Variant report

Variant	rs555742
Chromosome Location	chr6:11582292-11582293
allele	A/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 105 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:104)

rs_ID	r²[population]
rs11751931	0.86[EUR][1000 genomes]
rs16871371	0.86[EUR][1000 genomes]
rs17607537	0.86[EUR][1000 genomes]
rs17607558	0.86[EUR][1000 genomes]
rs17675742	0.86[EUR][1000 genomes]
rs17675772	0.86[EUR][1000 genomes]
rs2140109	0.86[EUR][1000 genomes]
rs2177158	0.86[EUR][1000 genomes]
rs2177159	0.85[EUR][1000 genomes]
rs34066851	0.86[EUR][1000 genomes]
rs34255222	0.86[EUR][1000 genomes]
rs34336996	0.86[EUR][1000 genomes]
rs34342746	0.86[EUR][1000 genomes]
rs34363244	0.86[EUR][1000 genomes]
rs34486680	0.86[EUR][1000 genomes]
rs34586980	0.86[EUR][1000 genomes]
rs34630993	0.86[EUR][1000 genomes]
rs34678413	0.86[EUR][1000 genomes]
rs34793558	0.85[EUR][1000 genomes]
rs34951511	0.85[EUR][1000 genomes]
rs35074878	0.86[EUR][1000 genomes]
rs35087778	0.86[EUR][1000 genomes]
rs35100959	0.86[EUR][1000 genomes]
rs35160576	0.81[EUR][1000 genomes]
rs35250180	0.86[EUR][1000 genomes]
rs35491413	0.86[EUR][1000 genomes]
rs35658210	0.86[EUR][1000 genomes]
rs35877256	0.85[EUR][1000 genomes]
rs35938392	0.86[EUR][1000 genomes]
rs36021289	0.86[EUR][1000 genomes]
rs36023953	0.86[EUR][1000 genomes]
rs36053861	0.86[EUR][1000 genomes]
rs36120363	0.86[EUR][1000 genomes]
rs3942485	0.86[EUR][1000 genomes]
rs4711303	0.94[CEU][hapmap];0.95[JPT][hapmap];0.86[EUR][1000 genomes]
rs4713556	0.86[EUR][1000 genomes]
rs4713562	0.94[CEU][hapmap];0.95[JPT][hapmap];0.86[EUR][1000 genomes]
rs4713569	0.86[EUR][1000 genomes]
rs4713577	0.94[CEU][hapmap];0.94[JPT][hapmap]
rs4713579	0.94[CEU][hapmap];0.88[CHB][hapmap];0.94[JPT][hapmap];0.90[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs471560	0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs471752	0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs478147	1.00[CEU][hapmap];0.94[CHB][hapmap];0.95[JPT][hapmap]
rs483637	0.88[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs490466	1.00[CEU][hapmap];0.94[CHB][hapmap];1.00[JPT][hapmap];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs509971	0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs513870	0.80[CEU][hapmap];0.88[CHB][hapmap];0.83[JPT][hapmap]
rs519140	0.93[AMR][1000 genomes];0.95[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs524159	0.95[AMR][1000 genomes];0.94[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs528679	0.88[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs538808	0.87[ASN][1000 genomes]
rs539160	0.90[AMR][1000 genomes];0.95[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs552681	0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs554671	1.00[CEU][hapmap];0.88[CHB][hapmap];0.94[JPT][hapmap];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs555034	1.00[CEU][hapmap];0.93[CHB][hapmap];0.95[JPT][hapmap];0.90[AMR][1000 genomes];0.94[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs566237	0.81[CEU][hapmap];0.87[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs571683	0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs573082	0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs574254	0.93[AMR][1000 genomes];0.95[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs578507	0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs581285	0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs598907	1.00[CEU][hapmap];0.94[CHB][hapmap];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs605058	0.88[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs606402	1.00[CEU][hapmap];0.94[CHB][hapmap];0.94[JPT][hapmap]
rs620729	0.80[CEU][hapmap];0.88[CHB][hapmap];0.83[JPT][hapmap]
rs62394918	0.84[EUR][1000 genomes]
rs62394920	0.86[EUR][1000 genomes]
rs62394921	0.86[EUR][1000 genomes]
rs62394922	0.86[EUR][1000 genomes]
rs62394924	0.80[EUR][1000 genomes]
rs62394925	0.86[EUR][1000 genomes]
rs62394927	0.80[EUR][1000 genomes]
rs62394928	0.80[EUR][1000 genomes]
rs628980	1.00[CEU][hapmap];0.94[CHB][hapmap];0.94[JPT][hapmap];0.90[AMR][1000 genomes];0.95[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs637564	0.90[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs645198	0.82[ASN][1000 genomes]
rs6457608	0.86[EUR][1000 genomes]
rs661055	0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs662296	0.82[ASN][1000 genomes]
rs663283	0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs66502560	0.86[EUR][1000 genomes]
rs67452935	0.86[EUR][1000 genomes]
rs675565	1.00[CEU][hapmap];0.88[CHB][hapmap];0.94[JPT][hapmap];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs67807015	0.85[EUR][1000 genomes]
rs678862	1.00[CEU][hapmap];0.88[CHB][hapmap];0.95[JPT][hapmap];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs685384	1.00[CEU][hapmap];0.94[CHB][hapmap];1.00[JPT][hapmap];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs687163	0.90[AMR][1000 genomes];0.95[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs6904209	0.84[EUR][1000 genomes]
rs6907890	0.86[EUR][1000 genomes]
rs6907900	0.86[EUR][1000 genomes]
rs6907944	0.86[EUR][1000 genomes]
rs6923613	0.86[EUR][1000 genomes]
rs6923798	0.84[EUR][1000 genomes]
rs6936326	0.88[CHB][hapmap];0.84[JPT][hapmap]
rs7752671	0.84[EUR][1000 genomes]
rs821443	0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs9348893	0.87[AMR][1000 genomes];0.94[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs9357151	0.80[AMR][1000 genomes];0.90[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs9366802	0.86[EUR][1000 genomes]
rs9368729	0.89[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs9380321	0.88[AMR][1000 genomes];0.95[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs9394108	0.86[EUR][1000 genomes]
rs9394109	0.94[CEU][hapmap];0.88[CHB][hapmap];0.95[JPT][hapmap];0.82[AMR][1000 genomes];0.90[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs9394115	1.00[CEU][hapmap];0.94[CHB][hapmap];0.94[JPT][hapmap];0.88[AMR][1000 genomes];0.95[EUR][1000 genomes];0.87[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	nsv1015234	chr6:11545582-11583516	Active TSS Weak transcription Strong transcription Enhancers Genic enhancers Flanking Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	Chromatin interactive region lncRNA miRNA target site	3 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs555742	TMEM170B	cis	Adipose Subcutaneous	GTEx

Chromatin state (count:21 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:11567600-11582600	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
2	chr6:11567600-11586200	Weak transcription	Fetal Intestine Small	intestine
3	chr6:11567600-11586400	Weak transcription	Fetal Stomach	stomach
4	chr6:11567600-11586600	Weak transcription	Skeletal Muscle Female	skeletal muscle
5	chr6:11567800-11584200	Weak transcription	HSMMtube	muscle
6	chr6:11567800-11586400	Weak transcription	Breast Myoepithelial Primary Cells	Breast
7	chr6:11568000-11586200	Weak transcription	Liver	Liver
8	chr6:11568000-11586600	Weak transcription	Brain Angular Gyrus	brain
9	chr6:11568600-11586800	Weak transcription	Cortex derived primary cultured neurospheres	brain
10	chr6:11571800-11586600	Weak transcription	Ovary	ovary
11	chr6:11575800-11584400	Weak transcription	HSMM	muscle
12	chr6:11575800-11586200	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
13	chr6:11576000-11582600	Weak transcription	Primary hematopoietic stem cells short term culture	blood
14	chr6:11576000-11584600	Weak transcription	ES-I3 Cell Line	embryonic stem cell
15	chr6:11576000-11586200	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
16	chr6:11576000-11586400	Weak transcription	HepG2	liver
17	chr6:11578600-11583200	Enhancers	Primary neutrophils fromperipheralblood	blood
18	chr6:11579200-11586400	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
19	chr6:11580200-11582800	Enhancers	Primary monocytes fromperipheralblood	blood
20	chr6:11580200-11586400	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
21	chr6:11582200-11582600	Enhancers	Monocytes-CD14+_RO01746	blood

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