Variant report

Variant	rs11117687
Chromosome Location	chr1:216997113-216997114
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 22 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:21)

rs_ID	r²[population]
rs1126021	0.94[CHD][hapmap];1.00[JPT][hapmap];0.89[ASN][1000 genomes]
rs12568029	0.90[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12723353	0.88[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.91[GIH][hapmap];1.00[JPT][hapmap];0.87[MEX][hapmap];0.95[TSI][hapmap];0.94[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs12727957	0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12733125	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12742081	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs12745662	0.94[CHB][hapmap];0.83[EUR][1000 genomes]
rs12753723	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.93[GIH][hapmap];1.00[JPT][hapmap];0.96[MEX][hapmap];1.00[TSI][hapmap];0.89[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12760372	0.85[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.91[GIH][hapmap];1.00[JPT][hapmap];0.87[MEX][hapmap];0.95[TSI][hapmap];0.93[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs1344874	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.93[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1545109	0.94[ASW][hapmap];1.00[CEU][hapmap];0.95[CHB][hapmap];0.94[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];0.80[LWK][hapmap];0.96[MEX][hapmap];1.00[TSI][hapmap];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1545110	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1821787	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1971804	0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2164613	0.88[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.94[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];0.96[MEX][hapmap];1.00[TSI][hapmap];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2164614	0.94[CHB][hapmap];0.94[CHD][hapmap];1.00[JPT][hapmap];0.97[ASN][1000 genomes]
rs6604646	0.94[ASW][hapmap];0.88[CEU][hapmap];1.00[CHB][hapmap];0.96[CHD][hapmap];1.00[JPT][hapmap];0.85[LWK][hapmap];0.95[TSI][hapmap];0.82[YRI][hapmap];0.88[AFR][1000 genomes];0.81[AMR][1000 genomes];0.93[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7526618	0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7528362	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.85[YRI][hapmap];0.85[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7531310	0.88[ASW][hapmap];1.00[CEU][hapmap];0.95[CHB][hapmap];0.91[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.96[MEX][hapmap];1.00[TSI][hapmap];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7543938	0.83[CHB][hapmap];0.82[JPT][hapmap];0.87[ASN][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	esv2762163	chr1:216982140-217015625	Enhancers Weak transcription ZNF genes & repeats Flanking Active TSS Active TSS Bivalent Enhancer Genic enhancers	TF binding region CpG island Chromatin interactive region	2 gene(s)	inside rSNPs	n/a

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs11117687	C1orf97	cis	cerebellum	SCAN

Chromatin state (count:21 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:216988000-216997200	Weak transcription	Breast Myoepithelial Primary Cells	Breast
2	chr1:216989000-217005800	Weak transcription	Left Ventricle	heart
3	chr1:216989400-216998200	Weak transcription	H9 Cell Line	embryonic stem cell
4	chr1:216989600-216997800	Weak transcription	Duodenum Mucosa	Duodenum
5	chr1:216989600-216998000	Weak transcription	H1 Cell Line	embryonic stem cell
6	chr1:216989600-217000600	Weak transcription	Psoas Muscle	Psoas
7	chr1:216990000-216998000	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
8	chr1:216994200-216998000	Weak transcription	ES-I3 Cell Line	embryonic stem cell
9	chr1:216994400-216998200	Weak transcription	Small Intestine	intestine
10	chr1:216994600-217004000	Weak transcription	iPS-20b Cell Line	embryonic stem cell
11	chr1:216994800-216998600	Weak transcription	Fetal Heart	heart
12	chr1:216995400-216997200	Enhancers	HUES64 Cell Line	embryonic stem cell
13	chr1:216995800-216997200	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
14	chr1:216996400-217000400	Enhancers	Fetal Intestine Small	intestine
15	chr1:216996400-217004400	Weak transcription	iPS-18 Cell Line	embryonic stem cell
16	chr1:216996600-216997400	Enhancers	Fetal Lung	lung
17	chr1:216996600-216998000	Weak transcription	HUES6 Cell Line	embryonic stem cell
18	chr1:216996600-216998200	Weak transcription	iPS-15b Cell Line	embryonic stem cell
19	chr1:216996800-216997800	Weak transcription	HUES48 Cell Line	embryonic stem cell
20	chr1:216997000-216997400	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
21	chr1:216997000-216999600	Enhancers	Fetal Intestine Large	intestine

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