Variant report

Variant	rs566237
Chromosome Location	chr6:11543342-11543343
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr6:11537385..11540114-chr6:11542769..11544308,2	K562	blood:
2	chr6:11537112..11540314-chr6:11541089..11545769,6	MCF-7	breast:
3	chr6:11537155..11540056-chr6:11540130..11543939,4	MCF-7	breast:

Variant related genes	Relation type
ENSG00000205269	Chromatin interaction

Extended variants
information (count: 50 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:46)

rs_ID	r²[population]
rs2327440	1.00[JPT][hapmap]
rs4711303	0.85[JPT][hapmap]
rs4713562	0.85[JPT][hapmap]
rs4713577	0.84[JPT][hapmap]
rs4713579	0.84[JPT][hapmap]
rs471560	0.90[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs471752	0.90[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs478147	0.81[CEU][hapmap];0.85[JPT][hapmap]
rs483637	0.86[AMR][1000 genomes];0.84[ASN][1000 genomes]
rs490466	0.80[CEU][hapmap];0.90[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs509971	0.90[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs513870	1.00[CEU][hapmap];0.83[CHB][hapmap];0.95[JPT][hapmap];0.88[AMR][1000 genomes];0.91[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs519140	0.87[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs524159	0.92[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs528679	0.82[AMR][1000 genomes]
rs539160	0.84[AMR][1000 genomes]
rs552681	0.90[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs554671	0.80[CEU][hapmap];0.83[CHB][hapmap];0.84[JPT][hapmap];0.90[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs555034	0.85[CEU][hapmap];0.85[JPT][hapmap];0.84[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs555742	0.81[CEU][hapmap];0.87[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs56055084	0.83[ASN][1000 genomes]
rs571683	0.87[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs573082	0.90[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs574254	0.87[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs578507	0.90[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs581285	0.86[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs588062	0.82[CEU][hapmap]
rs598907	0.81[CEU][hapmap];0.90[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs605058	0.82[AMR][1000 genomes]
rs606402	0.80[CEU][hapmap];0.84[JPT][hapmap]
rs620729	1.00[CEU][hapmap];0.83[CHB][hapmap];0.95[JPT][hapmap]
rs628980	0.80[CEU][hapmap];0.84[JPT][hapmap];0.84[AMR][1000 genomes]
rs637564	0.84[AMR][1000 genomes]
rs661055	0.87[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs663283	0.87[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs675565	0.80[CEU][hapmap];0.83[CHB][hapmap];0.84[JPT][hapmap];0.90[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs678862	0.81[CEU][hapmap];0.84[CHB][hapmap];0.85[JPT][hapmap];0.90[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs685384	0.81[CEU][hapmap];0.90[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs687163	0.84[AMR][1000 genomes]
rs6936326	0.84[CHB][hapmap];0.95[JPT][hapmap];0.96[ASN][1000 genomes]
rs821443	0.87[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs9348893	0.81[AMR][1000 genomes]
rs9380321	0.82[AMR][1000 genomes]
rs9394109	0.85[JPT][hapmap]
rs9394115	0.80[CEU][hapmap];0.84[JPT][hapmap];0.82[AMR][1000 genomes]
rs9394119	0.89[CHB][hapmap];1.00[JPT][hapmap];0.96[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:4 , 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

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs566237	TMEM170B	cis	Adipose Subcutaneous	GTEx

Chromatin state (count:22 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:11539600-11547000	Weak transcription	Duodenum Smooth Muscle	Duodenum
2	chr6:11540200-11545400	Weak transcription	Fetal Brain Male	brain
3	chr6:11540200-11547000	Weak transcription	Adipose Nuclei	Adipose
4	chr6:11540200-11547000	Weak transcription	Pancreatic Islets	Pancreatic Islet
5	chr6:11540200-11552000	Weak transcription	Brain Cingulate Gyrus	brain
6	chr6:11540400-11543800	Weak transcription	Liver	Liver
7	chr6:11540400-11544600	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
8	chr6:11540400-11544800	Weak transcription	Brain Germinal Matrix	brain
9	chr6:11540400-11551600	Weak transcription	Primary hematopoietic stem cells short term culture	blood
10	chr6:11540400-11552600	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
11	chr6:11540600-11543800	Weak transcription	Primary hematopoietic stem cells	blood
12	chr6:11540600-11544400	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
13	chr6:11540600-11566600	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
14	chr6:11540800-11551200	Weak transcription	Brain Substantia Nigra	brain
15	chr6:11541000-11544800	Weak transcription	Brain Anterior Caudate	brain
16	chr6:11541400-11544400	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
17	chr6:11541400-11544600	Weak transcription	Fetal Brain Female	brain
18	chr6:11541400-11556000	Enhancers	Primary neutrophils fromperipheralblood	blood
19	chr6:11542400-11546400	Flanking Active TSS	Monocytes-CD14+_RO01746	blood
20	chr6:11542800-11543400	Enhancers	Cortex derived primary cultured neurospheres	brain
21	chr6:11543000-11543400	Enhancers	Primary monocytes fromperipheralblood	blood
22	chr6:11543200-11545000	Enhancers	Primary B cells from cord blood	blood

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links