Variant report

Variant	rs2036861
Chromosome Location	chr4:120102289-120102290
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr4:120100153..120102490-chr4:120128940..120130617,2	MCF-7	breast:

Extended variants
information (count: 58 )
Associated
traits (count: 5 )

rSNPs within LD-proxies of this variant (count:49)

rs_ID	r²[population]
rs10006304	0.81[CHB][hapmap];1.00[JPT][hapmap];0.91[ASN][1000 genomes]
rs10013032	0.95[CHB][hapmap];0.87[JPT][hapmap];0.89[ASN][1000 genomes]
rs10022508	0.86[CHB][hapmap];0.91[JPT][hapmap];0.94[ASN][1000 genomes]
rs1033087	0.96[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11098486	0.91[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs11098489	0.96[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs11098490	0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs11098491	0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs11098492	0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs11098493	0.94[AFR][1000 genomes];0.99[ASN][1000 genomes]
rs11729978	0.92[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs11730138	0.89[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs11731008	0.92[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs11733239	0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs11733525	0.95[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs12502503	0.94[ASN][1000 genomes]
rs12508316	0.92[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs12509054	0.95[CHB][hapmap];0.93[CHD][hapmap];0.95[JPT][hapmap];0.92[ASN][1000 genomes]
rs12513191	0.98[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs13120560	0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs13123591	0.94[ASN][1000 genomes]
rs13126596	0.90[ASN][1000 genomes]
rs13136593	0.91[AMR][1000 genomes];0.95[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs13138782	0.82[ASN][1000 genomes]
rs1459055	0.84[CEU][hapmap];0.82[GIH][hapmap];0.89[MEX][hapmap];0.87[TSI][hapmap];0.88[EUR][1000 genomes]
rs17839089	0.95[CHB][hapmap];0.95[JPT][hapmap];0.94[ASN][1000 genomes]
rs2203039	0.95[CHB][hapmap];0.93[CHD][hapmap];0.87[JPT][hapmap];0.89[ASN][1000 genomes]
rs28452522	0.94[ASN][1000 genomes]
rs4334737	0.92[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs4355373	0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4833612	0.89[ASN][1000 genomes]
rs4833613	0.83[CHB][hapmap];0.80[ASN][1000 genomes]
rs56122576	0.91[ASN][1000 genomes]
rs6534130	0.95[CHB][hapmap];0.87[JPT][hapmap];0.89[ASN][1000 genomes]
rs68128210	0.90[ASN][1000 genomes]
rs6822498	0.92[ASN][1000 genomes]
rs6826823	0.92[ASN][1000 genomes]
rs6832670	0.95[CHB][hapmap];0.95[JPT][hapmap];0.92[ASN][1000 genomes]
rs6838674	0.92[ASN][1000 genomes]
rs6851130	0.87[ASN][1000 genomes]
rs6851169	0.94[ASN][1000 genomes]
rs7441137	0.89[ASN][1000 genomes]
rs7661020	0.94[CHB][hapmap];0.94[JPT][hapmap];0.94[ASN][1000 genomes]
rs7696877	0.95[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs951570	0.89[ASN][1000 genomes]
rs9884728	0.89[ASN][1000 genomes]
rs9993110	0.90[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs9995277	0.95[CHB][hapmap];0.97[CHD][hapmap];0.95[JPT][hapmap];0.94[ASN][1000 genomes]
rs9996382	0.88[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:5)

SNP	Gene	Cis/trans	Tissue	Source
rs2036861	FLJ14186///LOC284701///LOC441124///LOC728624	Cis_1M	lymphoblastoid	RTeQTL
rs2036861	RP11-384K6.6	cis	Artery Tibial	GTEx
rs2036861	SPATA5	cis	cerebellum	SCAN
rs2036861	LOC645513	Cis_1M	lymphoblastoid	RTeQTL
rs2036861	MYOZ2	cis	parietal	SCAN

Chromatin state (count:9 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:120070800-120109200	Weak transcription	Psoas Muscle	Psoas
2	chr4:120077000-120107800	Weak transcription	Fetal Muscle Trunk	muscle
3	chr4:120079800-120114200	Weak transcription	Aorta	Aorta
4	chr4:120087800-120103400	Weak transcription	Right Ventricle	heart
5	chr4:120087800-120111800	Weak transcription	HSMMtube	muscle
6	chr4:120088800-120110200	Weak transcription	Skeletal Muscle Female	skeletal muscle
7	chr4:120090000-120109800	Weak transcription	Fetal Heart	heart
8	chr4:120101000-120132400	Weak transcription	Left Ventricle	heart
9	chr4:120101200-120107600	Weak transcription	Skeletal Muscle Male	skeletal muscle

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links