Variant report

Variant	rs652049
Chromosome Location	chr6:33711420-33711421
allele	C/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:11)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

(count:11 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr6:33710780..33712378-chr6:33728766..33730415,2	K562	blood:
2	chr6:33706317..33709748-chr6:33710509..33712632,5	MCF-7	breast:
3	chr6:33710698..33713860-chr6:33753568..33757560,4	MCF-7	breast:
4	chr6:33706241..33709561-chr6:33709640..33714031,4	MCF-7	breast:
5	chr6:33710878..33712572-chr6:33728483..33730415,2	K562	blood:
6	chr6:33710782..33712479-chr6:33760281..33762991,2	MCF-7	breast:
7	chr6:33708535..33711845-chr6:33715070..33719242,6	MCF-7	breast:
8	chr6:33587417..33588935-chr6:33710962..33713150,2	MCF-7	breast:
9	chr6:33711077..33714000-chr6:33723904..33727038,3	MCF-7	breast:
10	chr6:33704170..33706170-chr6:33708932..33711756,3	MCF-7	breast:
11	chr6:33667241..33669923-chr6:33710850..33712681,2	K562	blood:

No data

Variant related genes	Relation type
ENSG00000161904	Chromatin interaction
ENSG00000096433	Chromatin interaction

Extended variants
information (count: 42 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:41)

rs_ID	r²[population]
rs10947428	0.94[CEU][hapmap]
rs10947436	0.92[ASW][hapmap];0.89[CEU][hapmap];1.00[GIH][hapmap];0.88[LWK][hapmap];0.90[MEX][hapmap];0.86[TSI][hapmap];0.96[YRI][hapmap];0.81[AFR][1000 genomes];0.85[AMR][1000 genomes];0.80[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs10947446	0.83[CEU][hapmap]
rs11751943	0.90[AFR][1000 genomes];0.87[AMR][1000 genomes];0.84[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs1536500	0.83[EUR][1000 genomes]
rs1536501	1.00[ASW][hapmap];0.94[CEU][hapmap];1.00[GIH][hapmap];0.97[LWK][hapmap];0.90[MEX][hapmap];0.93[TSI][hapmap];1.00[YRI][hapmap];0.90[AFR][1000 genomes];0.87[AMR][1000 genomes];0.85[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs1547668	0.84[ASW][hapmap];0.89[CEU][hapmap];0.80[LWK][hapmap];0.81[MEX][hapmap];0.80[AFR][1000 genomes];0.82[AMR][1000 genomes]
rs1998949	0.83[CEU][hapmap];0.82[EUR][1000 genomes]
rs2182658	0.92[ASW][hapmap];0.96[YRI][hapmap]
rs2182659	0.92[ASW][hapmap];0.89[CEU][hapmap];1.00[GIH][hapmap];0.88[LWK][hapmap];0.90[MEX][hapmap];0.86[TSI][hapmap];0.96[YRI][hapmap];0.81[AFR][1000 genomes];0.85[AMR][1000 genomes];0.80[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs2395401	0.92[ASW][hapmap];0.89[CEU][hapmap];1.00[GIH][hapmap];0.81[LWK][hapmap];0.90[MEX][hapmap];0.86[TSI][hapmap];0.96[YRI][hapmap];0.85[AMR][1000 genomes];0.80[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs2395447	0.81[AFR][1000 genomes];0.82[AMR][1000 genomes];0.80[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs2395448	0.89[CEU][hapmap]
rs4711350	0.89[CEU][hapmap];1.00[GIH][hapmap];0.90[MEX][hapmap];0.86[TSI][hapmap];0.82[AMR][1000 genomes];0.80[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs487835	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs530614	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[GIH][hapmap];0.95[LWK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs549652	0.89[CEU][hapmap];0.83[CHD][hapmap];0.88[GIH][hapmap]
rs570749	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs597386	0.88[GIH][hapmap]
rs597723	0.91[EUR][1000 genomes]
rs602399	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[GIH][hapmap];0.97[LWK][hapmap];0.90[MEX][hapmap];0.88[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs608971	0.82[CEU][hapmap];1.00[CHB][hapmap]
rs623813	0.82[CEU][hapmap];1.00[GIH][hapmap];0.82[EUR][1000 genomes]
rs658087	0.89[CEU][hapmap];0.88[GIH][hapmap]
rs680608	0.82[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs684119	0.89[CEU][hapmap];0.83[CHD][hapmap];0.88[GIH][hapmap]
rs688209	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]
rs6915136	0.89[CEU][hapmap];0.88[GIH][hapmap]
rs751727	0.89[CEU][hapmap];0.85[AMR][1000 genomes];0.80[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs756138	0.92[YRI][hapmap]
rs756139	0.92[ASW][hapmap];0.92[YRI][hapmap]
rs7739273	0.91[YRI][hapmap]
rs7752348	0.90[EUR][1000 genomes]
rs791904	0.99[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs942496	0.84[ASW][hapmap];0.83[CEU][hapmap];0.83[LWK][hapmap]
rs943463	0.89[CEU][hapmap];0.87[TSI][hapmap];0.86[EUR][1000 genomes]
rs943464	0.89[CEU][hapmap];1.00[GIH][hapmap];0.81[MEX][hapmap];0.87[TSI][hapmap];0.82[YRI][hapmap];0.82[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs943472	0.92[ASW][hapmap];0.89[CEU][hapmap];1.00[GIH][hapmap];0.88[LWK][hapmap];0.90[MEX][hapmap];0.86[TSI][hapmap];0.96[YRI][hapmap];0.81[AFR][1000 genomes];0.85[AMR][1000 genomes];0.83[ASN][1000 genomes]
rs943476	1.00[ASW][hapmap];0.96[YRI][hapmap]
rs9461905	0.89[CEU][hapmap];0.83[EUR][1000 genomes]
rs9461907	0.82[EUR][1000 genomes]

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

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	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
rs652049	C6orf125	cis	cerebellum	SCAN
rs652049	BAK1	cis	Skin Sun Exposed Lower leg	GTEx

Chromatin state (count:61 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:33691800-33711600	Weak transcription	Duodenum Smooth Muscle	Duodenum
2	chr6:33693600-33712000	Weak transcription	ES-I3 Cell Line	embryonic stem cell
3	chr6:33695600-33711800	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
4	chr6:33705400-33712000	Weak transcription	Placenta Amnion	Placenta Amnion
5	chr6:33706600-33715800	Enhancers	Fetal Intestine Large	intestine
6	chr6:33707400-33714000	Weak transcription	Spleen	Spleen
7	chr6:33708600-33711600	Weak transcription	HMEC	breast
8	chr6:33709000-33711600	Weak transcription	Primary neutrophils fromperipheralblood	blood
9	chr6:33709000-33711600	Weak transcription	HepG2	liver
10	chr6:33709000-33711800	Weak transcription	Hela-S3	cervix
11	chr6:33709000-33712000	Weak transcription	Gastric	stomach
12	chr6:33709000-33712400	Weak transcription	Fetal Heart	heart
13	chr6:33709200-33711800	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
14	chr6:33710000-33711600	Transcr. at gene 5' and 3'	Skeletal Muscle Male	skeletal muscle
15	chr6:33710000-33711800	Bivalent Enhancer	Fetal Muscle Trunk	muscle
16	chr6:33710000-33712600	Transcr. at gene 5' and 3'	HSMM	muscle
17	chr6:33710200-33712000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
18	chr6:33710400-33711600	Weak transcription	Stomach Mucosa	stomach
19	chr6:33710400-33712000	Enhancers	Brain Hippocampus Middle	brain
20	chr6:33710400-33712000	Enhancers	Brain Substantia Nigra	brain
21	chr6:33710400-33712000	Enhancers	Fetal Lung	lung
22	chr6:33710400-33712200	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
23	chr6:33710600-33711600	Transcr. at gene 5' and 3'	Muscle Satellite Cultured Cells	--
24	chr6:33710600-33711800	Enhancers	Brain Anterior Caudate	brain
25	chr6:33710600-33712000	Enhancers	Brain Angular Gyrus	brain
26	chr6:33710600-33712000	Enhancers	Brain Inferior Temporal Lobe	brain
27	chr6:33710600-33713200	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
28	chr6:33710600-33715200	Enhancers	Breast Myoepithelial Primary Cells	Breast
29	chr6:33710800-33711800	Weak transcription	HUES6 Cell Line	embryonic stem cell
30	chr6:33710800-33711800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
31	chr6:33710800-33711800	Weak transcription	HSMMtube	muscle
32	chr6:33710800-33712000	Weak transcription	H1 Cell Line	embryonic stem cell
33	chr6:33710800-33712000	Weak transcription	HUES48 Cell Line	embryonic stem cell
34	chr6:33710800-33712000	Weak transcription	HUES64 Cell Line	embryonic stem cell
35	chr6:33710800-33712000	Enhancers	Brain Cingulate Gyrus	brain
36	chr6:33710800-33712400	Weak transcription	iPS-18 Cell Line	embryonic stem cell
37	chr6:33710800-33712400	Weak transcription	Colon Smooth Muscle	Colon
38	chr6:33710800-33714200	Enhancers	Pancreas	Pancrea
39	chr6:33710800-33716600	Active TSS	Psoas Muscle	Psoas
40	chr6:33711000-33711800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
41	chr6:33711000-33711800	Weak transcription	Left Ventricle	heart
42	chr6:33711000-33712000	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
43	chr6:33711000-33712000	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
44	chr6:33711000-33712000	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
45	chr6:33711000-33712000	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
46	chr6:33711000-33712000	Weak transcription	Right Atrium	heart
47	chr6:33711000-33712000	Active TSS	Right Ventricle	heart
48	chr6:33711000-33712800	Weak transcription	Lung	lung
49	chr6:33711200-33711600	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
50	chr6:33711200-33711600	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell

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