Variant report

Variant	rs4390169
Chromosome Location	chr1:155106054-155106055
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:17)
CpG islands
(count:0)
Chromatin interactive
region (count:7)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:17 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	NR2F2	chr1:155105739-155106290	K562	blood:	n/a	n/a
2	POLR2A	chr1:155105642-155108644	HepG2	liver:	n/a	n/a
3	POLR2A	chr1:155105844-155108967	HepG2	liver:	n/a	n/a
4	MYBL2	chr1:155105949-155106627	HepG2	liver:	n/a	n/a
5	POLR2A	chr1:155105587-155108949	HepG2	liver:	n/a	n/a
6	POLR2A	chr1:155105878-155108823	A549	lung:	n/a	n/a
7	POLR2A	chr1:155105749-155108991	HUVEC	blood vessel:	n/a	n/a
8	NR2F2	chr1:155105755-155106192	K562	blood:	n/a	n/a
9	HDAC2	chr1:155105886-155106133	K562	blood:	n/a	n/a
10	POLR2A	chr1:155104784-155113272	HepG2	liver:	n/a	n/a
11	POLR2A	chr1:155105627-155108964	HepG2	liver:	n/a	n/a
12	POLR2A	chr1:155105888-155106082	MCF10A-Er-Src	breast:	n/a	n/a
13	NR2F2	chr1:155105902-155109005	HepG2	liver:	n/a	chr1:155106405-155106420
14	POLR2A	chr1:155105869-155106161	K562	blood:	n/a	n/a
15	NR2F2	chr1:155105970-155106799	MCF-7	breast:	n/a	chr1:155106405-155106420
16	HEY1	chr1:155105595-155109009	HepG2	liver:	n/a	chr1:155108266-155108281
17	POLR2A	chr1:155105850-155108982	HepG2	liver:	n/a	n/a

No data

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

No.	Distal block	Cell Line	Cell type
1	chr1:155049589..155073019-chr1:155085330..155115362,149	MCF-7	breast:
2	chr1:155095314..155110392-chr1:155134312..155151496,72	MCF-7	breast:
3	chr1:155105664..155110180-chr1:155143584..155151850,15	MCF-7	breast:
4	chr1:155103694..155106243-chr1:155163809..155165755,2	MCF-7	breast:
5	chr1:155105295..155110704-chr1:155161873..155165835,7	K562	blood:
6	chr1:155066527..155067288-chr1:155106043..155106834,2	MCF-7	breast:
7	chr1:154944220..154948259-chr1:155103576..155107473,5	MCF-7	breast:

No data

Variant related genes	Relation type
SLC50A1	TF binding region
ENSG00000173207	Chromatin interaction
ENSG00000264349	Chromatin interaction
ENSG00000143590	Chromatin interaction
ENSG00000271748	Chromatin interaction
ENSG00000160691	Chromatin interaction
ENSG00000163463	Chromatin interaction
ENSG00000163462	Chromatin interaction
ENSG00000185499	Chromatin interaction

Extended variants
information (count: 31 )
Associated
traits (count: 7 )

rSNPs within LD-proxies of this variant (count:22)

rs_ID	r²[population]
rs10157801	0.94[ASN][1000 genomes]
rs11264328	0.87[EUR][1000 genomes]
rs11264329	0.87[EUR][1000 genomes]
rs11264333	1.00[ASN][1000 genomes]
rs11799962	0.94[ASN][1000 genomes]
rs12028043	0.94[ASN][1000 genomes]
rs12040970	0.87[EUR][1000 genomes]
rs12127609	0.94[ASN][1000 genomes]
rs12904	1.00[ASN][1000 genomes]
rs34257409	0.89[ASN][1000 genomes]
rs34815285	0.82[EUR][1000 genomes]
rs4246529	1.00[ASN][1000 genomes]
rs4276913	0.94[ASN][1000 genomes]
rs4745	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4971066	0.85[ASN][1000 genomes]
rs4971073	0.85[ASN][1000 genomes]
rs4971076	0.94[ASN][1000 genomes]
rs4971079	0.84[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6676150	0.89[ASN][1000 genomes]
rs7364524	0.94[ASN][1000 genomes]
rs9297	1.00[ASN][1000 genomes]
rs9330263	0.87[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:9 , 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	nsv872455	chr1:155003954-155106550	Enhancers Active TSS Flanking Active TSS Weak transcription Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Strong transcription Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	74 gene(s)	inside rSNPs	diseases
4	nsv998756	chr1:155080090-155136545	Bivalent Enhancer Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Enhancers Flanking Active TSS Strong transcription Active TSS Weak transcription Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	72 gene(s)	inside rSNPs	diseases
5	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
6	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
7	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
8	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
9	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

mRNA abundance (count:7)

SNP	Gene	Cis/trans	Tissue	Source
rs4390169	THBS3	cis	Whole Blood	GTEx
rs4390169	GBAP1	cis	Artery Tibial	GTEx
rs4390169	GBAP1	cis	Esophagus Mucosa	GTEx
rs4390169	GBA	cis	Esophagus Mucosa	GTEx
rs4390169	GBAP1	cis	Thyroid	GTEx
rs4390169	GBAP1	cis	Adipose Subcutaneous	GTEx
rs4390169	GBAP1	cis	lung	GTEx

Chromatin state (count:102 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:155102400-155106800	Weak transcription	Dnd41	blood
2	chr1:155102400-155107000	Weak transcription	HSMM	muscle
3	chr1:155102400-155107400	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
4	chr1:155102400-155107400	Weak transcription	Primary T helper naive cells from peripheral blood	blood
5	chr1:155102600-155107400	Weak transcription	Primary T killer memory cells from peripheral blood	blood
6	chr1:155102800-155107000	Weak transcription	Muscle Satellite Cultured Cells	--
7	chr1:155102800-155107000	Weak transcription	NH-A	brain
8	chr1:155102800-155107200	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
9	chr1:155102800-155107400	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
10	chr1:155103000-155107200	Weak transcription	Primary T helper cells fromperipheralblood	blood
11	chr1:155103000-155107400	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
12	chr1:155103200-155106200	Weak transcription	Small Intestine	intestine
13	chr1:155103200-155106800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
14	chr1:155103400-155107000	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
15	chr1:155103400-155107000	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
16	chr1:155103400-155107200	Weak transcription	Primary T helper cells PMA-I stimulated	--
17	chr1:155103600-155106800	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
18	chr1:155103600-155107000	Weak transcription	HUES64 Cell Line	embryonic stem cell
19	chr1:155103600-155107000	Weak transcription	Pancreatic Islets	Pancreatic Islet
20	chr1:155103800-155106400	Strong transcription	Foreskin Melanocyte Primary Cells skin01	Skin
21	chr1:155103800-155107000	Strong transcription	Fetal Stomach	stomach
22	chr1:155103800-155107200	Weak transcription	HUES48 Cell Line	embryonic stem cell
23	chr1:155103800-155107200	Weak transcription	Fetal Brain Female	brain
24	chr1:155103800-155107200	Strong transcription	Thymus	Thymus
25	chr1:155103800-155107400	Genic enhancers	Fetal Intestine Large	intestine
26	chr1:155104000-155106600	Strong transcription	Fetal Thymus	thymus
27	chr1:155104000-155106800	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
28	chr1:155104000-155106800	Genic enhancers	Skeletal Muscle Male	skeletal muscle
29	chr1:155104000-155107200	Genic enhancers	Fetal Intestine Small	intestine
30	chr1:155104000-155107400	Genic enhancers	HUVEC	blood vessel
31	chr1:155104200-155106400	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
32	chr1:155104200-155106400	Weak transcription	Psoas Muscle	Psoas
33	chr1:155104200-155106800	Weak transcription	Primary hematopoietic stem cells	blood
34	chr1:155104200-155107200	Weak transcription	iPS-18 Cell Line	embryonic stem cell
35	chr1:155104200-155107400	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
36	chr1:155104200-155107400	Weak transcription	Aorta	Aorta
37	chr1:155104400-155106800	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
38	chr1:155104400-155107000	Weak transcription	HUES6 Cell Line	embryonic stem cell
39	chr1:155104400-155107000	Weak transcription	iPS-20b Cell Line	embryonic stem cell
40	chr1:155104400-155107400	Genic enhancers	Left Ventricle	heart
41	chr1:155104600-155106200	Strong transcription	Brain Anterior Caudate	brain
42	chr1:155104600-155106200	Strong transcription	NHEK	skin
43	chr1:155104600-155106400	Weak transcription	Fetal Heart	heart
44	chr1:155104600-155106600	Strong transcription	Brain Cingulate Gyrus	brain
45	chr1:155104600-155106600	Strong transcription	Placenta	Placenta
46	chr1:155104600-155106800	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
47	chr1:155104600-155106800	Genic enhancers	Right Ventricle	heart
48	chr1:155104600-155106800	Strong transcription	Stomach Smooth Muscle	stomach
49	chr1:155104600-155107000	Genic enhancers	Duodenum Mucosa	Duodenum
50	chr1:155104600-155107000	Weak transcription	Fetal Lung	lung

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links