Variant report

Variant	rs4656718
Chromosome Location	chr1:169753458-169753459
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr1:169751349..169757764-chr1:169760418..169766538,11	K562	blood:
2	chr1:169750643..169754945-chr1:169761592..169765030,6	MCF-7	breast:
3	chr1:169751762..169754671-chr1:169756355..169758348,3	K562	blood:

Variant related genes	Relation type
ENSG00000171806	Chromatin interaction
ENSG00000000460	Chromatin interaction

Extended variants
information (count: 43 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:42)

rs_ID	r²[population]
rs11577641	0.89[ASW][hapmap]
rs11579102	0.89[ASW][hapmap]
rs11588380	0.80[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs11590604	0.88[ASW][hapmap]
rs12072966	1.00[CEU][hapmap];0.90[CHB][hapmap];0.90[JPT][hapmap]
rs12076368	0.84[CHB][hapmap]
rs12087033	1.00[CEU][hapmap];0.90[CHB][hapmap];0.90[JPT][hapmap]
rs16862661	0.81[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs16862672	0.86[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs16862705	0.81[AFR][1000 genomes]
rs1883229	0.84[CHB][hapmap]
rs2205849	0.84[CHB][hapmap]
rs2298899	1.00[CEU][hapmap];0.90[CHB][hapmap];0.90[JPT][hapmap]
rs2420510	0.89[ASW][hapmap]
rs2420511	0.89[ASW][hapmap]
rs3753312	1.00[ASW][hapmap]
rs3766138	0.89[ASW][hapmap]
rs3766145	0.89[ASW][hapmap]
rs3766150	0.89[ASW][hapmap]
rs3817859	0.89[ASW][hapmap]
rs3917405	0.87[ASN][1000 genomes]
rs3917428	0.87[CEU][hapmap];0.90[CHB][hapmap];0.85[CHD][hapmap];0.85[GIH][hapmap];0.90[JPT][hapmap];0.83[ASN][1000 genomes]
rs3917430	0.84[CHB][hapmap]
rs3917432	0.87[CEU][hapmap];0.90[CHB][hapmap];0.90[JPT][hapmap];0.84[ASN][1000 genomes]
rs4656726	0.89[ASW][hapmap]
rs4987298	0.84[CHB][hapmap]
rs4987301	1.00[CEU][hapmap];0.90[CHB][hapmap];0.85[CHD][hapmap];0.92[GIH][hapmap];0.90[JPT][hapmap];0.82[MEX][hapmap];0.87[TSI][hapmap]
rs4987306	1.00[CEU][hapmap];0.90[CHB][hapmap];0.90[JPT][hapmap]
rs4987314	1.00[CEU][hapmap];0.90[CHB][hapmap];0.85[CHD][hapmap];0.92[GIH][hapmap];0.90[JPT][hapmap];0.82[MEX][hapmap];0.87[TSI][hapmap]
rs4987320	1.00[CEU][hapmap];0.90[CHB][hapmap];0.90[JPT][hapmap]
rs4987322	1.00[CEU][hapmap];0.90[CHB][hapmap];0.90[JPT][hapmap]
rs4987328	1.00[CEU][hapmap];0.90[CHB][hapmap];0.85[CHD][hapmap];0.92[GIH][hapmap];0.90[JPT][hapmap];0.82[MEX][hapmap];0.86[TSI][hapmap]
rs5356	1.00[CEU][hapmap];0.80[CHB][hapmap];0.81[CHD][hapmap];0.92[GIH][hapmap];0.90[JPT][hapmap];0.82[MEX][hapmap];0.87[TSI][hapmap];0.80[ASN][1000 genomes]
rs5359	0.84[CHB][hapmap]
rs5368	1.00[CEU][hapmap];1.00[CHB][hapmap];0.93[CHD][hapmap];0.92[GIH][hapmap];0.90[JPT][hapmap];0.82[MEX][hapmap];0.83[TSI][hapmap];0.87[ASN][1000 genomes]
rs57793783	0.86[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs61807818	0.82[AFR][1000 genomes]
rs7418242	1.00[CEU][hapmap];0.90[CHB][hapmap];0.90[JPT][hapmap]
rs7523520	0.83[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs964555	1.00[CEU][hapmap];0.90[CHB][hapmap];0.85[CHD][hapmap];0.92[GIH][hapmap];0.90[JPT][hapmap];0.82[MEX][hapmap];0.87[TSI][hapmap]
rs964556	1.00[CEU][hapmap];0.90[CHB][hapmap];0.85[CHD][hapmap];0.92[GIH][hapmap];0.90[JPT][hapmap];0.82[MEX][hapmap];0.87[TSI][hapmap]
rs964557	1.00[CEU][hapmap];0.90[CHB][hapmap];0.85[CHD][hapmap];0.92[GIH][hapmap];0.90[JPT][hapmap];0.82[MEX][hapmap];0.87[TSI][hapmap]

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

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv3451367	chr1:169630075-169976964	Strong transcription Flanking Active TSS Genic enhancers Enhancers Weak transcription Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	37 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs4656718	C1orf112	cis	cerebellum	SCAN

Chromatin state (count:10 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:169748200-169753600	Enhancers	HUVEC	blood vessel
2	chr1:169749400-169761400	Weak transcription	Liver	Liver
3	chr1:169750400-169754400	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
4	chr1:169750800-169762800	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
5	chr1:169751600-169760200	Weak transcription	HUES48 Cell Line	embryonic stem cell
6	chr1:169751600-169762600	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
7	chr1:169752600-169760200	Weak transcription	Placenta Amnion	Placenta Amnion
8	chr1:169753000-169753600	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
9	chr1:169753000-169754000	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
10	chr1:169753200-169753600	Enhancers	HMEC	breast

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