Variant report

Variant	rs570749
Chromosome Location	chr6:33710229-33710230
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr6:33706241..33709561-chr6:33709640..33714031,4	MCF-7	breast:
2	chr6:33708694..33710403-chr6:33728367..33730684,2	MCF-7	breast:
3	chr6:33708535..33711845-chr6:33715070..33719242,6	MCF-7	breast:
4	chr6:33704170..33706170-chr6:33708932..33711756,3	MCF-7	breast:

Extended variants
information (count: 32 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:29)

rs_ID	r²[population]
rs10947436	0.83[AFR][1000 genomes];0.85[AMR][1000 genomes];0.94[ASN][1000 genomes]
rs11751943	0.92[AFR][1000 genomes];0.87[AMR][1000 genomes];0.82[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1536500	0.82[EUR][1000 genomes]
rs1536501	0.92[AFR][1000 genomes];0.87[AMR][1000 genomes];0.84[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1547668	0.82[AFR][1000 genomes];0.82[AMR][1000 genomes]
rs1998949	0.81[EUR][1000 genomes]
rs2182659	0.83[AFR][1000 genomes];0.85[AMR][1000 genomes];0.94[ASN][1000 genomes]
rs2395401	0.80[AFR][1000 genomes];0.85[AMR][1000 genomes];0.94[ASN][1000 genomes]
rs2395447	0.83[AFR][1000 genomes];0.82[AMR][1000 genomes];0.94[ASN][1000 genomes]
rs4711350	0.82[AMR][1000 genomes];0.94[ASN][1000 genomes]
rs4713687	0.81[AFR][1000 genomes]
rs4713688	0.81[AFR][1000 genomes]
rs487835	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs530614	0.98[AFR][1000 genomes];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs597723	0.89[EUR][1000 genomes]
rs602399	0.98[AFR][1000 genomes];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs623813	0.80[EUR][1000 genomes]
rs652049	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs680608	0.80[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs688209	0.86[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs751727	0.81[AFR][1000 genomes];0.85[AMR][1000 genomes];0.94[ASN][1000 genomes]
rs7752348	0.89[EUR][1000 genomes]
rs791904	0.97[AFR][1000 genomes];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs942496	0.81[AFR][1000 genomes]
rs943463	0.84[EUR][1000 genomes]
rs943464	0.81[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs943472	0.83[AFR][1000 genomes];0.85[AMR][1000 genomes];0.94[ASN][1000 genomes]
rs9461905	0.82[EUR][1000 genomes]
rs9461907	0.81[EUR][1000 genomes]

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
rs570749	BAK1	cis	Skin Sun Exposed Lower leg	GTEx
rs570749	RXRB	cis	Skin Sun Exposed Lower leg	GTEx

Chromatin state (count:55 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:33686400-33710600	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
2	chr6:33691800-33711600	Weak transcription	Duodenum Smooth Muscle	Duodenum
3	chr6:33693600-33712000	Weak transcription	ES-I3 Cell Line	embryonic stem cell
4	chr6:33694000-33710600	Weak transcription	HUES6 Cell Line	embryonic stem cell
5	chr6:33695600-33711800	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
6	chr6:33705400-33712000	Weak transcription	Placenta Amnion	Placenta Amnion
7	chr6:33705800-33711000	Strong transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
8	chr6:33706600-33715800	Enhancers	Fetal Intestine Large	intestine
9	chr6:33706800-33711400	Weak transcription	Rectal Mucosa Donor 31	rectum
10	chr6:33707200-33711400	Enhancers	Fetal Brain Male	brain
11	chr6:33707400-33714000	Weak transcription	Spleen	Spleen
12	chr6:33707600-33711000	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
13	chr6:33707800-33710600	Genic enhancers	Muscle Satellite Cultured Cells	--
14	chr6:33708200-33710400	Enhancers	Stomach Mucosa	stomach
15	chr6:33708600-33710800	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
16	chr6:33708600-33711600	Weak transcription	HMEC	breast
17	chr6:33708800-33710400	Weak transcription	Fetal Lung	lung
18	chr6:33709000-33710600	Weak transcription	Breast Myoepithelial Primary Cells	Breast
19	chr6:33709000-33710600	Weak transcription	Brain Inferior Temporal Lobe	brain
20	chr6:33709000-33711400	Weak transcription	Liver	Liver
21	chr6:33709000-33711600	Weak transcription	Primary neutrophils fromperipheralblood	blood
22	chr6:33709000-33711600	Weak transcription	HepG2	liver
23	chr6:33709000-33711800	Weak transcription	Hela-S3	cervix
24	chr6:33709000-33712000	Weak transcription	Gastric	stomach
25	chr6:33709000-33712400	Weak transcription	Fetal Heart	heart
26	chr6:33709200-33710400	Weak transcription	Fetal Brain Female	brain
27	chr6:33709200-33710600	Weak transcription	Brain Angular Gyrus	brain
28	chr6:33709200-33710600	Weak transcription	Brain Anterior Caudate	brain
29	chr6:33709200-33710800	Weak transcription	Pancreas	Pancrea
30	chr6:33709200-33711800	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
31	chr6:33709400-33710400	Strong transcription	Foreskin Melanocyte Primary Cells skin01	Skin
32	chr6:33709800-33710800	Enhancers	HSMMtube	muscle
33	chr6:33709800-33711000	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
34	chr6:33709800-33711200	Enhancers	Placenta	Placenta
35	chr6:33710000-33710400	Strong transcription	Brain Cingulate Gyrus	brain
36	chr6:33710000-33710400	Genic enhancers	Brain Hippocampus Middle	brain
37	chr6:33710000-33710600	Genic enhancers	Left Ventricle	heart
38	chr6:33710000-33711000	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
39	chr6:33710000-33711000	Transcr. at gene 5' and 3'	Right Ventricle	heart
40	chr6:33710000-33711200	Enhancers	iPS DF 19.11 Cell Line	embryonic stem cell
41	chr6:33710000-33711200	Transcr. at gene 5' and 3'	Skeletal Muscle Female	skeletal muscle
42	chr6:33710000-33711600	Transcr. at gene 5' and 3'	Skeletal Muscle Male	skeletal muscle
43	chr6:33710000-33711800	Bivalent Enhancer	Fetal Muscle Trunk	muscle
44	chr6:33710000-33712600	Transcr. at gene 5' and 3'	HSMM	muscle
45	chr6:33710200-33710400	Genic enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
46	chr6:33710200-33710400	Flanking Active TSS	Brain Substantia Nigra	brain
47	chr6:33710200-33710400	Bivalent Enhancer	Fetal Stomach	stomach
48	chr6:33710200-33710400	Flanking Active TSS	Psoas Muscle	Psoas
49	chr6:33710200-33710400	Weak transcription	Right Atrium	heart
50	chr6:33710200-33710800	Enhancers	H1 Cell Line	embryonic stem cell

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