Variant report

Variant	rs202069
Chromosome Location	chr6:13267241-13267242
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr6:13266277..13270174-chr6:13278637..13282022,4	MCF-7	breast:
2	chr6:13258559..13263124-chr6:13265994..13271116,8	K562	blood:
3	chr6:13265469..13267865-chr6:13268622..13270348,2	K562	blood:
4	chr6:13259737..13263124-chr6:13265994..13271257,6	K562	blood:

Extended variants
information (count: 29 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:24)

rs_ID	r²[population]
rs1150623	0.80[ASN][1000 genomes]
rs12194742	0.80[GIH][hapmap];0.87[JPT][hapmap];0.93[TSI][hapmap];0.84[EUR][1000 genomes]
rs1223393	0.90[CEU][hapmap];0.87[CHB][hapmap];0.85[CHD][hapmap];0.95[GIH][hapmap];0.91[JPT][hapmap];1.00[TSI][hapmap];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1232381	0.87[JPT][hapmap];0.86[TSI][hapmap];0.83[EUR][1000 genomes]
rs1550526	0.90[CEU][hapmap]
rs182148	1.00[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];0.80[MEX][hapmap];1.00[TSI][hapmap];0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs202025	0.90[EUR][1000 genomes]
rs202027	0.87[JPT][hapmap];0.90[EUR][1000 genomes]
rs202030	0.90[CEU][hapmap];0.81[EUR][1000 genomes]
rs202038	0.90[CEU][hapmap];0.80[MEX][hapmap];0.82[TSI][hapmap];0.81[EUR][1000 genomes]
rs202040	0.90[CEU][hapmap];0.81[EUR][1000 genomes]
rs202048	0.89[EUR][1000 genomes]
rs202064	0.90[CEU][hapmap];0.82[CHB][hapmap];0.93[TSI][hapmap];0.95[EUR][1000 genomes]
rs202068	0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs202070	0.87[CHB][hapmap];0.95[JPT][hapmap];0.94[ASN][1000 genomes]
rs202071	0.87[CHB][hapmap];0.95[JPT][hapmap];0.94[ASN][1000 genomes]
rs202072	0.87[CHB][hapmap];0.93[CHD][hapmap];0.95[JPT][hapmap];0.94[ASN][1000 genomes]
rs202073	0.87[CHB][hapmap];0.93[CHD][hapmap];0.95[JPT][hapmap];0.94[ASN][1000 genomes]
rs366904	1.00[CHB][hapmap];0.97[CHD][hapmap];1.00[JPT][hapmap];0.86[TSI][hapmap];0.89[AMR][1000 genomes];0.99[ASN][1000 genomes]
rs453695	0.90[CEU][hapmap];0.95[CHB][hapmap];0.83[GIH][hapmap];0.87[JPT][hapmap];0.86[TSI][hapmap];0.95[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs454563	0.90[CEU][hapmap]
rs4602719	0.90[CEU][hapmap]
rs536208	0.92[EUR][1000 genomes]
rs8541	0.90[CEU][hapmap];0.80[MEX][hapmap];0.82[TSI][hapmap];0.81[EUR][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	nsv532021	chr6:13232627-13805381	Active TSS Genic enhancers Strong transcription Enhancers Flanking Active TSS Weak transcription Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	74 gene(s)	inside rSNPs	diseases
2	nsv1028533	chr6:13239059-13484814	Enhancers Strong transcription Weak transcription ZNF genes & repeats Active TSS Flanking Active TSS Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	23 gene(s)	inside rSNPs	diseases
3	nsv538136	chr6:13239059-13484814	Strong transcription Weak transcription Enhancers Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Active TSS Genic enhancers ZNF genes & repeats Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	23 gene(s)	inside rSNPs	diseases
4	nsv1034016	chr6:13248122-13418225	Enhancers Flanking Active TSS Strong transcription Weak transcription Genic enhancers Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	22 gene(s)	inside rSNPs	diseases
5	esv2761063	chr6:13265334-13268211	Weak transcription Strong transcription ZNF genes & repeats Enhancers Genic enhancers	TF binding region Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs202069	TBC1D7,LOC100130357	cis	brain	BrainEAC

Chromatin state (count:44 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:13249200-13272200	Weak transcription	Brain Inferior Temporal Lobe	brain
2	chr6:13249800-13287000	Weak transcription	Fetal Brain Male	brain
3	chr6:13256600-13268800	Weak transcription	Right Ventricle	heart
4	chr6:13256600-13272200	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
5	chr6:13256600-13273200	Weak transcription	Duodenum Smooth Muscle	Duodenum
6	chr6:13256600-13278200	Weak transcription	Pancreas	Pancrea
7	chr6:13258800-13272200	Weak transcription	Left Ventricle	heart
8	chr6:13259400-13267400	Weak transcription	Fetal Heart	heart
9	chr6:13261000-13268800	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
10	chr6:13261400-13272200	Weak transcription	Brain Angular Gyrus	brain
11	chr6:13261400-13272200	Weak transcription	Brain Cingulate Gyrus	brain
12	chr6:13261400-13273000	Weak transcription	Adipose Nuclei	Adipose
13	chr6:13261600-13272200	Weak transcription	Brain Hippocampus Middle	brain
14	chr6:13262600-13272400	Enhancers	Primary B cells from peripheral blood	blood
15	chr6:13262600-13272800	Weak transcription	Primary T cells from cord blood	blood
16	chr6:13263200-13269200	Weak transcription	iPS-15b Cell Line	embryonic stem cell
17	chr6:13263400-13268800	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
18	chr6:13263400-13272400	Weak transcription	Spleen	Spleen
19	chr6:13263800-13267800	Weak transcription	Monocytes-CD14+_RO01746	blood
20	chr6:13264200-13267600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
21	chr6:13264600-13272200	Weak transcription	Fetal Muscle Leg	muscle
22	chr6:13265400-13267800	Strong transcription	Stomach Smooth Muscle	stomach
23	chr6:13265800-13267800	Strong transcription	Brain Anterior Caudate	brain
24	chr6:13266000-13267400	ZNF genes & repeats	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
25	chr6:13266000-13267400	Strong transcription	Fetal Brain Female	brain
26	chr6:13266200-13267400	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
27	chr6:13266200-13267800	Strong transcription	Primary hematopoietic stem cells	blood
28	chr6:13266400-13267400	ZNF genes & repeats	Primary hematopoietic stem cells short term culture	blood
29	chr6:13266600-13267400	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
30	chr6:13266600-13267400	ZNF genes & repeats	Foreskin Melanocyte Primary Cells skin03	Skin
31	chr6:13266600-13267400	Strong transcription	Brain Germinal Matrix	brain
32	chr6:13266800-13267600	ZNF genes & repeats	Primary neutrophils fromperipheralblood	blood
33	chr6:13266800-13268000	ZNF genes & repeats	K562	blood
34	chr6:13267000-13267400	Strong transcription	Fetal Stomach	stomach
35	chr6:13267000-13269800	Weak transcription	Lung	lung
36	chr6:13267000-13274200	Weak transcription	Gastric	stomach
37	chr6:13267200-13267400	Genic enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
38	chr6:13267200-13268000	Enhancers	Foreskin Fibroblast Primary Cells skin02	Skin
39	chr6:13267200-13268000	Enhancers	HSMMtube	muscle
40	chr6:13267200-13268600	Enhancers	HSMM	muscle
41	chr6:13267200-13268800	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
42	chr6:13267200-13268800	Weak transcription	Aorta	Aorta
43	chr6:13267200-13269000	Weak transcription	HUES6 Cell Line	embryonic stem cell
44	chr6:13267200-13272000	Enhancers	Primary B cells from cord blood	blood

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