Variant report

Variant	rs1344671
Chromosome Location	chr3:54795064-54795065
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 40 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:36)

rs_ID	r²[population]
rs10510773	1.00[CHB][hapmap];1.00[CHD][hapmap];0.88[GIH][hapmap];1.00[JPT][hapmap];0.90[MEX][hapmap];0.88[TSI][hapmap];0.85[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs12488046	0.94[CEU][hapmap];0.90[CHB][hapmap];1.00[JPT][hapmap];0.82[AMR][1000 genomes];0.86[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs12490327	0.89[CEU][hapmap];1.00[CHB][hapmap];0.94[CHD][hapmap];0.83[GIH][hapmap];1.00[JPT][hapmap];0.81[MEX][hapmap];0.82[TSI][hapmap]
rs12490953	0.84[CEU][hapmap];0.90[CHB][hapmap];1.00[JPT][hapmap];0.82[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs12496821	1.00[CHB][hapmap];0.94[CHD][hapmap]
rs13068008	0.84[CEU][hapmap];0.90[CHB][hapmap];0.94[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];0.81[MEX][hapmap]
rs13070126	0.89[CEU][hapmap]
rs13070262	0.81[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs13083683	0.94[CEU][hapmap];0.90[CHB][hapmap];1.00[JPT][hapmap]
rs13084347	0.82[CHD][hapmap]
rs13084602	0.84[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs13086256	0.90[CHB][hapmap];0.94[CHD][hapmap];0.83[GIH][hapmap];1.00[JPT][hapmap];0.81[MEX][hapmap]
rs13088416	0.94[CEU][hapmap];0.90[CHB][hapmap];1.00[JPT][hapmap]
rs13090131	0.91[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs13092066	0.85[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs13095178	1.00[CHB][hapmap];0.94[CHD][hapmap];1.00[JPT][hapmap];0.80[ASN][1000 genomes]
rs13100029	0.90[CHB][hapmap];1.00[JPT][hapmap];0.86[AMR][1000 genomes];0.87[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs1520575	1.00[CHB][hapmap];0.94[CHD][hapmap];1.00[JPT][hapmap]
rs17815840	1.00[CHB][hapmap];0.94[CHD][hapmap];1.00[JPT][hapmap]
rs1882320	1.00[CHB][hapmap];1.00[JPT][hapmap];0.84[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs1882322	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.94[TSI][hapmap];0.80[AMR][1000 genomes];0.91[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs1921548	0.94[CEU][hapmap];0.90[CHB][hapmap];1.00[CHD][hapmap];0.88[GIH][hapmap];1.00[JPT][hapmap];0.95[MEX][hapmap];0.97[TSI][hapmap];0.81[AMR][1000 genomes];0.89[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2099019	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs3852006	0.84[CEU][hapmap];0.90[CHB][hapmap];1.00[JPT][hapmap]
rs3864001	0.84[CEU][hapmap];0.90[CHB][hapmap];0.94[CHD][hapmap];0.83[GIH][hapmap];1.00[JPT][hapmap];0.91[MEX][hapmap];0.82[TSI][hapmap]
rs3868872	0.89[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs3906509	0.90[CHB][hapmap];0.94[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];0.85[MEX][hapmap];0.82[TSI][hapmap]
rs4025824	0.81[AMR][1000 genomes];0.90[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs4083342	0.84[CEU][hapmap];0.80[CHB][hapmap];0.94[CHD][hapmap];0.83[GIH][hapmap];1.00[JPT][hapmap];0.86[MEX][hapmap]
rs6808464	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs6809269	0.91[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs6809715	0.91[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs7618235	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs7618991	0.91[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs7623961	0.84[CEU][hapmap];1.00[CHB][hapmap];0.94[CHD][hapmap];0.83[GIH][hapmap];0.90[JPT][hapmap];0.86[MEX][hapmap];0.82[TSI][hapmap]
rs7636321	0.90[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.98[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1014595	chr3:53944473-54846754	Enhancers Bivalent Enhancer Weak transcription Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS Flanking Active TSS Genic enhancers Strong transcription Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
2	nsv834700	chr3:54637374-54803896	Weak transcription Enhancers Transcr. at gene 5' and 3' Genic enhancers Bivalent Enhancer Strong transcription Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
3	nsv522779	chr3:54793450-54803521	Enhancers Weak transcription ZNF genes & repeats Bivalent Enhancer	n/a	n/a	inside rSNPs	diseases
4	nsv524822	chr3:54793450-54803521	Enhancers Weak transcription Bivalent Enhancer ZNF genes & repeats	n/a	n/a	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs1344671	DNAH12	cis	cerebellum	SCAN
rs1344671	PRKCD	cis	cerebellum	SCAN

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:54784600-54797200	Weak transcription	Skeletal Muscle Female	skeletal muscle
2	chr3:54785800-54798200	Weak transcription	H9 Cell Line	embryonic stem cell
3	chr3:54787400-54800200	Weak transcription	Stomach Smooth Muscle	stomach
4	chr3:54787600-54804600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
5	chr3:54793800-54795800	Enhancers	Foreskin Fibroblast Primary Cells skin02	Skin
6	chr3:54793800-54796600	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
7	chr3:54794000-54796200	Enhancers	NHDF-Ad	bronchial
8	chr3:54794200-54796200	Enhancers	NHLF	lung
9	chr3:54794200-54806800	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
10	chr3:54794400-54795600	Weak transcription	Fetal Stomach	stomach
11	chr3:54794400-54795800	Enhancers	Psoas Muscle	Psoas
12	chr3:54794400-54801400	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
13	chr3:54794400-54806600	Weak transcription	HUES6 Cell Line	embryonic stem cell
14	chr3:54794600-54795600	Weak transcription	ES-I3 Cell Line	embryonic stem cell
15	chr3:54794600-54795800	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
16	chr3:54795000-54795800	Weak transcription	Fetal Muscle Leg	muscle

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