Variant report

Variant	rs17617508
Chromosome Location	chr7:16417094-16417095
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr7:16413371..16417158-chr7:16459644..16462038,3	MCF-7	breast:
2	chr7:16406566..16408387-chr7:16416040..16418438,2	K562	blood:

Variant related genes	Relation type
ENSG00000214960	Chromatin interaction

Extended variants
information (count: 30 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:20)

rs_ID	r²[population]
rs10464288	0.92[AFR][1000 genomes];0.87[AMR][1000 genomes];0.86[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs17674339	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1921840	1.00[CEU][hapmap];0.89[CHB][hapmap];0.88[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs1921843	0.84[EUR][1000 genomes]
rs1921845	0.94[CEU][hapmap];0.85[CHB][hapmap];0.86[CHD][hapmap];0.83[GIH][hapmap];0.86[JPT][hapmap];0.91[MKK][hapmap];0.91[TSI][hapmap];0.84[AMR][1000 genomes];0.88[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2389632	0.91[AMR][1000 genomes];0.95[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs2389633	1.00[AFR][1000 genomes];0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2389638	0.82[AMR][1000 genomes];0.87[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs55746209	1.00[AFR][1000 genomes];0.87[AMR][1000 genomes];0.90[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs55790136	0.98[ASN][1000 genomes]
rs55944246	1.00[AFR][1000 genomes];0.87[AMR][1000 genomes];0.87[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs56061198	0.89[AFR][1000 genomes];0.84[AMR][1000 genomes];0.87[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs56176134	1.00[AFR][1000 genomes];0.87[AMR][1000 genomes];0.87[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs56199980	1.00[AFR][1000 genomes];0.87[AMR][1000 genomes];0.90[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs59379368	1.00[AFR][1000 genomes];0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs60255112	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6461247	1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs67088819	0.94[AFR][1000 genomes];0.84[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs73071078	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7791775	1.00[CEU][hapmap];0.92[CHB][hapmap];0.86[JPT][hapmap];0.89[AFR][1000 genomes];0.82[AMR][1000 genomes];0.87[EUR][1000 genomes];0.92[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:10 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1016642	chr7:15884061-16799788	Genic enhancers Weak transcription Flanking Active TSS Active TSS Enhancers Strong transcription ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	56 gene(s)	inside rSNPs	diseases
2	esv2759514	chr7:16236162-16527390	Flanking Active TSS Enhancers Active TSS Strong transcription Weak transcription ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	21 gene(s)	inside rSNPs	diseases
3	nsv1022388	chr7:16251992-16431864	Enhancers ZNF genes & repeats Weak transcription Genic enhancers Active TSS Flanking Active TSS Strong transcription Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	14 gene(s)	inside rSNPs	diseases
4	esv2758105	chr7:16272822-16527390	Enhancers Weak transcription ZNF genes & repeats Active TSS Flanking Active TSS Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh Strong transcription Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	18 gene(s)	inside rSNPs	diseases
5	esv2757215	chr7:16346139-16458474	Weak transcription Enhancers ZNF genes & repeats Flanking Active TSS Active TSS Strong transcription Bivalent Enhancer Transcr. at gene 5' and 3' Genic enhancers Bivalent/Poised TSS	Chromatin interactive region	4 gene(s)	inside rSNPs	diseases
6	nsv508447	chr7:16360614-16446053	Enhancers Weak transcription ZNF genes & repeats Strong transcription Flanking Active TSS Bivalent Enhancer Genic enhancers Active TSS Bivalent/Poised TSS	Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
7	nsv1031019	chr7:16377519-16458474	Enhancers Weak transcription ZNF genes & repeats Strong transcription Flanking Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS Active TSS Genic enhancers	Chromatin interactive region	4 gene(s)	inside rSNPs	diseases
8	nsv1028556	chr7:16404615-16440024	Weak transcription Enhancers ZNF genes & repeats Strong transcription Bivalent/Poised TSS Active TSS Genic enhancers Flanking Active TSS	Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
9	nsv523408	chr7:16413481-16438357	Weak transcription ZNF genes & repeats Enhancers Bivalent/Poised TSS Strong transcription	Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
10	nsv1034151	chr7:16415497-16578081	ZNF genes & repeats Enhancers Flanking Active TSS Weak transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Genic enhancers Active TSS Strong transcription Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region	11 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs17617508	SOSTDC1	cis	parietal	SCAN

Chromatin state (count:9 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr7:16398000-16417400	Weak transcription	Gastric	stomach
2	chr7:16405000-16417400	Weak transcription	Right Ventricle	heart
3	chr7:16410800-16418200	Weak transcription	Primary hematopoietic stem cells	blood
4	chr7:16412600-16427000	Weak transcription	Adipose Nuclei	Adipose
5	chr7:16414400-16425400	Weak transcription	Aorta	Aorta
6	chr7:16415600-16423400	Weak transcription	Ovary	ovary
7	chr7:16416000-16417400	Weak transcription	Left Ventricle	heart
8	chr7:16416600-16417600	Enhancers	Stomach Mucosa	stomach
9	chr7:16416800-16417400	Enhancers	K562	blood

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links