:15207935-15207936
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 25 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:18)

rs_ID	r²[population]
rs13961	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.82[GIH][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs170742	0.97[ASN][1000 genomes]
rs170743	0.97[ASN][1000 genomes]
rs170744	0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs2305959	1.00[CEU][hapmap]
rs230893	1.00[CEU][hapmap]
rs230898	0.83[LWK][hapmap]
rs230951	0.97[ASN][1000 genomes]
rs230952	0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs230953	0.80[EUR][1000 genomes]
rs230955	0.97[ASN][1000 genomes]
rs230956	0.83[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs230957	0.90[ASN][1000 genomes]
rs230958	0.88[ASN][1000 genomes]
rs230960	0.98[ASN][1000 genomes]
rs230961	0.84[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2531950	1.00[CEU][hapmap]
rs7226363	1.00[CEU][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:3)

SNP	Gene	Cis/trans	Tissue	Source
rs230966	CDRT1	cis	parietal	SCAN
rs230966	UBB	cis	cerebellum	SCAN
rs230966	SMCR8	cis	parietal	SCAN

Chromatin state (count:17 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr17:15201800-15208200	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
2	chr17:15202000-15208000	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
3	chr17:15202000-15208800	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
4	chr17:15202000-15209400	Weak transcription	Osteobl	bone
5	chr17:15202400-15209400	Weak transcription	NHDF-Ad	bronchial
6	chr17:15205400-15213400	Enhancers	Fetal Stomach	stomach
7	chr17:15205600-15210000	Weak transcription	HSMMtube	muscle
8	chr17:15206800-15209000	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
9	chr17:15206800-15209600	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
10	chr17:15207000-15208200	Weak transcription	Rectal Smooth Muscle	rectum
11	chr17:15207200-15209000	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
12	chr17:15207400-15209400	Weak transcription	Cortex derived primary cultured neurospheres	brain
13	chr17:15207400-15209800	Enhancers	Fetal Lung	lung
14	chr17:15207400-15211800	Weak transcription	Brain Germinal Matrix	brain
15	chr17:15207600-15210400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
16	chr17:15207600-15210400	Weak transcription	Fetal Brain Male	brain
17	chr17:15207800-15210000	Enhancers	Colon Smooth Muscle	Colon

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Input of quick search could be:

dbSNP/dbVar ID: rs12345 /nsv7879
a single nucleotide as 0-based coordinates: chr1:12345
chromosomal regions: chr1:12345-34567

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