Variant report

Variant	rs10864152
Chromosome Location	chr1:215269410-215269411
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 99 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:97)

rs_ID	r²[population]
rs10127521	0.83[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs10127656	0.95[CEU][hapmap];0.90[CHB][hapmap];0.93[CHD][hapmap];0.95[GIH][hapmap];0.91[MEX][hapmap];0.97[TSI][hapmap];0.84[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs10746454	0.90[CEU][hapmap];0.86[CHB][hapmap];0.82[JPT][hapmap];0.84[AMR][1000 genomes];0.87[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs10746455	0.90[CEU][hapmap];0.81[CHB][hapmap];0.84[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs10779639	0.90[CHB][hapmap]
rs10779640	0.95[CEU][hapmap];0.90[CHB][hapmap];0.84[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs10779642	0.90[CEU][hapmap];0.81[CHB][hapmap];0.83[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs10779643	0.90[CEU][hapmap];0.81[CHB][hapmap];0.83[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs10779644	0.90[CHB][hapmap]
rs10779645	0.89[CHB][hapmap]
rs10779646	0.81[CHB][hapmap]
rs10779647	0.90[CHB][hapmap];0.87[CHD][hapmap]
rs10779649	0.90[CEU][hapmap];0.81[CHB][hapmap];0.85[CHD][hapmap];0.91[MEX][hapmap];0.84[TSI][hapmap]
rs10779650	0.81[CHB][hapmap]
rs10779651	0.81[CHB][hapmap];0.85[CHD][hapmap];0.81[MEX][hapmap]
rs10864150	0.95[CEU][hapmap];0.95[CHB][hapmap];0.84[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs10864153	0.80[ASN][1000 genomes]
rs10864154	0.84[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs11120495	0.90[CEU][hapmap];0.84[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs11120497	0.81[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs11120499	0.90[CHB][hapmap];0.93[CHD][hapmap]
rs11120500	0.83[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs11120508	0.90[CHB][hapmap];0.90[CHD][hapmap]
rs11120511	0.90[CHB][hapmap]
rs11120513	0.90[CHB][hapmap];0.90[CHD][hapmap]
rs1112101	0.90[CEU][hapmap];0.81[CHB][hapmap];0.85[CHD][hapmap];0.84[TSI][hapmap]
rs12031308	0.95[CHB][hapmap]
rs12039875	0.90[CHB][hapmap];0.95[CHD][hapmap];0.82[JPT][hapmap];0.84[ASN][1000 genomes]
rs12120091	1.00[CEU][hapmap];0.90[CHB][hapmap];0.83[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs12121761	0.90[CHB][hapmap]
rs12135076	0.90[CEU][hapmap];0.81[CHB][hapmap];0.83[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs12141874	0.90[CEU][hapmap];0.81[CHB][hapmap]
rs12143339	0.90[CHB][hapmap]
rs12410041	0.81[CHB][hapmap];0.85[EUR][1000 genomes]
rs12411068	0.81[CHD][hapmap]
rs12567520	0.81[CHB][hapmap];0.85[CHD][hapmap]
rs12742137	0.84[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs1339405	0.90[CHB][hapmap]
rs1339406	0.90[CHB][hapmap]
rs1416647	0.90[CEU][hapmap];0.81[CHB][hapmap]
rs2363554	0.89[CHB][hapmap]
rs2363556	0.90[CEU][hapmap];0.81[CHB][hapmap]
rs2363557	0.90[CEU][hapmap];0.81[CHB][hapmap];0.83[CHD][hapmap];0.90[MEX][hapmap];0.82[TSI][hapmap];0.83[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs2363558	0.86[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs2363559	0.86[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs2363560	0.86[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs2363564	0.90[CHB][hapmap];0.90[CHD][hapmap];0.80[ASN][1000 genomes]
rs2363565	0.90[CHB][hapmap];0.90[CHD][hapmap]
rs2363566	0.90[CEU][hapmap];0.81[CHB][hapmap];0.85[CHD][hapmap];0.91[MEX][hapmap];0.84[TSI][hapmap]
rs2363567	0.90[CEU][hapmap];0.81[CHB][hapmap];0.85[CHD][hapmap];0.91[MEX][hapmap];0.84[TSI][hapmap]
rs2885812	0.94[CHB][hapmap]
rs2885813	0.83[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs2885815	0.95[CEU][hapmap];0.90[CHB][hapmap];0.83[AMR][1000 genomes];0.94[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs4262516	0.86[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs4269745	0.83[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs4271184	0.95[CHB][hapmap];0.97[CHD][hapmap];1.00[JPT][hapmap];0.96[ASN][1000 genomes]
rs4300189	0.90[CEU][hapmap];0.81[CHB][hapmap];0.84[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs4303048	0.90[CEU][hapmap];0.81[CHB][hapmap];0.85[CHD][hapmap];0.90[MEX][hapmap];0.82[TSI][hapmap];0.83[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs4375232	0.95[CEU][hapmap];0.81[CHB][hapmap];1.00[MEX][hapmap];0.84[TSI][hapmap];0.95[AMR][1000 genomes];0.88[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs4411107	0.90[CHB][hapmap];0.93[CHD][hapmap]
rs4497183	0.81[CEU][hapmap];0.90[CHB][hapmap];0.93[CHD][hapmap]
rs4509553	1.00[CEU][hapmap];0.90[CHB][hapmap];0.94[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs4531266	0.94[CEU][hapmap];0.89[CHB][hapmap];0.85[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs4556330	0.95[CHB][hapmap];1.00[JPT][hapmap];0.96[ASN][1000 genomes]
rs4571941	0.85[AMR][1000 genomes];0.94[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs4607848	0.84[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs4634877	0.95[CHB][hapmap];0.93[CHD][hapmap];0.95[JPT][hapmap];0.88[ASN][1000 genomes]
rs4655277	0.81[CHB][hapmap]
rs4655391	0.90[CHB][hapmap]
rs4655392	0.90[CHB][hapmap]
rs4655393	0.95[CEU][hapmap];0.81[CHB][hapmap];0.82[AMR][1000 genomes]
rs4655394	0.81[CHB][hapmap];0.83[CHD][hapmap]
rs4655395	0.85[CEU][hapmap];0.81[CHB][hapmap]
rs61818320	0.85[EUR][1000 genomes]
rs61818328	0.83[EUR][1000 genomes]
rs6657313	0.90[CEU][hapmap];0.81[CHB][hapmap]
rs6662353	0.90[CEU][hapmap];0.81[CHB][hapmap];0.88[CHD][hapmap];0.91[MEX][hapmap];0.84[TSI][hapmap];0.83[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs6666828	0.90[CHB][hapmap]
rs6667764	0.90[CHB][hapmap];0.80[ASN][1000 genomes]
rs6672978	0.90[CHB][hapmap];0.90[CHD][hapmap]
rs6673739	0.85[CEU][hapmap];0.81[CHB][hapmap]
rs6675926	0.90[CEU][hapmap];0.81[CHB][hapmap];0.83[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs6678758	0.84[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs6684084	0.81[CHB][hapmap];0.85[CHD][hapmap]
rs6688713	0.95[CEU][hapmap];0.95[CHB][hapmap];0.89[GIH][hapmap];0.86[MEX][hapmap];0.95[TSI][hapmap];0.86[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs6695967	0.86[CEU][hapmap];0.83[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs6696333	0.90[CEU][hapmap];0.81[CHB][hapmap];0.83[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs6699161	0.86[CHB][hapmap];0.93[CHD][hapmap];0.82[JPT][hapmap];0.82[ASN][1000 genomes]
rs7417100	0.90[CHB][hapmap]
rs7513709	0.95[CEU][hapmap];0.90[CHB][hapmap];0.84[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs7516689	0.95[CEU][hapmap];0.95[CHB][hapmap];0.85[CHD][hapmap];0.91[GIH][hapmap];0.95[JPT][hapmap];0.91[MEX][hapmap];0.95[TSI][hapmap];0.87[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs7541543	0.95[CEU][hapmap];0.90[CHB][hapmap];0.93[CHD][hapmap];0.95[GIH][hapmap];0.91[MEX][hapmap];0.97[TSI][hapmap];0.84[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs7547572	0.81[CHB][hapmap]
rs7547655	0.90[CEU][hapmap];0.85[CHB][hapmap];0.88[CHD][hapmap];0.91[MEX][hapmap];0.85[TSI][hapmap];0.82[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs7549136	0.90[CHB][hapmap]
rs7555013	0.85[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs7555727	0.86[EUR][1000 genomes];0.81[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:2 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv2754411	chr1:215235605-215281605	Bivalent/Poised TSS Active TSS Enhancers Flanking Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Strong transcription Weak transcription ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
2	nsv873169	chr1:215264486-215453286	Weak transcription Active TSS Strong transcription Enhancers Flanking Active TSS ZNF genes & repeats Genic enhancers Bivalent/Poised TSS	Chromatin interactive region miRNA target site	n/a	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs10864152	SYT14	cis	parietal	SCAN
rs10864152	FDX1	trans	cerebellum	SCAN

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:215258200-215277600	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
2	chr1:215258400-215277600	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
3	chr1:215265400-215280800	Weak transcription	Cortex derived primary cultured neurospheres	brain
4	chr1:215266600-215276000	Weak transcription	NHDF-Ad	bronchial
5	chr1:215267800-215269600	Enhancers	Fetal Brain Male	brain
6	chr1:215268000-215270200	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
7	chr1:215268600-215269800	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
8	chr1:215268600-215270600	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
9	chr1:215269400-215270200	Genic enhancers	Fetal Brain Female	brain
10	chr1:215269400-215273200	Weak transcription	Osteobl	bone

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links