Variant report

Variant	rs524159
Chromosome Location	chr6:11554181-11554182
allele	C/G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr6:11552654..11554519-chr6:11555824..11557962,2	MCF-7	breast:

Extended variants
information (count: 96 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:91)

rs_ID	r²[population]
rs11751931	0.81[EUR][1000 genomes]
rs16871371	0.81[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs17607537	0.81[EUR][1000 genomes]
rs17607558	0.81[EUR][1000 genomes]
rs17675742	0.81[EUR][1000 genomes]
rs17675772	0.81[EUR][1000 genomes]
rs2140109	0.81[EUR][1000 genomes]
rs2177158	0.81[EUR][1000 genomes]
rs2177159	0.80[EUR][1000 genomes]
rs34066851	0.81[EUR][1000 genomes]
rs34255222	0.81[EUR][1000 genomes]
rs34336996	0.81[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs34342746	0.81[EUR][1000 genomes]
rs34363244	0.81[EUR][1000 genomes]
rs34486680	0.81[EUR][1000 genomes]
rs34586980	0.81[EUR][1000 genomes]
rs34630993	0.81[EUR][1000 genomes]
rs34678413	0.81[EUR][1000 genomes]
rs34793558	0.81[EUR][1000 genomes]
rs34951511	0.80[EUR][1000 genomes]
rs35074878	0.81[EUR][1000 genomes]
rs35087778	0.81[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs35100959	0.81[EUR][1000 genomes]
rs35250180	0.81[EUR][1000 genomes]
rs35491413	0.81[EUR][1000 genomes]
rs35658210	0.81[EUR][1000 genomes]
rs35877256	0.80[EUR][1000 genomes]
rs35938392	0.81[EUR][1000 genomes]
rs36021289	0.81[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs36023953	0.81[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs36053861	0.81[EUR][1000 genomes]
rs36120363	0.81[EUR][1000 genomes]
rs3942485	0.81[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs4711303	0.81[EUR][1000 genomes]
rs4713556	0.81[EUR][1000 genomes]
rs4713562	0.81[EUR][1000 genomes]
rs4713569	0.81[EUR][1000 genomes]
rs4713579	0.85[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs471560	0.96[AFR][1000 genomes];0.98[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs471752	0.96[AFR][1000 genomes];0.98[AMR][1000 genomes];0.94[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs483637	0.84[AFR][1000 genomes];0.90[AMR][1000 genomes];0.90[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs490466	0.96[AFR][1000 genomes];0.98[AMR][1000 genomes];0.94[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs509971	0.96[AFR][1000 genomes];0.98[AMR][1000 genomes];0.94[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs513870	0.80[AMR][1000 genomes];0.80[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs519140	0.96[AFR][1000 genomes];0.95[AMR][1000 genomes];0.92[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs528679	0.90[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs538808	0.97[ASN][1000 genomes]
rs539160	0.96[AFR][1000 genomes];0.91[AMR][1000 genomes];0.90[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs552681	0.96[AFR][1000 genomes];0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs554671	0.96[AFR][1000 genomes];0.98[AMR][1000 genomes];0.95[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs555034	0.96[AFR][1000 genomes];0.91[AMR][1000 genomes];0.91[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs555742	0.95[AMR][1000 genomes];0.94[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs56055084	0.82[ASN][1000 genomes]
rs566237	0.92[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs571683	0.96[AFR][1000 genomes];0.95[AMR][1000 genomes];0.94[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs573082	0.96[AFR][1000 genomes];0.98[AMR][1000 genomes];0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs574254	0.89[AFR][1000 genomes];0.95[AMR][1000 genomes];0.92[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs578507	0.96[AFR][1000 genomes];0.98[AMR][1000 genomes];0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs581285	0.96[AFR][1000 genomes];0.93[AMR][1000 genomes];0.94[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs586105	0.80[AMR][1000 genomes];0.87[ASN][1000 genomes]
rs598907	0.81[AFR][1000 genomes];0.98[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs605058	0.90[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs62394920	0.81[EUR][1000 genomes]
rs62394921	0.81[EUR][1000 genomes]
rs62394922	0.81[EUR][1000 genomes]
rs62394925	0.81[EUR][1000 genomes]
rs628980	0.96[AFR][1000 genomes];0.91[AMR][1000 genomes];0.90[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs637564	0.92[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs6457608	0.81[EUR][1000 genomes]
rs661055	0.96[AFR][1000 genomes];0.95[AMR][1000 genomes];0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs663283	0.95[AMR][1000 genomes];0.94[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs66502560	0.81[EUR][1000 genomes]
rs67452935	0.81[EUR][1000 genomes]
rs675565	0.96[AFR][1000 genomes];0.98[AMR][1000 genomes];0.95[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs67807015	0.80[EUR][1000 genomes]
rs678862	0.96[AFR][1000 genomes];0.98[AMR][1000 genomes];0.95[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs685384	0.96[AFR][1000 genomes];0.98[AMR][1000 genomes];0.94[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs687163	0.96[AFR][1000 genomes];0.91[AMR][1000 genomes];0.90[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6907890	0.81[EUR][1000 genomes]
rs6907900	0.81[EUR][1000 genomes]
rs6907944	0.81[EUR][1000 genomes]
rs6923613	0.81[EUR][1000 genomes]
rs821443	0.89[AFR][1000 genomes];0.95[AMR][1000 genomes];0.94[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs9348893	0.88[AMR][1000 genomes];0.90[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs9357151	0.82[AMR][1000 genomes];0.86[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs9366802	0.81[EUR][1000 genomes]
rs9368729	0.80[AMR][1000 genomes];0.86[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs9380321	0.96[AFR][1000 genomes];0.90[AMR][1000 genomes];0.90[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs9394108	0.81[EUR][1000 genomes]
rs9394109	0.83[AMR][1000 genomes];0.86[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs9394115	0.96[AFR][1000 genomes];0.90[AMR][1000 genomes];0.90[EUR][1000 genomes];0.96[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:5 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1021078	chr6:10819083-11558560	Enhancers Strong transcription Active TSS Flanking Active TSS Weak transcription Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	47 gene(s)	inside rSNPs	diseases
2	nsv538135	chr6:10819083-11558560	Weak transcription Enhancers Strong transcription Flanking Active TSS Bivalent Enhancer Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	47 gene(s)	inside rSNPs	diseases
3	nsv432848	chr6:11371614-11560114	Enhancers Active TSS Weak transcription ZNF genes & repeats Flanking Active TSS Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	13 gene(s)	inside rSNPs	diseases
4	nsv600989	chr6:11509323-11581990	Enhancers Active TSS Weak transcription Flanking Active TSS Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Strong transcription Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	7 gene(s)	inside rSNPs	diseases
5	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
rs524159	TMEM170B	cis	Adipose Subcutaneous	GTEx

Chromatin state (count:25 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:11540600-11566600	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
2	chr6:11541400-11556000	Enhancers	Primary neutrophils fromperipheralblood	blood
3	chr6:11544400-11554400	Enhancers	Primary monocytes fromperipheralblood	blood
4	chr6:11545600-11554600	Weak transcription	Fetal Brain Female	brain
5	chr6:11548000-11566600	Weak transcription	Placenta	Placenta
6	chr6:11548200-11565800	Weak transcription	Primary B cells from cord blood	blood
7	chr6:11551600-11566600	Weak transcription	Aorta	Aorta
8	chr6:11552800-11566800	Weak transcription	Brain Anterior Caudate	brain
9	chr6:11553000-11556400	Weak transcription	HUES64 Cell Line	embryonic stem cell
10	chr6:11553200-11556400	Weak transcription	HUES48 Cell Line	embryonic stem cell
11	chr6:11553200-11556400	Weak transcription	iPS-18 Cell Line	embryonic stem cell
12	chr6:11553200-11556600	Weak transcription	H9 Cell Line	embryonic stem cell
13	chr6:11553200-11556600	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
14	chr6:11553200-11556600	Weak transcription	Brain Substantia Nigra	brain
15	chr6:11553200-11565000	Weak transcription	Brain Cingulate Gyrus	brain
16	chr6:11553400-11556000	Enhancers	Monocytes-CD14+_RO01746	blood
17	chr6:11553400-11556400	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
18	chr6:11553400-11556600	Weak transcription	H1 Cell Line	embryonic stem cell
19	chr6:11553400-11565800	Weak transcription	Cortex derived primary cultured neurospheres	brain
20	chr6:11553400-11566600	Weak transcription	Primary hematopoietic stem cells short term culture	blood
21	chr6:11553400-11566800	Weak transcription	Gastric	stomach
22	chr6:11553400-11567000	Weak transcription	Brain Inferior Temporal Lobe	brain
23	chr6:11553600-11556400	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
24	chr6:11554000-11554200	Enhancers	Stomach Mucosa	stomach
25	chr6:11554000-11554400	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin

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