Variant report

Variant	rs6842840
Chromosome Location	chr4:100887972-100887973
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr4:100866837..100874072-chr4:100882881..100890630,13	K562	blood:
2	chr4:100870527..100872651-chr4:100887647..100889251,3	K562	blood:
3	chr4:100869808..100871466-chr4:100887382..100890165,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000164032	Chromatin interaction
ENSG00000245322	Chromatin interaction
ENSG00000164031	Chromatin interaction

Extended variants
information (count: 90 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:89)

rs_ID	r²[population]
rs1044044	0.81[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs10516458	0.82[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.92[MEX][hapmap];0.95[TSI][hapmap];0.83[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs11097679	0.82[AMR][1000 genomes];0.92[ASN][1000 genomes]
rs11097680	0.84[AMR][1000 genomes];0.83[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs11097681	0.86[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.95[TSI][hapmap];0.83[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs11097682	0.84[AMR][1000 genomes];0.83[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs11097683	0.98[ASN][1000 genomes]
rs11097685	0.85[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs11097686	0.81[AMR][1000 genomes];0.88[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs11723286	1.00[CEU][hapmap];0.94[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.92[MEX][hapmap];1.00[TSI][hapmap];0.86[AMR][1000 genomes];0.87[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs11736218	0.82[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.95[TSI][hapmap];0.85[AMR][1000 genomes];0.88[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11736750	0.82[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.84[AMR][1000 genomes];0.90[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs11931053	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.92[MEX][hapmap];1.00[TSI][hapmap];0.89[AMR][1000 genomes];0.92[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs11931551	0.95[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs11932783	0.82[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[AMR][1000 genomes];0.90[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs11935458	0.81[CHB][hapmap];0.92[JPT][hapmap];0.83[ASN][1000 genomes]
rs11935615	0.81[CHB][hapmap];1.00[JPT][hapmap];0.83[ASN][1000 genomes]
rs11936309	0.85[AMR][1000 genomes];0.88[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11936580	0.86[AMR][1000 genomes];0.99[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs11937985	0.82[CEU][hapmap];0.89[CHB][hapmap];0.94[CHD][hapmap];1.00[JPT][hapmap];0.95[TSI][hapmap];0.82[AMR][1000 genomes];0.80[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs11938952	0.84[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11939538	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.92[MEX][hapmap];1.00[TSI][hapmap];0.89[AMR][1000 genomes];0.92[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs11941520	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11941799	0.81[CHB][hapmap];1.00[JPT][hapmap];0.85[MEX][hapmap];0.87[TSI][hapmap];0.83[ASN][1000 genomes]
rs11942532	0.87[CHB][hapmap];0.84[JPT][hapmap]
rs11944405	0.82[CEU][hapmap];0.94[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.92[MEX][hapmap];0.95[TSI][hapmap];0.82[AMR][1000 genomes];0.92[ASN][1000 genomes]
rs11944656	0.82[CEU][hapmap];0.81[CHB][hapmap];1.00[JPT][hapmap];0.83[ASN][1000 genomes]
rs11945303	0.82[CEU][hapmap];0.94[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.92[MEX][hapmap];0.95[TSI][hapmap];0.82[AMR][1000 genomes];0.80[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs11947295	0.82[CEU][hapmap];0.83[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[MEX][hapmap];0.82[TSI][hapmap];0.83[ASN][1000 genomes]
rs17029662	0.95[CEU][hapmap];1.00[CHB][hapmap];0.94[CHD][hapmap];1.00[JPT][hapmap];0.92[MEX][hapmap];1.00[TSI][hapmap];0.86[AMR][1000 genomes];0.92[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs17029673	0.82[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.95[TSI][hapmap];0.85[AMR][1000 genomes];0.88[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs17029724	0.94[ASN][1000 genomes]
rs2017707	0.81[CEU][hapmap];0.94[CHB][hapmap];1.00[JPT][hapmap];0.82[AMR][1000 genomes];0.88[ASN][1000 genomes]
rs2070738	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]
rs2081626	0.82[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.84[MEX][hapmap];0.95[TSI][hapmap];0.83[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2081627	0.84[AMR][1000 genomes];0.83[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2162386	0.92[JPT][hapmap]
rs2276939	0.82[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.92[MEX][hapmap];0.95[TSI][hapmap];0.80[AMR][1000 genomes];0.87[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2866179	0.85[AMR][1000 genomes];0.90[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs34453741	0.82[AMR][1000 genomes];0.88[ASN][1000 genomes]
rs3733463	0.92[JPT][hapmap]
rs3737484	0.82[CEU][hapmap];0.94[CHB][hapmap];0.88[CHD][hapmap];1.00[JPT][hapmap];0.85[MEX][hapmap];0.82[TSI][hapmap];0.82[AMR][1000 genomes];0.92[ASN][1000 genomes]
rs3756087	0.88[ASW][hapmap];0.81[LWK][hapmap]
rs3775512	0.84[JPT][hapmap]
rs3822103	0.92[JPT][hapmap]
rs4320141	0.85[AMR][1000 genomes];0.90[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4536938	0.83[ASN][1000 genomes]
rs5015717	0.98[AFR][1000 genomes];0.99[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs55726736	0.84[AMR][1000 genomes];0.83[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs55797991	0.81[ASN][1000 genomes]
rs55888547	0.84[AMR][1000 genomes];0.99[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs56007968	0.85[AMR][1000 genomes];0.90[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs56140620	0.90[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs57322716	0.90[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs58304154	0.83[ASN][1000 genomes]
rs60070547	0.81[AMR][1000 genomes];0.90[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs61191235	0.85[ASN][1000 genomes]
rs61203457	0.85[AMR][1000 genomes];0.87[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs62305038	0.83[ASN][1000 genomes]
rs62306101	0.96[ASN][1000 genomes]
rs6532834	0.88[CHB][hapmap];0.94[CHD][hapmap];1.00[JPT][hapmap];0.87[TSI][hapmap];0.82[AMR][1000 genomes];0.92[ASN][1000 genomes]
rs6532837	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6532839	0.94[ASN][1000 genomes]
rs6532840	0.84[AMR][1000 genomes];0.99[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6814140	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6814181	0.86[JPT][hapmap]
rs6816635	1.00[CEU][hapmap];1.00[CHB][hapmap];0.94[CHD][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.97[TSI][hapmap];0.90[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6824513	0.80[AFR][1000 genomes];0.96[ASN][1000 genomes]
rs6829912	0.82[CEU][hapmap];0.94[CHB][hapmap];0.94[CHD][hapmap];1.00[JPT][hapmap];0.92[MEX][hapmap];0.90[TSI][hapmap];0.82[AMR][1000 genomes];0.92[ASN][1000 genomes]
rs6831193	0.83[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs6832726	0.82[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.84[AMR][1000 genomes];0.83[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs6838495	0.82[AFR][1000 genomes];0.99[ASN][1000 genomes]
rs6843247	0.83[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6845556	0.94[CHB][hapmap];1.00[JPT][hapmap];0.81[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6848666	0.81[CHB][hapmap];1.00[JPT][hapmap];0.87[TSI][hapmap];0.83[ASN][1000 genomes]
rs72686215	0.90[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs732386	0.99[ASN][1000 genomes]
rs73832925	0.83[AMR][1000 genomes];0.88[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7660185	0.80[AFR][1000 genomes];0.96[ASN][1000 genomes]
rs7666156	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7666192	0.95[AFR][1000 genomes];0.85[ASN][1000 genomes]
rs7686565	0.92[JPT][hapmap]
rs7687287	0.82[CHB][hapmap];0.84[JPT][hapmap]
rs7692416	0.88[ASW][hapmap];0.81[LWK][hapmap]
rs890486	0.82[AMR][1000 genomes];0.92[ASN][1000 genomes]

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	esv3397740	chr4:100887913-100888396	Weak transcription Enhancers	Chromatin interactive region	3 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs6842840	MAPKSP1	cis	parietal	SCAN
rs6842840	H2AFZ	cis	cerebellum	SCAN
rs6842840	MAPKSP1	cis	cerebellum	SCAN

Chromatin state (count:12 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:100880400-100889600	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
2	chr4:100882600-100889000	Weak transcription	Osteobl	bone
3	chr4:100882800-100888400	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
4	chr4:100882800-100892800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
5	chr4:100883000-100889000	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
6	chr4:100887000-100890000	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
7	chr4:100887200-100888400	Enhancers	NHLF	lung
8	chr4:100887400-100888000	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
9	chr4:100887400-100888400	Enhancers	Dnd41	blood
10	chr4:100887800-100888200	Enhancers	Muscle Satellite Cultured Cells	--
11	chr4:100887800-100889800	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
12	chr4:100887800-100890200	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived

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