Variant report

Variant	rs3445
Chromosome Location	chr6:33246518-33246519
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:20)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

(count:20 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr6:33214775..33224346-chr6:33236521..33248678,40	K562	blood:
2	chr6:33163540..33178083-chr6:33236797..33246926,29	MCF-7	breast:
3	chr6:33243392..33248315-chr6:33357393..33361975,11	K562	blood:
4	chr6:33242863..33248981-chr6:33374531..33379553,10	MCF-7	breast:
5	chr6:33237079..33247876-chr6:33369927..33381738,26	K562	blood:
6	chr6:33174484..33176596-chr6:33246131..33248374,2	K562	blood:
7	chr6:33244147..33247113-chr6:33398461..33400467,3	K562	blood:
8	chr3:186500386..186502524-chr6:33245530..33247369,2	MCF-7	breast:
9	chr6:33243260..33246626-chr6:33279357..33283682,8	MCF-7	breast:
10	chr6:33165702..33182742-chr6:33234718..33250379,54	K562	blood:
11	chr6:33237732..33247113-chr6:33390735..33401356,31	K562	blood:
12	chr6:32939187..32940741-chr6:33244329..33246573,2	K562	blood:
13	chr6:33237328..33248026-chr6:33370896..33379989,29	K562	blood:
14	chr6:33245204..33246812-chr6:33420469..33423462,2	MCF-7	breast:
15	chr6:33242365..33247657-chr6:33386109..33388284,6	K562	blood:
16	chr6:33244680..33251060-chr6:33375427..33382644,12	MCF-7	breast:
17	chr6:33237283..33247485-chr6:33356185..33362256,17	K562	blood:
18	chr6:33241747..33248128-chr6:33380775..33386072,13	K562	blood:
19	chr6:33242542..33249529-chr6:33381747..33388277,18	K562	blood:
20	chr6:33243431..33246571-chr6:33357252..33359910,3	MCF-7	breast:

No data

Variant related genes	Relation type
ENSG00000232940	Chromatin interaction
ENSG00000204227	Chromatin interaction
ENSG00000202441	Chromatin interaction
ENSG00000112473	Chromatin interaction
ENSG00000156976	Chromatin interaction
ENSG00000263756	Chromatin interaction
ENSG00000199036	Chromatin interaction
ENSG00000204228	Chromatin interaction
ENSG00000112514	Chromatin interaction
ENSG00000237649	Chromatin interaction
ENSG00000231925	Chromatin interaction
ENSG00000204256	Chromatin interaction
ENSG00000204231	Chromatin interaction
ENSG00000213588	Chromatin interaction
ENSG00000263826	Chromatin interaction
ENSG00000197283	Chromatin interaction
ENSG00000225644	Chromatin interaction
ENSG00000112511	Chromatin interaction

Extended variants
information (count: 18 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:10)

rs_ID	r²[population]
rs1061801	0.81[ASN][1000 genomes]
rs458434	0.95[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs460568	0.85[EUR][1000 genomes]
rs461338	0.86[AMR][1000 genomes];0.94[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs462618	0.86[AMR][1000 genomes];0.94[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs464921	0.86[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs466886	0.86[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs9277956	0.86[AMR][1000 genomes];0.92[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs9277958	0.86[AMR][1000 genomes];0.94[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs9277965	0.86[AMR][1000 genomes];0.92[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:8 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv462893	chr6:33142539-33256471	Weak transcription Enhancers Transcr. at gene 5' and 3' Genic enhancers Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh Strong transcription Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	104 gene(s)	inside rSNPs	diseases
2	nsv602830	chr6:33142539-33256471	Enhancers Bivalent Enhancer Flanking Active TSS Genic enhancers Strong transcription Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Weak transcription Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	104 gene(s)	inside rSNPs	diseases
3	nsv830634	chr6:33161217-33330745	Flanking Active TSS Genic enhancers Active TSS Strong transcription Weak transcription Enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	139 gene(s)	inside rSNPs	diseases
4	nsv462894	chr6:33174783-33254665	Weak transcription Transcr. at gene 5' and 3' Flanking Active TSS Strong transcription Genic enhancers Bivalent/Poised TSS Active TSS Bivalent Enhancer Enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA	87 gene(s)	inside rSNPs	diseases
5	nsv602831	chr6:33174783-33254665	Enhancers Bivalent Enhancer Weak transcription Flanking Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS Strong transcription Active TSS Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA	87 gene(s)	inside rSNPs	diseases
6	nsv5249	chr6:33231743-33249478	Strong transcription Weak transcription Transcr. at gene 5' and 3' Enhancers Flanking Active TSS Genic enhancers Active TSS Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region	62 gene(s)	inside rSNPs	diseases
7	nsv830635	chr6:33238005-33413787	Active TSS Flanking Bivalent TSS/Enh Weak transcription Genic enhancers Transcr. at gene 5' and 3' Enhancers Strong transcription Flanking Active TSS ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	129 gene(s)	inside rSNPs	diseases
8	nsv970109	chr6:33241506-33248502	Strong transcription Active TSS Genic enhancers Transcr. at gene 5' and 3' Weak transcription Enhancers Flanking Active TSS	TF binding region CpG island Chromatin interactive region	36 gene(s)	inside rSNPs	diseases

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs3445	ENSG00000204222	cis	multi-tissue	Pritchard
rs3445	B3GALT4	cis	Cerebellum	GTEx
rs3445	B3GALT4	cis	multi-tissue	Pritchard
rs3445	STK38	cis	parietal	SCAN

Chromatin state (count:127 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:33240600-33248800	Transcr. at gene 5' and 3'	Foreskin Fibroblast Primary Cells skin01	Skin
2	chr6:33241800-33248800	Transcr. at gene 5' and 3'	Foreskin Fibroblast Primary Cells skin02	Skin
3	chr6:33244800-33247000	Enhancers	Fetal Brain Male	brain
4	chr6:33244800-33249200	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
5	chr6:33245000-33246600	Weak transcription	HepG2	liver
6	chr6:33245200-33248200	Weak transcription	HSMMtube	muscle
7	chr6:33245400-33247000	Weak transcription	HSMM	muscle
8	chr6:33245400-33247200	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
9	chr6:33245400-33248800	Strong transcription	Muscle Satellite Cultured Cells	--
10	chr6:33245600-33247000	Weak transcription	Ovary	ovary
11	chr6:33245600-33247600	Strong transcription	A549	lung
12	chr6:33245600-33249400	Strong transcription	HMEC	breast
13	chr6:33245600-33250400	Strong transcription	NHLF	lung
14	chr6:33245600-33251400	Weak transcription	NHDF-Ad	bronchial
15	chr6:33245600-33255200	Strong transcription	NHEK	skin
16	chr6:33245600-33255400	Strong transcription	Breast Myoepithelial Primary Cells	Breast
17	chr6:33245800-33246600	Transcr. at gene 5' and 3'	Foreskin Melanocyte Primary Cells skin01	Skin
18	chr6:33245800-33246600	Enhancers	Brain Inferior Temporal Lobe	brain
19	chr6:33245800-33246600	Enhancers	Fetal Heart	heart
20	chr6:33245800-33246600	Enhancers	Stomach Mucosa	stomach
21	chr6:33245800-33246800	Weak transcription	Left Ventricle	heart
22	chr6:33245800-33247000	Weak transcription	Aorta	Aorta
23	chr6:33245800-33247200	Genic enhancers	Fetal Muscle Leg	muscle
24	chr6:33245800-33247600	Strong transcription	Fetal Intestine Small	intestine
25	chr6:33245800-33247600	Weak transcription	Hela-S3	cervix
26	chr6:33245800-33248000	Weak transcription	K562	blood
27	chr6:33245800-33248600	Genic enhancers	Skeletal Muscle Female	skeletal muscle
28	chr6:33245800-33248800	Genic enhancers	Spleen	Spleen
29	chr6:33245800-33250400	Weak transcription	HUVEC	blood vessel
30	chr6:33245800-33254400	Weak transcription	Fetal Kidney	kidney
31	chr6:33245800-33255600	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
32	chr6:33245800-33255800	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
33	chr6:33245800-33255800	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
34	chr6:33245800-33256000	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
35	chr6:33245800-33256000	Weak transcription	Pancreatic Islets	Pancreatic Islet
36	chr6:33245800-33256400	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
37	chr6:33246000-33246600	Genic enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
38	chr6:33246000-33246600	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
39	chr6:33246000-33246600	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
40	chr6:33246000-33246600	Enhancers	Primary T helper cells PMA-I stimulated	--
41	chr6:33246000-33246600	Enhancers	Primary T cells effector/memory enriched fromperipheralblood	blood
42	chr6:33246000-33246600	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
43	chr6:33246000-33246600	Genic enhancers	Thymus	Thymus
44	chr6:33246000-33246800	Enhancers	Primary B cells from peripheral blood	blood
45	chr6:33246000-33246800	Enhancers	Placenta Amnion	Placenta Amnion
46	chr6:33246000-33246800	Transcr. at gene 5' and 3'	Skeletal Muscle Male	skeletal muscle
47	chr6:33246000-33247000	Genic enhancers	ES-UCSF4 Cell Line	embryonic stem cell
48	chr6:33246000-33247000	Genic enhancers	Primary T helper naive cells from peripheral blood	blood
49	chr6:33246000-33247000	Weak transcription	Brain Angular Gyrus	brain
50	chr6:33246000-33247200	Genic enhancers	Fetal Adrenal Gland	Adrenal Gland

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