Variant report

Variant	rs2297480
Chromosome Location	chr1:155279482-155279483
allele	A/C
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	chr1:155245586..155250751-chr1:155275814..155280484,11	K562	blood:
2	chr1:155241469..155243385-chr1:155277012..155279531,3	MCF-7	breast:
3	chr1:155240186..155244594-chr1:155276068..155280700,10	MCF-7	breast:
4	chr1:155245586..155248343-chr1:155278550..155280734,4	K562	blood:
5	chr1:155278802..155279780-chr4:128885897..128886684,2	Hela-S3	cervix:
6	chr1:155179163..155181119-chr1:155277191..155279761,2	K562	blood:
7	chr1:155177882..155179907-chr1:155278093..155280074,2	MCF-7	breast:
8	chr1:155241171..155245021-chr1:155277000..155280071,7	K562	blood:
9	chr1:155211622..155214565-chr1:155278095..155280494,4	MCF-7	breast:
10	chr1:155161598..155164529-chr1:155278690..155280381,2	MCF-7	breast:
11	chr1:155195759..155198427-chr1:155276824..155279493,2	K562	blood:
12	chr1:155228693..155233633-chr1:155276892..155283389,6	K562	blood:
13	chr1:155245052..155250020-chr1:155276306..155280611,10	MCF-7	breast:
14	chr1:155270092..155273127-chr1:155275751..155279798,4	K562	blood:
15	chr1:155246042..155249168-chr1:155274467..155279979,9	MCF-7	breast:
16	chr1:155195750..155198407-chr1:155276763..155279696,2	K562	blood:
17	chr1:155223569..155227620-chr1:155275954..155279861,5	K562	blood:
18	chr1:155220090..155222745-chr1:155275911..155279698,3	K562	blood:
19	chr1:155223569..155226696-chr1:155275954..155279861,6	K562	blood:
20	chr1:155241810..155244486-chr1:155276710..155279928,5	K562	blood:

No data

Variant related genes	Relation type
ENSG00000116521	Chromatin interaction
ENSG00000143630	Chromatin interaction
ENSG00000160767	Chromatin interaction
ENSG00000164073	Chromatin interaction
ENSG00000164074	Chromatin interaction
ENSG00000173171	Chromatin interaction
ENSG00000177628	Chromatin interaction
ENSG00000185499	Chromatin interaction
ENSG00000143627	Chromatin interaction
ENSG00000160766	Chromatin interaction
ENSG00000176444	Chromatin interaction
ENSG00000169231	Chromatin interaction

Extended variants
information (count: 65 )
Associated
traits (count: 16 )

rSNPs within LD-proxies of this variant (count:58)

rs_ID	r²[population]
rs1052176	0.86[AMR][1000 genomes];0.84[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs1052177	0.86[AMR][1000 genomes];0.84[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs10796941	0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs10796943	0.82[CEU][hapmap];0.88[CHB][hapmap];0.82[GIH][hapmap];0.94[TSI][hapmap]
rs10796945	0.80[CEU][hapmap];0.89[CHB][hapmap];0.85[GIH][hapmap];0.88[TSI][hapmap]
rs10908461	0.94[AMR][1000 genomes];0.92[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs10908462	0.89[AMR][1000 genomes];0.98[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs10908463	1.00[CEU][hapmap];0.89[CHB][hapmap];0.83[CHD][hapmap];1.00[GIH][hapmap];1.00[MEX][hapmap];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs10908465	0.88[CEU][hapmap];0.89[CHB][hapmap];0.82[GIH][hapmap];0.90[MEX][hapmap];0.88[TSI][hapmap]
rs10908469	0.84[CEU][hapmap];0.89[CHB][hapmap]
rs11264349	0.82[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs11264352	0.81[EUR][1000 genomes]
rs11264353	0.81[EUR][1000 genomes]
rs11264354	0.80[EUR][1000 genomes]
rs11264355	0.84[AMR][1000 genomes];0.83[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs11264357	0.84[EUR][1000 genomes]
rs11264358	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11264359	0.96[CEU][hapmap];0.95[CHB][hapmap];0.81[CHD][hapmap];0.95[MEX][hapmap];0.94[TSI][hapmap];0.83[AMR][1000 genomes];0.91[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs11264360	0.86[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs11264361	1.00[CEU][hapmap];0.89[CHB][hapmap];0.84[CHD][hapmap];1.00[GIH][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs11264363	0.84[CHB][hapmap]
rs11264367	0.88[CEU][hapmap];0.89[CHB][hapmap]
rs11264369	0.84[CEU][hapmap];0.89[CHB][hapmap]
rs11264371	0.89[CHB][hapmap];0.85[MEX][hapmap]
rs11264372	0.89[CHB][hapmap];0.81[MEX][hapmap]
rs11264375	0.88[CEU][hapmap];0.89[CHB][hapmap];0.82[GIH][hapmap];0.95[MEX][hapmap];0.88[TSI][hapmap]
rs12026638	0.88[CEU][hapmap];0.95[CHB][hapmap];0.82[GIH][hapmap];0.85[MEX][hapmap];0.88[TSI][hapmap]
rs12032720	0.95[AMR][1000 genomes];0.92[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12041534	0.88[CEU][hapmap];0.89[CHB][hapmap];0.82[GIH][hapmap];0.95[MEX][hapmap];0.88[TSI][hapmap]
rs12044063	0.86[EUR][1000 genomes]
rs12049375	0.81[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs12067675	0.83[AMR][1000 genomes];0.85[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs12079134	0.84[CEU][hapmap];0.89[CHB][hapmap]
rs12239114	0.88[CEU][hapmap];0.89[CHB][hapmap];0.91[GIH][hapmap];0.95[MEX][hapmap];0.94[TSI][hapmap]
rs12724079	0.89[CHB][hapmap]
rs12724449	0.82[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs12749306	0.82[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs1325908	0.89[CHB][hapmap]
rs1360554	0.89[CHB][hapmap]
rs1886905	0.84[CEU][hapmap];0.82[MEX][hapmap]
rs2071053	0.83[AMR][1000 genomes];0.88[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs3020781	0.85[AMR][1000 genomes];0.91[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs3814318	0.86[AMR][1000 genomes];0.83[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs3814319	0.83[ASN][1000 genomes]
rs4620533	0.87[AMR][1000 genomes];0.86[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs4971072	0.98[ASN][1000 genomes]
rs5005770	0.88[CEU][hapmap];0.89[CHB][hapmap];0.82[GIH][hapmap];0.90[MEX][hapmap];0.88[TSI][hapmap]
rs6672284	0.87[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6688636	0.89[CHB][hapmap]
rs7520184	0.81[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs7524950	0.86[AMR][1000 genomes];0.87[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs7534795	0.82[AMR][1000 genomes];0.91[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7549276	0.81[EUR][1000 genomes]
rs7554780	0.82[EUR][1000 genomes]
rs8177968	0.86[AMR][1000 genomes];0.87[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs8847	0.86[AMR][1000 genomes];0.83[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs932972	0.86[AMR][1000 genomes];0.84[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs9426886	0.83[JPT][hapmap]

Variant overlapped rSNPs/rCNVs (count:7 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	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
2	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
3	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
4	nsv831625	chr1:155145634-155313409	Weak transcription Enhancers Flanking Active TSS Active TSS Strong transcription Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	407 gene(s)	inside rSNPs	diseases
5	nsv529709	chr1:155154933-155757219	Strong transcription Weak transcription Flanking Active TSS Enhancers Active TSS Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	450 gene(s)	inside rSNPs	diseases
6	nsv831636	chr1:155219223-155444864	Strong transcription Weak transcription Active TSS Flanking Active TSS Enhancers Genic enhancers ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	67 gene(s)	inside rSNPs	diseases
7	esv33869	chr1:155223283-155917961	Flanking Active TSS Strong transcription Weak transcription Active TSS Bivalent/Poised TSS Enhancers Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	187 gene(s)	inside rSNPs	diseases

mRNA abundance (count:16)

SNP	Gene	Cis/trans	Tissue	Source
rs2297480	GBAP1	cis	parietal	SCAN
rs2297480	C1orf104	cis	lymphoblastoid	seeQTL
rs2297480	SPRR2D	cis	parietal	SCAN
rs2297480	THBS3	cis	Whole Blood	GTEx
rs2297480	SPRR2A	cis	cerebellum	SCAN
rs2297480	THEM5	cis	parietal	SCAN
rs2297480	FDPS	cis	lymphoblastoid	seeQTL
rs2297480	GBA	cis	Esophagus Mucosa	GTEx
rs2297480	GBAP1	cis	Artery Tibial	GTEx
rs2297480	DCST1	cis	parietal	SCAN
rs2297480	YY1AP1	cis	cerebellum	SCAN
rs2297480	PKLR	cis	Nerve Tibial	GTEx
rs2297480	LCE1C	cis	parietal	SCAN
rs2297480	RIT1	cis	cerebellum	SCAN
rs2297480	RIT1	Cis_1M	lymphoblastoid	RTeQTL
rs2297480	FDPS	Cis_1M	lymphoblastoid	RTeQTL

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:155277400-155281000	Active TSS	HSMMtube	muscle
2	chr1:155277600-155279800	Active TSS	Fetal Kidney	kidney
3	chr1:155277600-155280000	Active TSS	iPS-15b Cell Line	embryonic stem cell
4	chr1:155277600-155280200	Active TSS	HUES64 Cell Line	embryonic stem cell
5	chr1:155277800-155279800	Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
6	chr1:155277800-155279800	Active TSS	K562	blood
7	chr1:155277800-155279800	Active TSS	NHEK	skin
8	chr1:155277800-155280000	Active TSS	HUES6 Cell Line	embryonic stem cell
9	chr1:155278000-155279600	Active TSS	ES-I3 Cell Line	embryonic stem cell
10	chr1:155278000-155279600	Active TSS	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
11	chr1:155278000-155279600	Active TSS	iPS-18 Cell Line	embryonic stem cell
12	chr1:155278000-155279600	Active TSS	Foreskin Melanocyte Primary Cells skin03	Skin
13	chr1:155278000-155279800	Active TSS	H9 Cell Line	embryonic stem cell
14	chr1:155278000-155279800	Active TSS	HUES48 Cell Line	embryonic stem cell
15	chr1:155278000-155279800	Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
16	chr1:155278000-155279800	Active TSS	A549	lung
17	chr1:155278000-155279800	Active TSS	HSMM	muscle
18	chr1:155278000-155280000	Active TSS	Left Ventricle	heart
19	chr1:155278000-155280200	Active TSS	iPS-20b Cell Line	embryonic stem cell
20	chr1:155278000-155280400	Active TSS	GM12878-XiMat	blood
21	chr1:155278000-155280400	Active TSS	NHDF-Ad	bronchial
22	chr1:155278200-155279800	Active TSS	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
23	chr1:155278200-155279800	Active TSS	Pancreatic Islets	Pancreatic Islet
24	chr1:155278400-155279600	Active TSS	Hela-S3	cervix
25	chr1:155278400-155279600	Active TSS	HMEC	breast
26	chr1:155278400-155279800	Active TSS	HUVEC	blood vessel
27	chr1:155278400-155279800	Active TSS	NHLF	lung
28	chr1:155278400-155283600	Transcr. at gene 5' and 3'	Foreskin Fibroblast Primary Cells skin02	Skin
29	chr1:155278600-155279600	Active TSS	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
30	chr1:155278600-155279600	Active TSS	Sigmoid Colon	Sigmoid Colon
31	chr1:155278600-155279800	Flanking Active TSS	Primary mononuclear cells fromperipheralblood	Blood
32	chr1:155278600-155279800	Active TSS	Small Intestine	intestine
33	chr1:155278800-155279600	Flanking Active TSS	Primary B cells from cord blood	blood
34	chr1:155278800-155279600	Flanking Active TSS	Primary Natural Killer cells fromperipheralblood	blood
35	chr1:155278800-155279600	Bivalent/Poised TSS	HepG2	liver
36	chr1:155278800-155279800	Flanking Active TSS	Primary T cells fromperipheralblood	blood
37	chr1:155278800-155279800	Flanking Active TSS	Primary T helper cells fromperipheralblood	blood
38	chr1:155278800-155279800	Flanking Active TSS	Primary T regulatory cells fromperipheralblood	blood
39	chr1:155278800-155280000	Flanking Active TSS	Primary hematopoietic stem cells	blood
40	chr1:155278800-155280000	Flanking Active TSS	Colonic Mucosa	Colon
41	chr1:155278800-155280200	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
42	chr1:155278800-155280200	Flanking Active TSS	Adipose Nuclei	Adipose
43	chr1:155279000-155279600	Flanking Active TSS	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
44	chr1:155279000-155279600	Flanking Active TSS	Primary monocytes fromperipheralblood	blood
45	chr1:155279000-155279600	Flanking Active TSS	Primary B cells from peripheral blood	blood
46	chr1:155279000-155279600	Flanking Active TSS	Primary T helper naive cells from peripheral blood	blood
47	chr1:155279000-155279800	Flanking Active TSS	Primary T helper naive cells fromperipheralblood	blood
48	chr1:155279000-155279800	Flanking Active TSS	Placenta	Placenta
49	chr1:155279000-155279800	Transcr. at gene 5' and 3'	Right Atrium	heart
50	chr1:155279000-155279800	Flanking Active TSS	Skeletal Muscle Male	skeletal muscle

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links