Variant report

Variant	rs465151
Chromosome Location	chr6:33255369-33255370
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:2)
CpG islands
(count:0)
Chromatin interactive
region (count:7)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:2 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	POLR2A	chr6:33255344-33255593	MCF-7	breast:	n/a	n/a
2	POLR2A	chr6:33255322-33255598	MCF-7	breast:	n/a	n/a

No data

(count:7 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr6:33255152..33256710-chr6:33377924..33379590,2	K562	blood:
2	chr6:33255047..33257514-chr6:33384371..33386134,2	K562	blood:
3	chr6:33170950..33173180-chr6:33254762..33258714,3	K562	blood:
4	chr6:33254516..33257651-chr6:33384634..33387572,3	K562	blood:
5	chr6:32937868..32940251-chr6:33254691..33256964,2	MCF-7	breast:
6	chr6:33254680..33257397-chr6:33405638..33407793,2	K562	blood:
7	chr6:33253660..33257073-chr6:33358023..33361324,4	K562	blood:

No data

Variant related genes	Relation type
PFDN6	TF binding region
WDR46	TF binding region
ENSG00000204256	Chromatin interaction
ENSG00000264085	Chromatin interaction
ENSG00000197283	Chromatin interaction
ENSG00000223837	Chromatin interaction
ENSG00000112511	Chromatin interaction
ENSG00000237649	Chromatin interaction
ENSG00000112514	Chromatin interaction
ENSG00000204228	Chromatin interaction

Extended variants
information (count: 7 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:3)

rs_ID	r²[population]
rs1704997	0.88[EUR][1000 genomes]
rs1704998	0.85[EUR][1000 genomes]
rs463302	0.87[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:4 , 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	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

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs465151	B3GALT4	cis	Cerebellum	GTEx
rs465151	STK38	cis	parietal	SCAN

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:33245600-33255400	Strong transcription	Breast Myoepithelial Primary Cells	Breast
2	chr6:33245800-33255600	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
3	chr6:33245800-33255800	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
4	chr6:33245800-33255800	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
5	chr6:33245800-33256000	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
6	chr6:33245800-33256000	Weak transcription	Pancreatic Islets	Pancreatic Islet
7	chr6:33245800-33256400	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
8	chr6:33246000-33255600	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
9	chr6:33246000-33255600	Strong transcription	Fetal Intestine Large	intestine
10	chr6:33246000-33255800	Strong transcription	Fetal Stomach	stomach
11	chr6:33246000-33255800	Weak transcription	Right Atrium	heart
12	chr6:33246200-33255800	Strong transcription	HUES64 Cell Line	embryonic stem cell
13	chr6:33246200-33255800	Strong transcription	Cortex derived primary cultured neurospheres	brain
14	chr6:33246200-33255800	Strong transcription	Brain Anterior Caudate	brain
15	chr6:33246400-33255400	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
16	chr6:33246400-33255400	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
17	chr6:33246400-33255400	Strong transcription	Lung	lung
18	chr6:33246400-33255800	Strong transcription	Sigmoid Colon	Sigmoid Colon
19	chr6:33246400-33255800	Strong transcription	Osteobl	bone
20	chr6:33246600-33255400	Strong transcription	HepG2	liver
21	chr6:33246600-33255600	Strong transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
22	chr6:33246600-33255600	Strong transcription	Ganglion Eminence derived primary cultured neurospheres	brain
23	chr6:33246600-33255600	Strong transcription	Liver	Liver
24	chr6:33246600-33255600	Strong transcription	Duodenum Mucosa	Duodenum
25	chr6:33246600-33255600	Weak transcription	Fetal Heart	heart
26	chr6:33246600-33255800	Strong transcription	iPS-20b Cell Line	embryonic stem cell
27	chr6:33246800-33255800	Strong transcription	Primary T helper 17 cells PMA-I stimulated	--
28	chr6:33247200-33255800	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
29	chr6:33247200-33255800	Strong transcription	Fetal Muscle Leg	muscle
30	chr6:33247400-33255600	Strong transcription	Primary T cells from cord blood	blood
31	chr6:33247800-33255600	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
32	chr6:33247800-33255600	Strong transcription	Placenta	Placenta
33	chr6:33248000-33255400	Strong transcription	Primary T helper naive cells fromperipheralblood	blood
34	chr6:33248000-33255600	Strong transcription	Adipose Nuclei	Adipose
35	chr6:33248000-33255600	Strong transcription	Stomach Smooth Muscle	stomach
36	chr6:33248000-33255600	Strong transcription	Monocytes-CD14+_RO01746	blood
37	chr6:33248000-33256000	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
38	chr6:33248200-33255400	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
39	chr6:33248200-33255800	Strong transcription	HUES6 Cell Line	embryonic stem cell
40	chr6:33248200-33255800	Strong transcription	Primary monocytes fromperipheralblood	blood
41	chr6:33248400-33255600	Strong transcription	Rectal Mucosa Donor 29	rectum
42	chr6:33248400-33255800	Strong transcription	Fetal Intestine Small	intestine
43	chr6:33248400-33255800	Strong transcription	Fetal Thymus	thymus
44	chr6:33248400-33256000	Strong transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
45	chr6:33248400-33256000	Strong transcription	HUES48 Cell Line	embryonic stem cell
46	chr6:33248600-33255600	Strong transcription	Primary hematopoietic stem cells short term culture	blood
47	chr6:33248600-33255600	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
48	chr6:33248600-33255800	Strong transcription	Fetal Muscle Trunk	muscle
49	chr6:33248800-33255400	Strong transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
50	chr6:33248800-33255400	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links