Variant report

Variant	rs11098490
Chromosome Location	chr4:120086883-120086884
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 57 )
Associated
traits (count: 6 )

rSNPs within LD-proxies of this variant (count:48)

rs_ID	r²[population]
rs10006304	0.81[CHB][hapmap];1.00[JPT][hapmap];0.87[ASN][1000 genomes]
rs10013032	0.95[CHB][hapmap];0.87[JPT][hapmap];0.85[ASN][1000 genomes]
rs10022508	0.86[CHB][hapmap];0.91[JPT][hapmap];0.90[ASN][1000 genomes]
rs1033087	1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs11098486	0.92[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs11098489	0.80[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs11098491	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11098492	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs11098493	0.95[ASN][1000 genomes]
rs11729978	0.93[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs11730138	0.90[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs11731008	0.93[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs11733239	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs11733525	0.96[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs12502503	0.90[ASN][1000 genomes]
rs12508316	0.93[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs12509054	0.95[CHB][hapmap];0.90[CHD][hapmap];0.95[JPT][hapmap];0.88[ASN][1000 genomes]
rs12513191	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs13120560	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs13123591	0.90[ASN][1000 genomes]
rs13126596	0.87[ASN][1000 genomes]
rs13136593	0.90[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1459055	0.88[CEU][hapmap];0.82[GIH][hapmap];0.89[MEX][hapmap];0.89[TSI][hapmap];0.89[EUR][1000 genomes]
rs17839089	0.95[CHB][hapmap];0.95[JPT][hapmap];0.90[ASN][1000 genomes]
rs2036861	0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2203039	0.95[CHB][hapmap];0.90[CHD][hapmap];0.87[JPT][hapmap];0.85[ASN][1000 genomes]
rs28452522	0.90[ASN][1000 genomes]
rs4334737	0.93[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs4355373	0.95[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4833612	0.85[ASN][1000 genomes]
rs4833613	0.83[CHB][hapmap]
rs56122576	0.87[ASN][1000 genomes]
rs6534130	0.95[CHB][hapmap];0.87[JPT][hapmap];0.85[ASN][1000 genomes]
rs68128210	0.87[ASN][1000 genomes]
rs6822498	0.88[ASN][1000 genomes]
rs6826823	0.88[ASN][1000 genomes]
rs6832670	0.95[CHB][hapmap];0.95[JPT][hapmap];0.88[ASN][1000 genomes]
rs6838674	0.88[ASN][1000 genomes]
rs6851130	0.83[ASN][1000 genomes]
rs6851169	0.90[ASN][1000 genomes]
rs7441137	0.85[ASN][1000 genomes]
rs7661020	0.94[CHB][hapmap];0.94[JPT][hapmap];0.90[ASN][1000 genomes]
rs7696877	0.96[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs951570	0.85[ASN][1000 genomes]
rs9884728	0.85[ASN][1000 genomes]
rs9993110	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs9995277	0.95[CHB][hapmap];0.95[CHD][hapmap];0.95[JPT][hapmap];0.90[ASN][1000 genomes]
rs9996382	0.84[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:9 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv916641	chr4:119780023-120777320	Strong transcription Weak transcription Enhancers Active TSS Flanking Active TSS Bivalent/Poised TSS Genic enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	72 gene(s)	inside rSNPs	diseases
2	nsv948802	chr4:119844269-120208926	Enhancers Weak transcription Strong transcription Active TSS Flanking Active TSS ZNF genes & repeats Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	54 gene(s)	inside rSNPs	diseases
3	nsv1007214	chr4:120007913-120112460	Enhancers Weak transcription Flanking Active TSS Genic enhancers Active TSS Transcr. at gene 5' and 3' Strong transcription ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
4	nsv1008115	chr4:120007913-120143849	Enhancers Weak transcription Flanking Active TSS Strong transcription Genic enhancers Active TSS Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	45 gene(s)	inside rSNPs	diseases
5	nsv1003827	chr4:120008227-120112460	Enhancers Weak transcription Active TSS Flanking Active TSS Strong transcription Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
6	nsv522386	chr4:120009147-120115379	Enhancers Strong transcription Weak transcription Genic enhancers Flanking Active TSS Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
7	nsv1012868	chr4:120014630-120464880	Enhancers Flanking Active TSS Active TSS Weak transcription Genic enhancers ZNF genes & repeats Strong transcription Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	58 gene(s)	inside rSNPs	diseases
8	nsv537232	chr4:120014630-120464880	Weak transcription Enhancers Strong transcription ZNF genes & repeats Genic enhancers Active TSS Flanking Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	58 gene(s)	inside rSNPs	diseases
9	nsv1007619	chr4:120014898-120112460	Enhancers Weak transcription Genic enhancers Flanking Active TSS Active TSS Strong transcription Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases

mRNA abundance (count:6)

SNP	Gene	Cis/trans	Tissue	Source
rs11098490	RP11-384K6.6	cis	Whole Blood	GTEx
rs11098490	FLJ14186///LOC284701///LOC441124///LOC728624	Cis_1M	lymphoblastoid	RTeQTL
rs11098490	RP11-384K6.6	cis	Artery Tibial	GTEx
rs11098490	SPATA5	cis	cerebellum	SCAN
rs11098490	MYOZ2	cis	parietal	SCAN
rs11098490	LOC645513	Cis_1M	lymphoblastoid	RTeQTL

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:120061400-120089200	Weak transcription	Fetal Muscle Leg	muscle
2	chr4:120066800-120087000	Weak transcription	Skeletal Muscle Female	skeletal muscle
3	chr4:120070800-120109200	Weak transcription	Psoas Muscle	Psoas
4	chr4:120071000-120088600	Weak transcription	Right Atrium	heart
5	chr4:120075400-120087000	Weak transcription	Fetal Heart	heart
6	chr4:120077000-120107800	Weak transcription	Fetal Muscle Trunk	muscle
7	chr4:120079800-120114200	Weak transcription	Aorta	Aorta
8	chr4:120083600-120088000	Weak transcription	Pancreas	Pancrea
9	chr4:120083800-120087400	Weak transcription	Right Ventricle	heart
10	chr4:120085200-120087000	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
11	chr4:120085400-120087400	Weak transcription	HSMMtube	muscle
12	chr4:120086200-120089000	Strong transcription	Left Ventricle	heart
13	chr4:120086400-120089000	Strong transcription	Skeletal Muscle Male	skeletal muscle

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links