Variant report

Variant	rs688209
Chromosome Location	chr6:33700376-33700377
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:0)
CpG islands
(count:0)
Chromatin interactive
region (count:8)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

(count:8 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr6:33699067..33701380-chr6:33760767..33763233,2	MCF-7	breast:
2	chr12:115690369..115693198-chr6:33698849..33701409,2	MCF-7	breast:
3	chr6:33700010..33701892-chr6:33765256..33768196,2	MCF-7	breast:
4	chr6:33698259..33701003-chr6:33736395..33738930,2	K562	blood:
5	chr6:33697890..33700582-chr6:35133101..35134719,2	MCF-7	breast:
6	chr6:33694998..33697623-chr6:33697893..33701266,3	K562	blood:
7	chr6:33673158..33676456-chr6:33698317..33701048,3	MCF-7	breast:
8	chr6:33699163..33701430-chr6:33753710..33757640,3	MCF-7	breast:

No data

Variant related genes	Relation type
ENSG00000161904	Chromatin interaction

Extended variants
information (count: 41 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:38)

rs_ID	r²[population]
rs10672	1.00[JPT][hapmap]
rs10947428	1.00[CEU][hapmap];0.81[TSI][hapmap];0.81[EUR][1000 genomes]
rs10947436	0.84[CEU][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap]
rs1536500	0.82[EUR][1000 genomes]
rs1536501	0.89[CEU][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.83[TSI][hapmap];0.81[EUR][1000 genomes]
rs1547668	0.84[CEU][hapmap]
rs1998949	0.89[CEU][hapmap];1.00[JPT][hapmap];0.82[EUR][1000 genomes]
rs2182659	0.84[CEU][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap]
rs2395401	0.84[CEU][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap]
rs2395448	0.83[CEU][hapmap];1.00[JPT][hapmap]
rs2967	1.00[CHB][hapmap];1.00[JPT][hapmap];0.80[ASN][1000 genomes]
rs4711350	0.84[CEU][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap]
rs487835	0.86[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs498114	1.00[JPT][hapmap]
rs530614	0.94[CEU][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.90[TSI][hapmap];0.88[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs549652	0.84[CEU][hapmap];0.88[GIH][hapmap];1.00[JPT][hapmap];0.88[ASN][1000 genomes]
rs570749	0.86[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs597386	0.88[GIH][hapmap];1.00[JPT][hapmap]
rs597723	0.82[AFR][1000 genomes];0.89[AMR][1000 genomes];0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs602399	0.94[CEU][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.91[MEX][hapmap];0.90[TSI][hapmap];0.88[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs608971	1.00[JPT][hapmap];0.94[ASN][1000 genomes]
rs623813	1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.94[ASN][1000 genomes]
rs652049	0.94[CEU][hapmap];1.00[GIH][hapmap];0.81[MEX][hapmap];0.90[TSI][hapmap];0.86[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs654682	1.00[JPT][hapmap]
rs658087	0.84[CEU][hapmap];0.88[GIH][hapmap];1.00[JPT][hapmap];0.88[ASN][1000 genomes]
rs684119	0.84[CEU][hapmap];0.88[GIH][hapmap];1.00[JPT][hapmap];0.88[ASN][1000 genomes]
rs6913517	1.00[JPT][hapmap]
rs6915136	0.84[CEU][hapmap];0.88[GIH][hapmap];1.00[JPT][hapmap]
rs751727	0.84[CEU][hapmap];1.00[JPT][hapmap]
rs764753	1.00[JPT][hapmap]
rs7752348	0.85[EUR][1000 genomes]
rs791904	0.86[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs943463	0.94[CEU][hapmap];1.00[JPT][hapmap];0.90[TSI][hapmap];0.85[EUR][1000 genomes]
rs943464	0.84[CEU][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap]
rs943472	0.84[CEU][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap]
rs9461905	0.94[CEU][hapmap];1.00[JPT][hapmap];0.82[EUR][1000 genomes]
rs9461907	0.83[EUR][1000 genomes]
rs9469542	1.00[JPT][hapmap]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv830638	chr6:33551202-33711346	Enhancers Weak transcription Active TSS Flanking Active TSS Genic enhancers Bivalent/Poised TSS Strong transcription ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA	46 gene(s)	inside rSNPs	diseases
2	nsv830639	chr6:33592022-33711346	Strong transcription Enhancers Flanking Active TSS Weak transcription Transcr. at gene 5' and 3' Active TSS Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA	30 gene(s)	inside rSNPs	diseases
3	nsv885772	chr6:33638180-33767727	Bivalent Enhancer Genic enhancers Strong transcription Enhancers Weak transcription Transcr. at gene 5' and 3' Flanking Active TSS Active TSS Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA	28 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs688209	BAK1	cis	Skin Sun Exposed Lower leg	GTEx
rs688209	C6orf125	cis	cerebellum	SCAN

Chromatin state (count:52 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:33680000-33705000	Weak transcription	Brain Angular Gyrus	brain
2	chr6:33686400-33710600	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
3	chr6:33690800-33708200	Weak transcription	Gastric	stomach
4	chr6:33691800-33711600	Weak transcription	Duodenum Smooth Muscle	Duodenum
5	chr6:33692000-33706800	Weak transcription	Fetal Intestine Small	intestine
6	chr6:33692000-33710200	Weak transcription	Colon Smooth Muscle	Colon
7	chr6:33692800-33701000	Weak transcription	Fetal Brain Female	brain
8	chr6:33693200-33700800	Strong transcription	Fetal Muscle Leg	muscle
9	chr6:33693400-33701200	Enhancers	Breast Myoepithelial Primary Cells	Breast
10	chr6:33693600-33712000	Weak transcription	ES-I3 Cell Line	embryonic stem cell
11	chr6:33694000-33710600	Weak transcription	HUES6 Cell Line	embryonic stem cell
12	chr6:33695000-33702400	Weak transcription	Brain Anterior Caudate	brain
13	chr6:33695600-33711800	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
14	chr6:33696600-33700400	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
15	chr6:33697200-33700400	Weak transcription	Brain Inferior Temporal Lobe	brain
16	chr6:33697800-33701000	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
17	chr6:33698200-33700400	Enhancers	Lung	lung
18	chr6:33698200-33700600	Enhancers	Right Atrium	heart
19	chr6:33698200-33700800	Genic enhancers	Brain Substantia Nigra	brain
20	chr6:33698200-33700800	Strong transcription	Fetal Muscle Trunk	muscle
21	chr6:33698200-33701600	Genic enhancers	Left Ventricle	heart
22	chr6:33698200-33702400	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
23	chr6:33698400-33703000	Enhancers	Placenta Amnion	Placenta Amnion
24	chr6:33698400-33703400	Strong transcription	Spleen	Spleen
25	chr6:33698600-33700400	Strong transcription	Muscle Satellite Cultured Cells	--
26	chr6:33698600-33700800	Genic enhancers	Foreskin Melanocyte Primary Cells skin01	Skin
27	chr6:33698600-33701200	Genic enhancers	Brain Hippocampus Middle	brain
28	chr6:33699200-33710000	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
29	chr6:33699400-33700400	Enhancers	Esophagus	oesophagus
30	chr6:33699400-33700600	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
31	chr6:33699400-33701200	Genic enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
32	chr6:33699400-33703600	Genic enhancers	Right Ventricle	heart
33	chr6:33699600-33700600	Genic enhancers	Brain Cingulate Gyrus	brain
34	chr6:33699600-33701000	Weak transcription	Psoas Muscle	Psoas
35	chr6:33699600-33701200	Bivalent Enhancer	Foreskin Fibroblast Primary Cells skin01	Skin
36	chr6:33699800-33700800	Enhancers	HMEC	breast
37	chr6:33699800-33701000	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
38	chr6:33699800-33708000	Weak transcription	Fetal Lung	lung
39	chr6:33700000-33700600	Enhancers	iPS DF 19.11 Cell Line	embryonic stem cell
40	chr6:33700000-33700600	Flanking Active TSS	Skeletal Muscle Female	skeletal muscle
41	chr6:33700000-33700600	Genic enhancers	HSMM	muscle
42	chr6:33700000-33700600	Genic enhancers	HSMMtube	muscle
43	chr6:33700000-33701600	Genic enhancers	Placenta	Placenta
44	chr6:33700000-33701600	Transcr. at gene 5' and 3'	Skeletal Muscle Male	skeletal muscle
45	chr6:33700000-33705000	Weak transcription	Pancreas	Pancrea
46	chr6:33700200-33700600	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
47	chr6:33700200-33700600	Bivalent Enhancer	HepG2	liver
48	chr6:33700200-33701000	Genic enhancers	Foreskin Fibroblast Primary Cells skin02	Skin
49	chr6:33700200-33701000	Strong transcription	Liver	Liver
50	chr6:33700200-33701000	Enhancers	NHDF-Ad	bronchial

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