Variant report

Variant	rs17283717
Chromosome Location	chr7:12620804-12620805
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 51 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:43)

rs_ID	r²[population]
rs1034856	0.85[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.88[GIH][hapmap];0.94[JPT][hapmap];0.86[MEX][hapmap];0.95[MKK][hapmap];0.88[TSI][hapmap];0.87[YRI][hapmap];0.94[AMR][1000 genomes];0.85[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1118998	0.86[AMR][1000 genomes];0.84[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs11558844	0.89[AMR][1000 genomes];0.87[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs11973033	0.81[AMR][1000 genomes];0.83[ASN][1000 genomes]
rs17283696	0.96[CEU][hapmap];0.83[AMR][1000 genomes]
rs17355921	0.93[AMR][1000 genomes];0.87[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2240572	0.82[JPT][hapmap];0.82[ASN][1000 genomes]
rs2240574	0.88[JPT][hapmap];0.83[ASN][1000 genomes]
rs3735222	0.84[CHD][hapmap];0.88[JPT][hapmap];0.82[MEX][hapmap];0.81[AMR][1000 genomes];0.83[ASN][1000 genomes]
rs3735223	0.84[CHD][hapmap];0.88[JPT][hapmap];0.81[AMR][1000 genomes];0.83[ASN][1000 genomes]
rs41356146	0.88[JPT][hapmap];0.81[AMR][1000 genomes];0.82[ASN][1000 genomes]
rs41379149	0.84[CHD][hapmap];0.88[JPT][hapmap];0.83[ASN][1000 genomes]
rs4458754	0.85[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.88[GIH][hapmap];0.88[JPT][hapmap];0.86[MEX][hapmap];0.88[MKK][hapmap];0.88[TSI][hapmap];0.87[YRI][hapmap];0.94[AMR][1000 genomes];0.85[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs55682719	0.82[ASN][1000 genomes]
rs55829483	0.94[AMR][1000 genomes];0.86[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs55999874	0.83[ASN][1000 genomes]
rs56085455	0.92[AFR][1000 genomes];0.94[AMR][1000 genomes];0.84[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs56131067	0.91[AMR][1000 genomes];0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs56274604	0.82[ASN][1000 genomes]
rs56760264	0.81[AMR][1000 genomes];0.82[ASN][1000 genomes]
rs57778115	0.93[AFR][1000 genomes];0.94[AMR][1000 genomes];0.84[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs6460964	0.81[AMR][1000 genomes]
rs6460965	0.83[CHB][hapmap];0.82[ASN][1000 genomes]
rs6954111	0.82[CHB][hapmap];0.86[JPT][hapmap];0.82[ASN][1000 genomes]
rs6961909	0.86[AMR][1000 genomes]
rs6965970	0.88[JPT][hapmap];0.81[AMR][1000 genomes];0.82[ASN][1000 genomes]
rs6967031	0.83[CHB][hapmap];0.90[CHD][hapmap];0.94[JPT][hapmap];0.94[ASN][1000 genomes]
rs6972418	0.83[ASN][1000 genomes]
rs73060662	0.87[AMR][1000 genomes];0.84[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs73060664	0.87[AMR][1000 genomes];0.84[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs73060678	0.82[ASN][1000 genomes]
rs73060679	0.91[AMR][1000 genomes];0.84[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs73060680	0.91[AMR][1000 genomes];0.84[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs73060684	0.83[ASN][1000 genomes]
rs73060686	0.83[ASN][1000 genomes]
rs73062610	0.93[AFR][1000 genomes];0.94[AMR][1000 genomes];0.84[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs73062611	0.93[AMR][1000 genomes];0.84[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs73062639	0.81[AFR][1000 genomes];0.93[AMR][1000 genomes];0.87[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7782451	0.85[CEU][hapmap];1.00[CHB][hapmap];0.94[JPT][hapmap];0.87[AMR][1000 genomes];0.84[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7799976	0.83[AMR][1000 genomes];0.82[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7803810	0.84[CHD][hapmap];0.88[JPT][hapmap];0.82[MEX][hapmap];0.81[AMR][1000 genomes];0.83[ASN][1000 genomes]
rs7804260	0.85[CEU][hapmap];1.00[CHB][hapmap];0.96[CHD][hapmap];0.93[JPT][hapmap];0.86[TSI][hapmap];0.87[AMR][1000 genomes];0.84[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7811582	0.88[JPT][hapmap];0.83[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:8 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv534432	chr7:12148960-12693032	Enhancers Weak transcription Active TSS Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS Strong transcription Flanking Active TSS Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	23 gene(s)	inside rSNPs	diseases
2	nsv1024554	chr7:12214722-12967418	Active TSS Flanking Active TSS ZNF genes & repeats Weak transcription Enhancers Strong transcription Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Genic enhancers Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	58 gene(s)	inside rSNPs	diseases
3	nsv538735	chr7:12214722-12967418	Bivalent/Poised TSS Enhancers Weak transcription Active TSS Flanking Active TSS Bivalent Enhancer Strong transcription Genic enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	58 gene(s)	inside rSNPs	diseases
4	nsv1021371	chr7:12530491-12710429	Bivalent Enhancer Weak transcription Enhancers Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Active TSS Flanking Active TSS ZNF genes & repeats Strong transcription Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases
5	nsv1017577	chr7:12530491-12722947	Weak transcription Bivalent Enhancer Enhancers Flanking Bivalent TSS/Enh Flanking Active TSS Bivalent/Poised TSS Genic enhancers Active TSS Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases
6	nsv1030764	chr7:12532287-12710429	Flanking Bivalent TSS/Enh Bivalent/Poised TSS Enhancers Weak transcription Flanking Active TSS Active TSS Strong transcription Bivalent Enhancer Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases
7	nsv1018053	chr7:12580554-12632996	Enhancers Flanking Active TSS Bivalent Enhancer Weak transcription Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS Genic enhancers ZNF genes & repeats Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
8	nsv1020242	chr7:12605593-12641202	Flanking Bivalent TSS/Enh Bivalent/Poised TSS Weak transcription Active TSS Bivalent Enhancer Enhancers Flanking Active TSS Transcr. at gene 5' and 3' Genic enhancers ZNF genes & repeats Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs17283717	SOSTDC1	cis	cerebellum	SCAN
rs17283717	ZC3H15	trans	parietal	SCAN
rs17283717	SCIN	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:19 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr7:12611800-12637600	Weak transcription	Colonic Mucosa	Colon
2	chr7:12612000-12622000	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
3	chr7:12613200-12624200	Weak transcription	Adipose Nuclei	Adipose
4	chr7:12613400-12622000	Weak transcription	Fetal Kidney	kidney
5	chr7:12613400-12623000	Weak transcription	Rectal Mucosa Donor 29	rectum
6	chr7:12613800-12621600	Weak transcription	Rectal Mucosa Donor 31	rectum
7	chr7:12617400-12623000	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
8	chr7:12617600-12623000	Weak transcription	Gastric	stomach
9	chr7:12619800-12630400	Weak transcription	Esophagus	oesophagus
10	chr7:12620200-12622000	Enhancers	Fetal Heart	heart
11	chr7:12620200-12622600	Enhancers	K562	blood
12	chr7:12620200-12623400	Enhancers	Placenta	Placenta
13	chr7:12620600-12621200	Enhancers	Placenta Amnion	Placenta Amnion
14	chr7:12620600-12622600	Weak transcription	NHDF-Ad	bronchial
15	chr7:12620600-12624400	Enhancers	Monocytes-CD14+_RO01746	blood
16	chr7:12620600-12626600	Enhancers	Primary monocytes fromperipheralblood	blood
17	chr7:12620800-12623800	Weak transcription	Small Intestine	intestine
18	chr7:12620800-12624600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
19	chr7:12620800-12625800	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived

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