Variant report

Variant	rs12145362
Chromosome Location	chr1:155094013-155094014
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:9)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

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

No.	Distal block	Cell Line	Cell type
1	chr1:155093079..155097838-chr1:155098662..155101099,5	K562	blood:
2	chr1:155049589..155073019-chr1:155085330..155115362,149	MCF-7	breast:
3	chr1:154971203..154978007-chr1:155093683..155103687,24	MCF-7	breast:
4	chr1:155092552..155095095-chr1:155160179..155163739,4	MCF-7	breast:
5	chr1:155093596..155095413-chr6:32939859..32941605,2	MCF-7	breast:
6	chr1:154973177..154975569-chr1:155093743..155096509,2	MCF-7	breast:
7	chr1:155093588..155095174-chr1:155095538..155097841,2	K562	blood:
8	chr1:155089510..155091697-chr1:155093424..155095610,2	K562	blood:
9	chr1:155023157..155025347-chr1:155091508..155094393,2	MCF-7	breast:

No data

Variant related genes	Relation type
ENSG00000169242	Chromatin interaction
ENSG00000143590	Chromatin interaction
ENSG00000263756	Chromatin interaction
ENSG00000160685	Chromatin interaction
ENSG00000185499	Chromatin interaction
ENSG00000204256	Chromatin interaction
ENSG00000143537	Chromatin interaction

Extended variants
information (count: 75 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:69)

rs_ID	r²[population]
rs1001848	1.00[JPT][hapmap]
rs10157801	0.83[CEU][hapmap];0.85[JPT][hapmap]
rs10796938	0.93[ASN][1000 genomes]
rs10796939	0.95[AMR][1000 genomes];0.95[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs10908454	0.87[ASW][hapmap];1.00[CHB][hapmap];0.88[CHD][hapmap];1.00[JPT][hapmap];0.84[MKK][hapmap];0.93[ASN][1000 genomes]
rs10908455	0.88[ASW][hapmap];1.00[CHB][hapmap];0.88[CHD][hapmap];1.00[JPT][hapmap];0.93[ASN][1000 genomes]
rs10908456	0.81[ASW][hapmap];1.00[CHB][hapmap];0.83[CHD][hapmap];0.85[GIH][hapmap];1.00[JPT][hapmap];0.82[LWK][hapmap];0.86[MKK][hapmap];0.86[TSI][hapmap];0.84[AMR][1000 genomes];0.83[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs10908458	0.80[CEU][hapmap];0.85[JPT][hapmap]
rs11264304	0.85[JPT][hapmap]
rs11264306	1.00[JPT][hapmap]
rs11264312	0.93[ASN][1000 genomes]
rs11264313	0.90[ASN][1000 genomes]
rs11264314	1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[ASN][1000 genomes]
rs11264319	1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[ASN][1000 genomes]
rs11264321	0.87[AFR][1000 genomes];0.82[AMR][1000 genomes];0.83[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs11264322	0.80[AMR][1000 genomes];0.85[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs11264323	0.91[AFR][1000 genomes];0.86[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs11264327	0.99[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11264328	1.00[ASN][1000 genomes]
rs11264329	1.00[CHB][hapmap];0.94[CHD][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs11264333	0.83[EUR][1000 genomes]
rs11807418	0.97[AFR][1000 genomes];0.90[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs12025371	0.85[JPT][hapmap]
rs12026113	0.95[ASN][1000 genomes]
rs12028043	0.80[CEU][hapmap];0.85[JPT][hapmap]
rs12039316	0.82[AMR][1000 genomes];0.80[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs12040970	1.00[CHB][hapmap];0.94[CHD][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs12137164	0.96[AFR][1000 genomes];0.90[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs12904	0.84[CEU][hapmap];0.80[GIH][hapmap];0.85[JPT][hapmap];0.83[EUR][1000 genomes]
rs1462855	1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[ASN][1000 genomes]
rs1870939	1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[ASN][1000 genomes]
rs2306124	0.88[ASW][hapmap];1.00[CHB][hapmap];0.88[CHD][hapmap];1.00[JPT][hapmap];0.93[ASN][1000 genomes]
rs34815285	0.85[ASN][1000 genomes]
rs35902694	0.85[JPT][hapmap]
rs3765087	1.00[JPT][hapmap]
rs3766916	1.00[JPT][hapmap]
rs3766918	0.93[ASN][1000 genomes]
rs3806256	0.85[JPT][hapmap]
rs4045192	0.85[JPT][hapmap]
rs4246529	0.84[CEU][hapmap];0.80[GIH][hapmap];0.85[JPT][hapmap];0.81[EUR][1000 genomes]
rs4276913	0.80[CEU][hapmap];0.85[JPT][hapmap]
rs4303067	0.84[AMR][1000 genomes];0.84[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs4361977	0.81[AMR][1000 genomes];0.81[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs4625273	0.93[ASN][1000 genomes]
rs4745	0.85[JPT][hapmap]
rs4845407	1.00[JPT][hapmap]
rs4845408	1.00[CHB][hapmap];0.83[CHD][hapmap];1.00[JPT][hapmap];0.95[ASN][1000 genomes]
rs4971052	1.00[JPT][hapmap]
rs4971066	0.85[JPT][hapmap]
rs4971073	0.92[CEU][hapmap];0.91[GIH][hapmap];0.85[JPT][hapmap]
rs4971076	0.85[JPT][hapmap]
rs4971079	0.85[JPT][hapmap]
rs56112907	0.93[ASN][1000 genomes]
rs6427158	1.00[CHB][hapmap];0.83[CHD][hapmap];1.00[JPT][hapmap];0.93[ASN][1000 genomes]
rs6665822	1.00[CHB][hapmap];0.94[CHD][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs6693477	1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[ASN][1000 genomes]
rs7364524	0.85[JPT][hapmap]
rs7364869	0.93[ASN][1000 genomes]
rs7365544	1.00[CHB][hapmap];0.83[CHD][hapmap];1.00[JPT][hapmap];0.93[ASN][1000 genomes]
rs7366138	0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7366355	0.93[ASN][1000 genomes]
rs7367207	0.88[ASW][hapmap];1.00[CHB][hapmap];0.88[CHD][hapmap];1.00[JPT][hapmap];0.86[TSI][hapmap];0.81[AMR][1000 genomes];0.82[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7367758	0.95[ASN][1000 genomes]
rs7367897	1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[AMR][1000 genomes];0.82[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7368345	1.00[CHB][hapmap];0.83[CHD][hapmap];1.00[JPT][hapmap];0.93[ASN][1000 genomes]
rs7534162	1.00[CHB][hapmap];0.83[CHD][hapmap];1.00[JPT][hapmap];0.93[ASN][1000 genomes]
rs7548955	1.00[CHB][hapmap];0.82[CHD][hapmap];1.00[JPT][hapmap];0.93[ASN][1000 genomes]
rs9297	0.84[CEU][hapmap];0.80[GIH][hapmap];0.85[JPT][hapmap];0.83[EUR][1000 genomes]
rs9330263	0.95[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:6 , 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

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs12145362	GBAP1	cis	Artery Tibial	GTEx

Chromatin state (count:19 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:155078600-155098400	Weak transcription	Right Atrium	heart
2	chr1:155089200-155095000	Weak transcription	Hela-S3	cervix
3	chr1:155089600-155096800	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
4	chr1:155091400-155097000	Weak transcription	Sigmoid Colon	Sigmoid Colon
5	chr1:155091800-155097000	Weak transcription	Colonic Mucosa	Colon
6	chr1:155092200-155094200	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
7	chr1:155092600-155094200	Enhancers	Stomach Mucosa	stomach
8	chr1:155093000-155095600	Weak transcription	Rectal Mucosa Donor 29	rectum
9	chr1:155093000-155096200	Weak transcription	HepG2	liver
10	chr1:155093400-155097000	Weak transcription	Placenta Amnion	Placenta Amnion
11	chr1:155093600-155096600	Weak transcription	Placenta	Placenta
12	chr1:155093600-155096800	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
13	chr1:155093800-155097000	Weak transcription	Lung	lung
14	chr1:155094000-155096000	Weak transcription	Rectal Mucosa Donor 31	rectum
15	chr1:155094000-155096200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
16	chr1:155094000-155096200	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
17	chr1:155094000-155096200	Weak transcription	Fetal Intestine Large	intestine
18	chr1:155094000-155096400	Weak transcription	Gastric	stomach
19	chr1:155094000-155099200	Weak transcription	K562	blood

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