Variant report

Variant	rs1473711
Chromosome Location	chr1:94385591-94385592
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 80 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:79)

rs_ID	r²[population]
rs10159000	0.86[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10489607	0.86[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10874809	0.84[CHB][hapmap];0.82[JPT][hapmap]
rs10874811	0.81[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.91[GIH][hapmap];0.93[JPT][hapmap];0.83[MEX][hapmap];0.86[TSI][hapmap];0.89[AMR][1000 genomes];0.86[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs10874812	0.99[AFR][1000 genomes];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11165004	0.93[JPT][hapmap]
rs11165006	0.93[JPT][hapmap]
rs11165007	0.93[JPT][hapmap]
rs11165030	0.84[CHB][hapmap];0.82[JPT][hapmap]
rs11165031	1.00[CHB][hapmap];0.95[CHD][hapmap];1.00[JPT][hapmap];0.97[ASN][1000 genomes]
rs11165034	0.88[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11165037	0.85[AMR][1000 genomes];0.91[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12068168	0.88[ASN][1000 genomes]
rs12068345	0.98[ASN][1000 genomes]
rs12089163	0.97[ASN][1000 genomes]
rs12122176	1.00[JPT][hapmap]
rs12122406	0.93[ASN][1000 genomes]
rs12125068	0.93[JPT][hapmap]
rs12126518	0.81[GIH][hapmap]
rs12129986	0.86[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12130623	0.94[ASN][1000 genomes]
rs12131163	0.93[ASN][1000 genomes]
rs12131247	0.86[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12134159	0.93[JPT][hapmap]
rs12135187	0.93[JPT][hapmap]
rs12135991	0.88[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12139561	0.81[GIH][hapmap];0.93[JPT][hapmap]
rs12140014	0.93[JPT][hapmap]
rs12140097	0.82[AMR][1000 genomes];0.92[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12141697	0.89[JPT][hapmap]
rs12142384	0.93[JPT][hapmap]
rs12144277	0.86[JPT][hapmap]
rs12401354	0.90[ASN][1000 genomes]
rs12404613	0.82[CHB][hapmap];0.84[JPT][hapmap]
rs12406885	0.93[JPT][hapmap]
rs12407732	0.93[JPT][hapmap]
rs12410342	0.93[JPT][hapmap]
rs12410985	0.84[CHB][hapmap]
rs17100392	0.93[JPT][hapmap]
rs1852	0.90[CHB][hapmap]
rs1989020	0.86[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1989021	0.85[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2017736	0.88[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2092697	0.93[ASN][1000 genomes]
rs2143993	0.93[ASN][1000 genomes]
rs2273406	0.89[AMR][1000 genomes];0.93[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2391324	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.98[LWK][hapmap];0.96[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.99[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs3170633	0.84[CHB][hapmap]
rs35674584	0.94[ASN][1000 genomes]
rs3761912	0.84[CHB][hapmap];0.82[JPT][hapmap]
rs3827715	1.00[CHB][hapmap];0.91[CHD][hapmap];1.00[JPT][hapmap];0.99[ASN][1000 genomes]
rs41303970	0.89[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4573532	0.85[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4598495	0.97[ASN][1000 genomes]
rs57387172	0.86[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs60120441	0.97[ASN][1000 genomes]
rs61667071	0.97[ASN][1000 genomes]
rs6680027	0.95[ASN][1000 genomes]
rs6681078	0.97[ASN][1000 genomes]
rs6684128	0.81[GIH][hapmap]
rs6687387	0.84[CHB][hapmap];0.82[JPT][hapmap]
rs6688926	0.93[JPT][hapmap]
rs6696758	1.00[CEU][hapmap];1.00[CHB][hapmap];0.93[JPT][hapmap];0.86[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6699912	0.86[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6700112	0.97[ASN][1000 genomes]
rs718873	0.88[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs718874	0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs718875	1.00[CHB][hapmap];0.87[CHD][hapmap];1.00[JPT][hapmap];0.81[TSI][hapmap];0.84[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs743119	0.86[AMR][1000 genomes];0.92[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7515191	0.82[JPT][hapmap]
rs7517826	0.84[CHB][hapmap];0.82[JPT][hapmap]
rs7533596	0.84[CHB][hapmap];0.82[JPT][hapmap]
rs7536714	0.84[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7544883	0.93[JPT][hapmap]
rs7546315	0.93[JPT][hapmap]
rs7549683	0.84[CHB][hapmap];0.82[JPT][hapmap]
rs761889	0.88[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs769211	1.00[CHB][hapmap];0.91[CHD][hapmap];1.00[JPT][hapmap];0.97[ASN][1000 genomes]
rs960625	0.93[JPT][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	nsv523355	chr1:94351328-94385591	Enhancers Weak transcription Active TSS Strong transcription Flanking Active TSS Genic enhancers Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs1473711	CNN3	cis	cerebellum	SCAN
rs1473711	GCLM	Cis_1M	lymphoblastoid	RTeQTL
rs1473711	GCLM	cis	parietal	SCAN

Chromatin state (count:13 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:94375600-94421200	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
2	chr1:94384000-94387000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
3	chr1:94384800-94385600	Enhancers	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
4	chr1:94384800-94385600	Enhancers	H9 Cell Line	embryonic stem cell
5	chr1:94384800-94385800	Enhancers	HUES6 Cell Line	embryonic stem cell
6	chr1:94384800-94386000	Enhancers	ES-I3 Cell Line	embryonic stem cell
7	chr1:94385000-94385800	Enhancers	iPS-15b Cell Line	embryonic stem cell
8	chr1:94385000-94386000	Enhancers	HUES64 Cell Line	embryonic stem cell
9	chr1:94385000-94386000	Enhancers	iPS-18 Cell Line	embryonic stem cell
10	chr1:94385000-94386000	Enhancers	Pancreatic Islets	Pancreatic Islet
11	chr1:94385200-94385600	Flanking Active TSS	iPS-20b Cell Line	embryonic stem cell
12	chr1:94385200-94385800	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
13	chr1:94385400-94385600	Enhancers	HUES48 Cell Line	embryonic stem cell

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