Variant report

Variant	rs2070738
Chromosome Location	chr4:100873826-100873827
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr4:100870634..100872645-chr4:100873145..100874722,2	MCF-7	breast:
2	chr4:100867262..100869871-chr4:100873382..100875262,2	MCF-7	breast:
3	chr4:100870569..100872730-chr4:100873518..100875085,2	MCF-7	breast:
4	chr4:100810623..100827791-chr4:100865444..100874425,55	K562	blood:
5	chr4:100871315..100874297-chr4:103746830..103749271,3	K562	blood:

Variant related genes	Relation type
ENSG00000245322	Chromatin interaction
ENSG00000246560	Chromatin interaction
ENSG00000164032	Chromatin interaction
ENSG00000164031	Chromatin interaction
ENSG00000109332	Chromatin interaction
ENSG00000109270	Chromatin interaction

Extended variants
information (count: 99 )
Associated
traits (count: 6 )

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

rs_ID	r²[population]
rs1044044	1.00[CHB][hapmap];1.00[JPT][hapmap];0.98[ASN][1000 genomes]
rs10516458	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.98[ASN][1000 genomes]
rs11097679	0.94[ASN][1000 genomes]
rs11097680	0.94[ASN][1000 genomes]
rs11097681	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.98[ASN][1000 genomes]
rs11097682	0.98[ASN][1000 genomes]
rs11097683	0.86[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11097685	0.96[ASN][1000 genomes]
rs11097686	0.93[ASN][1000 genomes]
rs11723286	0.94[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.94[ASN][1000 genomes]
rs11732776	0.89[CEU][hapmap]
rs11736218	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs11736750	1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[ASN][1000 genomes]
rs11931053	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.98[ASN][1000 genomes]
rs11931551	0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11932783	1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[ASN][1000 genomes]
rs11935458	0.81[CHB][hapmap];0.92[JPT][hapmap];0.85[ASN][1000 genomes]
rs11935615	0.81[CHB][hapmap];1.00[JPT][hapmap];0.85[ASN][1000 genomes]
rs11936309	1.00[ASN][1000 genomes]
rs11936580	0.89[ASN][1000 genomes]
rs11937985	0.89[CHB][hapmap];0.94[CHD][hapmap];1.00[JPT][hapmap];0.94[ASN][1000 genomes]
rs11938952	1.00[ASN][1000 genomes]
rs11939538	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.98[ASN][1000 genomes]
rs11941520	1.00[CHB][hapmap];1.00[JPT][hapmap];0.98[ASN][1000 genomes]
rs11941799	0.81[CHB][hapmap];1.00[JPT][hapmap];0.85[ASN][1000 genomes]
rs11942532	0.87[CHB][hapmap];0.84[JPT][hapmap]
rs11944405	0.94[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.94[ASN][1000 genomes]
rs11944656	0.81[CHB][hapmap];1.00[JPT][hapmap];0.85[ASN][1000 genomes]
rs11945303	0.94[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.94[ASN][1000 genomes]
rs11947295	0.85[ASN][1000 genomes]
rs11947412	0.81[CHB][hapmap];0.81[JPT][hapmap]
rs1465518	0.92[JPT][hapmap]
rs1465519	0.91[JPT][hapmap]
rs17029573	0.81[CHB][hapmap];0.92[JPT][hapmap];0.85[ASN][1000 genomes]
rs17029662	1.00[CHB][hapmap];0.94[CHD][hapmap];1.00[JPT][hapmap];0.98[ASN][1000 genomes]
rs17029673	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs17029724	0.94[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs1896166	0.89[CEU][hapmap]
rs2017707	0.94[CHB][hapmap];1.00[JPT][hapmap];0.91[ASN][1000 genomes]
rs2081626	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.98[ASN][1000 genomes]
rs2081627	0.98[ASN][1000 genomes]
rs2162386	0.92[JPT][hapmap]
rs2276939	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs2298735	0.85[CEU][hapmap]
rs2866174	0.85[CEU][hapmap]
rs2866179	0.96[ASN][1000 genomes]
rs34453741	0.91[ASN][1000 genomes]
rs3733463	0.92[JPT][hapmap]
rs3737484	0.94[CHB][hapmap];0.89[CHD][hapmap];1.00[JPT][hapmap];0.94[ASN][1000 genomes]
rs3756087	0.88[ASW][hapmap];0.89[CEU][hapmap];0.86[GIH][hapmap];0.93[LWK][hapmap];0.85[MKK][hapmap];0.83[AFR][1000 genomes]
rs3775512	0.84[JPT][hapmap]
rs3822103	0.92[JPT][hapmap]
rs4320141	0.96[ASN][1000 genomes]
rs4536938	0.85[ASN][1000 genomes]
rs5015717	0.95[ASN][1000 genomes]
rs55726736	0.98[ASN][1000 genomes]
rs55797991	0.84[ASN][1000 genomes]
rs55888547	0.92[ASN][1000 genomes]
rs56007968	0.96[ASN][1000 genomes]
rs56140620	0.96[ASN][1000 genomes]
rs57322716	0.98[ASN][1000 genomes]
rs58304154	0.85[ASN][1000 genomes]
rs60070547	0.92[ASN][1000 genomes]
rs61191235	0.83[ASN][1000 genomes]
rs61203457	1.00[ASN][1000 genomes]
rs62305038	0.85[ASN][1000 genomes]
rs62306101	0.82[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6532834	0.88[CHB][hapmap];0.94[CHD][hapmap];1.00[JPT][hapmap];0.94[ASN][1000 genomes]
rs6532837	1.00[CHB][hapmap];1.00[JPT][hapmap];0.98[ASN][1000 genomes]
rs6532839	0.87[AFR][1000 genomes];0.95[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs6532840	0.92[ASN][1000 genomes]
rs6814140	0.98[ASN][1000 genomes]
rs6814181	0.86[JPT][hapmap]
rs6816635	1.00[CHB][hapmap];0.94[CHD][hapmap];1.00[JPT][hapmap];0.98[ASN][1000 genomes]
rs6824513	0.89[AFR][1000 genomes];0.84[AMR][1000 genomes];0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6829912	0.94[CHB][hapmap];0.94[CHD][hapmap];1.00[JPT][hapmap];0.94[ASN][1000 genomes]
rs6831193	0.92[AFR][1000 genomes];0.92[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6832726	1.00[CHB][hapmap];1.00[JPT][hapmap];0.98[ASN][1000 genomes]
rs6838495	0.91[AFR][1000 genomes];0.88[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6842840	1.00[ASW][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.87[LWK][hapmap];0.98[ASN][1000 genomes]
rs6843247	0.98[ASN][1000 genomes]
rs6845556	0.94[CHB][hapmap];1.00[JPT][hapmap];0.94[ASN][1000 genomes]
rs6848666	0.81[CHB][hapmap];1.00[JPT][hapmap];0.85[ASN][1000 genomes]
rs6854536	0.89[CEU][hapmap]
rs72686215	0.94[ASN][1000 genomes]
rs732386	0.83[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs73832925	1.00[ASN][1000 genomes]
rs7660185	0.89[AFR][1000 genomes];0.82[AMR][1000 genomes];0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7666156	1.00[CHB][hapmap];1.00[JPT][hapmap];0.98[ASN][1000 genomes]
rs7666192	0.83[AMR][1000 genomes];0.89[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs7676564	0.89[CEU][hapmap]
rs7686428	0.89[CEU][hapmap]
rs7686565	0.92[JPT][hapmap]
rs7687287	0.82[CHB][hapmap];0.84[JPT][hapmap]
rs7689566	0.89[CEU][hapmap]
rs7692416	0.88[ASW][hapmap];0.89[CEU][hapmap];0.86[GIH][hapmap];0.93[LWK][hapmap];0.84[MKK][hapmap]
rs890486	0.94[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	nsv879662	chr4:100849466-100876648	Enhancers Flanking Active TSS Transcr. at gene 5' and 3' Active TSS ZNF genes & repeats Weak transcription Strong transcription Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	51 gene(s)	inside rSNPs	diseases
2	nsv879663	chr4:100866460-100876648	Flanking Active TSS Active TSS Enhancers Transcr. at gene 5' and 3' Weak transcription Genic enhancers Bivalent/Poised TSS Strong transcription Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	51 gene(s)	inside rSNPs	diseases

mRNA abundance (count:6)

SNP	Gene	Cis/trans	Tissue	Source
rs2070738	MAPKSP1	cis	cerebellum	SCAN
rs2070738	MAPKSP1	cis	parietal	SCAN
rs2070738	DAPP1	Cis_1M	lymphoblastoid	RTeQTL
rs2070738	NHEDC1	cis	cerebellum	SCAN
rs2070738	NHEDC2	cis	cerebellum	SCAN
rs2070738	MTTP	cis	lymphoblastoid	seeQTL

Chromatin state (count:8 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:100872600-100875200	Weak transcription	Psoas Muscle	Psoas
2	chr4:100872600-100875200	Weak transcription	Skeletal Muscle Female	skeletal muscle
3	chr4:100872600-100876000	Weak transcription	Colon Smooth Muscle	Colon
4	chr4:100872600-100881800	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
5	chr4:100872600-100886000	Weak transcription	Primary T cells from cord blood	blood
6	chr4:100872600-100886000	Weak transcription	Primary T killer memory cells from peripheral blood	blood
7	chr4:100872600-100886200	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
8	chr4:100873000-100876800	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin

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