Variant report

Variant	rs4971091
Chromosome Location	chr1:155143768-155143769
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:3)
CpG islands
(count:0)
Chromatin interactive
region (count:9)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:3 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	POLR2A	chr1:155143718-155143862	K562	blood:	n/a	n/a
2	POLR2A	chr1:155143192-155143894	HepG2	liver:	n/a	n/a
3	CTCF	chr1:155143768-155143839	GM13976	blood:	n/a	n/a

No data

(count:9 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr1:155056284..155060443-chr1:155143066..155147437,8	MCF-7	breast:
2	chr1:155041712..155043919-chr1:155142054..155144015,2	K562	blood:
3	chr1:155056491..155066482-chr1:155136760..155147519,21	K562	blood:
4	chr1:155095314..155110392-chr1:155134312..155151496,72	MCF-7	breast:
5	chr1:155056751..155059603-chr1:155143653..155146036,8	MCF-7	breast:
6	chr1:155055553..155060043-chr1:155139937..155145817,8	K562	blood:
7	chr1:155105664..155110180-chr1:155143584..155151850,15	MCF-7	breast:
8	chr1:155094769..155105017-chr1:155135344..155151845,46	MCF-7	breast:
9	chr1:155061878..155067935-chr1:155138836..155144212,15	MCF-7	breast:

No data

Variant related genes	Relation type
TRIM46	TF binding region
ENSG00000169242	Chromatin interaction
ENSG00000143590	Chromatin interaction
ENSG00000169241	Chromatin interaction

Extended variants
information (count: 24 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:14)

rs_ID	r²[population]
rs10157801	0.82[AMR][1000 genomes]
rs11799962	0.87[AMR][1000 genomes]
rs12028043	0.86[AMR][1000 genomes]
rs12124306	0.92[AMR][1000 genomes]
rs12127609	0.86[AMR][1000 genomes]
rs34257409	0.87[AMR][1000 genomes]
rs3814316	0.85[AMR][1000 genomes];0.85[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs4276913	0.89[AMR][1000 genomes]
rs4644481	0.83[AMR][1000 genomes]
rs4971054	0.91[AMR][1000 genomes]
rs4971059	0.90[AMR][1000 genomes];0.91[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs4971076	0.87[AMR][1000 genomes]
rs4971093	0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs7364524	0.87[AMR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:10 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv532579	chr1:154548165-155262692	Flanking Active TSS Enhancers Strong transcription Flanking Bivalent TSS/Enh Active TSS Weak transcription Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	575 gene(s)	inside rSNPs	diseases
2	esv1823746	chr1:154965207-155231904	Enhancers Flanking Active TSS Active TSS Weak transcription Genic enhancers Strong transcription Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	469 gene(s)	inside rSNPs	diseases
3	nsv464084	chr1:155082298-155194980	Weak transcription Bivalent Enhancer Active TSS Strong transcription Enhancers Flanking Active TSS Transcr. at gene 5' and 3' Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	366 gene(s)	inside rSNPs	diseases
4	nsv547961	chr1:155082298-155194980	Active TSS Flanking Active TSS Enhancers Weak transcription Strong transcription Genic enhancers Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	366 gene(s)	inside rSNPs	diseases
5	nsv831614	chr1:155094978-155275031	Genic enhancers Weak transcription Enhancers Flanking Active TSS Strong transcription Flanking Bivalent TSS/Enh Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	434 gene(s)	inside rSNPs	diseases
6	esv2757756	chr1:155094978-155314807	Bivalent Enhancer Weak transcription Enhancers Active TSS Genic enhancers Flanking Active TSS Strong transcription Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	452 gene(s)	inside rSNPs	diseases
7	esv2758971	chr1:155094978-155314807	Active TSS Weak transcription Flanking Active TSS Bivalent Enhancer Strong transcription Enhancers Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	452 gene(s)	inside rSNPs	diseases
8	nsv470741	chr1:155115260-155230131	Flanking Active TSS Flanking Bivalent TSS/Enh Genic enhancers Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3' Strong transcription Enhancers Weak transcription Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	381 gene(s)	inside rSNPs	diseases
9	nsv1010146	chr1:155119096-155201064	ZNF genes & repeats Strong transcription Enhancers Flanking Active TSS Active TSS Weak transcription Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	368 gene(s)	inside rSNPs	diseases
10	nsv872457	chr1:155135335-155310443	Weak transcription Active TSS Enhancers Flanking Active TSS Strong transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	407 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs4971091	GBAP1	cis	Artery Tibial	GTEx
rs4971091	MUC1	cis	Whole Blood	GTEx

Chromatin state (count:123 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:155134200-155145000	Weak transcription	Small Intestine	intestine
2	chr1:155140400-155144800	Weak transcription	Psoas Muscle	Psoas
3	chr1:155140600-155144000	Weak transcription	Hela-S3	cervix
4	chr1:155140600-155144600	Weak transcription	ES-I3 Cell Line	embryonic stem cell
5	chr1:155140600-155144600	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
6	chr1:155140600-155144600	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
7	chr1:155140800-155144000	Weak transcription	HepG2	liver
8	chr1:155140800-155144200	Weak transcription	GM12878-XiMat	blood
9	chr1:155140800-155144600	Weak transcription	iPS-15b Cell Line	embryonic stem cell
10	chr1:155140800-155144600	Weak transcription	Stomach Mucosa	stomach
11	chr1:155141000-155143800	Strong transcription	Rectal Mucosa Donor 29	rectum
12	chr1:155141000-155144000	Strong transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
13	chr1:155141000-155144200	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
14	chr1:155141000-155144200	Strong transcription	Foreskin Fibroblast Primary Cells skin01	Skin
15	chr1:155141000-155144200	Strong transcription	Spleen	Spleen
16	chr1:155141000-155144600	Strong transcription	Fetal Intestine Small	intestine
17	chr1:155141200-155143800	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
18	chr1:155141200-155144000	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
19	chr1:155141200-155144000	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
20	chr1:155141200-155144000	Strong transcription	Fetal Muscle Leg	muscle
21	chr1:155141200-155144000	Strong transcription	Fetal Stomach	stomach
22	chr1:155141200-155144000	Strong transcription	Dnd41	blood
23	chr1:155141200-155144200	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
24	chr1:155141200-155144200	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
25	chr1:155141200-155144200	Strong transcription	Fetal Intestine Large	intestine
26	chr1:155141200-155144200	Strong transcription	Placenta	Placenta
27	chr1:155141200-155144200	Strong transcription	Lung	lung
28	chr1:155141200-155144400	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
29	chr1:155141200-155144400	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
30	chr1:155141200-155144400	Strong transcription	Fetal Muscle Trunk	muscle
31	chr1:155141400-155143800	Strong transcription	Primary T helper cells fromperipheralblood	blood
32	chr1:155141400-155143800	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
33	chr1:155141400-155143800	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
34	chr1:155141400-155143800	Strong transcription	Skeletal Muscle Female	skeletal muscle
35	chr1:155141400-155144000	Strong transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
36	chr1:155141400-155144000	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
37	chr1:155141400-155144400	Strong transcription	iPS-20b Cell Line	embryonic stem cell
38	chr1:155141400-155144400	Strong transcription	K562	blood
39	chr1:155141400-155144600	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
40	chr1:155141600-155143800	Strong transcription	HUES64 Cell Line	embryonic stem cell
41	chr1:155141800-155143800	Strong transcription	Ganglion Eminence derived primary cultured neurospheres	brain
42	chr1:155142200-155144400	Weak transcription	Primary T helper naive cells from peripheral blood	blood
43	chr1:155142200-155144400	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
44	chr1:155142200-155144800	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
45	chr1:155142400-155144000	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
46	chr1:155142400-155144400	Weak transcription	Fetal Heart	heart
47	chr1:155142400-155144600	Weak transcription	Colonic Mucosa	Colon
48	chr1:155142400-155144600	Weak transcription	Fetal Lung	lung
49	chr1:155142400-155144600	Weak transcription	Left Ventricle	heart
50	chr1:155142400-155144800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell

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