Variant report

Variant	rs7115967
Chromosome Location	chr11:45847088-45847089
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr11:45834030..45839103-chr11:45846096..45849299,4	K562	blood:
2	chr11:45845122..45847202-chr11:45850154..45851796,2	MCF-7	breast:
3	chr11:45845665..45849726-chr11:45853081..45856050,3	K562	blood:

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-SLC35C1-1	chr11:45846803-45847181	NONHSAT021141
2	lnc-SLC35C1-1	chr11:45846679-45847181	NONHSAT021142

Variant related genes	Relation type
ENSG00000255447	Chromatin interaction

Extended variants
information (count: 23 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:22)

rs_ID	r²[population]
rs10742769	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10838521	0.87[CHD][hapmap]
rs11038666	0.94[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs11038669	0.99[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs11038693	0.89[AMR][1000 genomes];1.00[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs1533614	1.00[CEU][hapmap];0.98[EUR][1000 genomes]
rs2056260	0.84[AMR][1000 genomes];0.83[ASN][1000 genomes]
rs2090602	0.82[CHD][hapmap]
rs2292913	1.00[CEU][hapmap];0.91[CHB][hapmap];0.87[CHD][hapmap];0.95[GIH][hapmap];0.82[JPT][hapmap];0.89[MEX][hapmap];0.89[MKK][hapmap];1.00[TSI][hapmap];0.82[YRI][hapmap];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs2666890	1.00[ASW][hapmap];0.91[YRI][hapmap]
rs4755344	1.00[CEU][hapmap];0.91[CHB][hapmap];0.82[JPT][hapmap];0.82[YRI][hapmap];0.88[AMR][1000 genomes];1.00[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs4755345	1.00[CEU][hapmap];0.91[CHB][hapmap];0.87[CHD][hapmap];0.95[GIH][hapmap];0.82[JPT][hapmap];0.89[MEX][hapmap];1.00[TSI][hapmap];0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs4756028	0.86[AFR][1000 genomes];0.97[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs4756035	1.00[CEU][hapmap];0.91[CHB][hapmap];0.87[CHD][hapmap];0.95[GIH][hapmap];0.82[JPT][hapmap];0.89[MEX][hapmap];0.89[MKK][hapmap];1.00[TSI][hapmap];0.82[YRI][hapmap];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs4756039	1.00[CEU][hapmap];0.95[GIH][hapmap];0.96[EUR][1000 genomes]
rs57989022	0.84[AMR][1000 genomes];1.00[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs6798	1.00[ASW][hapmap];0.91[CHB][hapmap];0.87[CHD][hapmap];0.82[JPT][hapmap];0.80[ASN][1000 genomes]
rs7108887	0.83[EUR][1000 genomes]
rs7482133	0.85[AFR][1000 genomes]
rs7943306	0.83[CHB][hapmap];0.91[JPT][hapmap]
rs9666007	0.92[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs9787929	0.87[AFR][1000 genomes]

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	nsv897314	chr11:45816020-45965129	Genic enhancers Weak transcription Flanking Bivalent TSS/Enh Strong transcription Bivalent Enhancer Enhancers Flanking Active TSS Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	46 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs7115967	CRY2	cis	multi-tissue	Pritchard

Chromatin state (count:16 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr11:45833600-45848000	Weak transcription	Right Ventricle	heart
2	chr11:45833800-45850000	Weak transcription	Brain Angular Gyrus	brain
3	chr11:45837600-45848200	Weak transcription	Sigmoid Colon	Sigmoid Colon
4	chr11:45845600-45847800	Weak transcription	ES-I3 Cell Line	embryonic stem cell
5	chr11:45845800-45847400	Weak transcription	K562	blood
6	chr11:45845800-45847600	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
7	chr11:45845800-45848000	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
8	chr11:45845800-45848000	Weak transcription	Gastric	stomach
9	chr11:45845800-45848000	Weak transcription	Lung	lung
10	chr11:45845800-45850400	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
11	chr11:45845800-45869000	Weak transcription	Right Atrium	heart
12	chr11:45846000-45855800	Weak transcription	Ovary	ovary
13	chr11:45846600-45848000	Weak transcription	Placenta	Placenta
14	chr11:45846800-45848000	Weak transcription	Primary T helper naive cells from peripheral blood	blood
15	chr11:45846800-45848000	Weak transcription	Primary T killer memory cells from peripheral blood	blood
16	chr11:45847000-45848000	Weak transcription	Left Ventricle	heart

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