Variant report

Variant	rs4759355
Chromosome Location	chr12:123316566-123316567
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr12:123313753..123316707-chr12:123318570..123321464,4	MCF-7	breast:
2	chr12:123311180..123313487-chr12:123316149..123318304,2	K562	blood:
3	chr12:123312382..123316622-chr12:123318766..123321741,4	MCF-7	breast:
4	chr12:123314439..123317163-chr12:123634963..123637139,2	K562	blood:
5	chr12:123303995..123306395-chr12:123315559..123318480,2	MCF-7	breast:
6	chr12:123278169..123279892-chr12:123315469..123318246,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000130787	Chromatin interaction

Extended variants
information (count: 110 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:104)

rs_ID	r²[population]
rs10744422	0.87[EUR][1000 genomes]
rs10744434	1.00[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs10773599	0.81[YRI][hapmap]
rs10773627	1.00[ASW][hapmap];1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.89[LWK][hapmap];0.94[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.95[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs10773657	0.86[AMR][1000 genomes];0.94[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs10847742	0.81[YRI][hapmap]
rs10847749	0.81[YRI][hapmap]
rs10847751	0.81[YRI][hapmap]
rs10847775	0.80[YRI][hapmap]
rs10847826	0.95[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs10847869	0.97[AFR][1000 genomes];0.95[AMR][1000 genomes];0.94[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs11060064	0.86[CHB][hapmap];0.87[CHD][hapmap];0.88[JPT][hapmap];0.81[ASN][1000 genomes]
rs11060065	0.86[CHB][hapmap];0.87[CHD][hapmap];0.88[JPT][hapmap];0.81[ASN][1000 genomes]
rs11060152	0.81[YRI][hapmap]
rs11060208	0.86[ASN][1000 genomes]
rs11060209	0.93[ASN][1000 genomes]
rs12255	1.00[CEU][hapmap];0.95[CHB][hapmap];0.97[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.85[MEX][hapmap];0.95[TSI][hapmap];0.94[AMR][1000 genomes];0.86[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs12298151	0.82[ASN][1000 genomes]
rs12298664	0.94[ASN][1000 genomes]
rs12299742	0.93[ASN][1000 genomes]
rs12313006	0.91[CHB][hapmap];0.81[CHD][hapmap];0.88[JPT][hapmap]
rs12314494	0.94[ASN][1000 genomes]
rs12314544	0.90[CHB][hapmap];0.94[JPT][hapmap];0.94[ASN][1000 genomes]
rs12319654	0.94[ASN][1000 genomes]
rs12321131	0.81[ASN][1000 genomes]
rs12426809	0.97[AFR][1000 genomes];0.95[AMR][1000 genomes];0.94[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1532835	0.94[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs1587856	0.80[AMR][1000 genomes];0.87[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs1671681	0.81[YRI][hapmap]
rs1671682	0.80[YRI][hapmap]
rs1671685	0.94[ASN][1000 genomes]
rs1696320	0.81[CHB][hapmap]
rs1696322	0.89[YRI][hapmap]
rs1696326	0.91[CHB][hapmap];0.89[CHD][hapmap];0.94[JPT][hapmap];0.94[ASN][1000 genomes]
rs1696349	0.94[ASN][1000 genomes]
rs1798561	0.81[YRI][hapmap]
rs1798569	0.81[YRI][hapmap]
rs1799618	0.91[CHB][hapmap];0.89[CHD][hapmap];0.94[JPT][hapmap];0.94[ASN][1000 genomes]
rs1979236	0.94[ASN][1000 genomes]
rs1979237	0.94[ASN][1000 genomes]
rs2061098	0.94[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs2061101	0.91[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs2100500	0.94[ASN][1000 genomes]
rs2135014	1.00[CEU][hapmap];0.91[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.94[JPT][hapmap];1.00[TSI][hapmap];0.94[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2271050	1.00[CEU][hapmap];0.91[CHB][hapmap];0.95[CHD][hapmap];0.97[GIH][hapmap];0.88[JPT][hapmap];0.82[TSI][hapmap]
rs2271051	0.91[CHB][hapmap];0.86[CHD][hapmap];0.93[JPT][hapmap];1.00[MEX][hapmap];0.80[ASN][1000 genomes]
rs2292131	0.94[ASN][1000 genomes]
rs2292132	0.92[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2292134	1.00[CEU][hapmap];0.91[CHB][hapmap];0.94[JPT][hapmap];0.94[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2292135	0.94[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2292136	0.83[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[ASN][1000 genomes]
rs2292138	0.87[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs2343108	0.93[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2343109	0.89[AFR][1000 genomes];1.00[AMR][1000 genomes];0.86[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs2343685	0.98[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2649908	0.94[ASN][1000 genomes]
rs2649909	0.94[ASN][1000 genomes]
rs2880678	0.98[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs3817094	0.92[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs3825143	0.94[ASW][hapmap];0.92[CEU][hapmap];0.95[CHB][hapmap];0.97[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.96[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];0.89[YRI][hapmap];1.00[AMR][1000 genomes];0.86[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs3844369	0.81[YRI][hapmap]
rs3852536	0.94[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs3852537	1.00[CEU][hapmap];0.95[CHB][hapmap];0.88[JPT][hapmap];0.89[YRI][hapmap];1.00[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs3896870	0.80[ASN][1000 genomes]
rs4307760	0.81[YRI][hapmap]
rs4759381	0.87[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs4759382	0.94[ASW][hapmap];1.00[CEU][hapmap];0.95[CHB][hapmap];0.97[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.83[LWK][hapmap];1.00[MEX][hapmap];0.89[MKK][hapmap];1.00[TSI][hapmap];0.84[YRI][hapmap];0.97[AMR][1000 genomes];0.87[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs4759386	0.82[AFR][1000 genomes];0.89[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs4759387	0.89[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs4759389	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.93[AFR][1000 genomes];0.89[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs4759392	0.80[AFR][1000 genomes];0.81[AMR][1000 genomes];0.87[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs4759393	0.81[ASW][hapmap];0.83[CEU][hapmap];0.91[CHB][hapmap];0.92[CHD][hapmap]
rs56272219	0.94[ASN][1000 genomes]
rs58182048	0.81[ASN][1000 genomes]
rs59192320	0.80[ASN][1000 genomes]
rs59922385	0.94[ASN][1000 genomes]
rs60308342	0.92[ASN][1000 genomes]
rs6489245	0.87[ASW][hapmap];1.00[CEU][hapmap];0.86[GIH][hapmap];0.85[MEX][hapmap];1.00[TSI][hapmap]
rs6489247	0.83[CEU][hapmap]
rs7138398	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.80[AMR][1000 genomes];0.87[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs7139055	1.00[CEU][hapmap];0.97[GIH][hapmap];0.85[MEX][hapmap];1.00[TSI][hapmap];0.85[EUR][1000 genomes]
rs7294991	0.87[ASW][hapmap];1.00[CEU][hapmap];0.95[CHB][hapmap];0.94[CHD][hapmap];0.94[JPT][hapmap];0.85[MEX][hapmap];0.85[TSI][hapmap];0.81[YRI][hapmap];0.83[AMR][1000 genomes];0.87[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs7303024	0.94[ASN][1000 genomes]
rs7309225	1.00[CEU][hapmap];0.95[CHB][hapmap];0.95[CHD][hapmap];0.94[JPT][hapmap];0.85[MEX][hapmap];0.85[TSI][hapmap];0.87[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs73421642	0.94[ASN][1000 genomes]
rs735378	0.94[ASN][1000 genomes]
rs7398546	0.91[AFR][1000 genomes];0.83[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs754080	0.94[ASN][1000 genomes]
rs7957643	0.81[CEU][hapmap];0.81[YRI][hapmap]
rs7959441	1.00[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs7972447	0.94[ASW][hapmap];1.00[CEU][hapmap];0.82[CHD][hapmap];1.00[GIH][hapmap];0.96[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];0.89[YRI][hapmap];0.94[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs7980541	0.94[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs839360	0.91[CHB][hapmap]
rs897385	0.80[AMR][1000 genomes];0.87[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs897386	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[YRI][hapmap];0.89[AFR][1000 genomes];1.00[AMR][1000 genomes];0.87[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs897391	1.00[ASW][hapmap];1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[CHD][hapmap];0.91[GIH][hapmap];1.00[JPT][hapmap];0.98[LWK][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];0.95[AMR][1000 genomes];0.94[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs897392	0.96[AFR][1000 genomes];0.83[AMR][1000 genomes];0.94[ASN][1000 genomes]
rs897393	1.00[ASW][hapmap];1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.89[LWK][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.95[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs921808	1.00[ASW][hapmap];1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.98[LWK][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];0.95[AMR][1000 genomes];0.93[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs936083	0.83[CEU][hapmap];0.80[AMR][1000 genomes];0.87[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs937520	0.93[ASN][1000 genomes]
rs937766	0.94[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs967281	0.80[YRI][hapmap]
rs9788290	0.81[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	nsv899571	chr12:123215734-123363562	Strong transcription Enhancers Flanking Active TSS Genic enhancers Active TSS Weak transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	25 gene(s)	inside rSNPs	diseases
2	esv3388790	chr12:123275902-123655103	Enhancers Strong transcription Weak transcription Flanking Active TSS Genic enhancers Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	55 gene(s)	inside rSNPs	diseases
3	nsv899572	chr12:123292503-123477311	Active TSS Strong transcription Enhancers Flanking Active TSS Genic enhancers Weak transcription Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	43 gene(s)	inside rSNPs	diseases
4	nsv899573	chr12:123312051-123528405	Enhancers Strong transcription Weak transcription Active TSS Flanking Active TSS Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	47 gene(s)	inside rSNPs	diseases
5	nsv517200	chr12:123312051-123654498	Strong transcription Weak transcription Flanking Active TSS Genic enhancers Enhancers Transcr. at gene 5' and 3' Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	55 gene(s)	inside rSNPs	diseases
6	nsv899574	chr12:123316566-123360151	Genic enhancers Weak transcription Enhancers Strong transcription Flanking Active TSS Bivalent/Poised TSS Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	15 gene(s)	inside rSNPs	diseases

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs4759355	VPS37B	cis	lymphoblastoid	seeQTL
rs4759355	HIP1R	cis	parietal	SCAN
rs4759355	ACADS	cis	parietal	SCAN
rs4759355	TMEM120B	cis	parietal	SCAN

Chromatin state (count:31 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:123305800-123318800	Weak transcription	Pancreas	Pancrea
2	chr12:123310400-123319200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
3	chr12:123311000-123318800	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
4	chr12:123311200-123318200	Weak transcription	Fetal Brain Female	brain
5	chr12:123311200-123319000	Weak transcription	Aorta	Aorta
6	chr12:123311400-123318800	Weak transcription	Duodenum Mucosa	Duodenum
7	chr12:123311600-123318800	Weak transcription	NHDF-Ad	bronchial
8	chr12:123312200-123318800	Weak transcription	Rectal Mucosa Donor 31	rectum
9	chr12:123312400-123318800	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
10	chr12:123312400-123318800	Weak transcription	Breast Myoepithelial Primary Cells	Breast
11	chr12:123312400-123318800	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
12	chr12:123312400-123318800	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
13	chr12:123312400-123318800	Weak transcription	Brain Substantia Nigra	brain
14	chr12:123312600-123318800	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
15	chr12:123313800-123319200	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
16	chr12:123315600-123319200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
17	chr12:123315800-123316600	Weak transcription	Stomach Mucosa	stomach
18	chr12:123315800-123318800	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
19	chr12:123315800-123318800	Weak transcription	A549	lung
20	chr12:123315800-123318800	Weak transcription	K562	blood
21	chr12:123315800-123318800	Weak transcription	NHLF	lung
22	chr12:123316000-123318800	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
23	chr12:123316000-123318800	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
24	chr12:123316000-123318800	Weak transcription	Muscle Satellite Cultured Cells	--
25	chr12:123316000-123318800	Weak transcription	Placenta	Placenta
26	chr12:123316000-123318800	Weak transcription	NHEK	skin
27	chr12:123316200-123318000	Weak transcription	Hela-S3	cervix
28	chr12:123316200-123318800	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
29	chr12:123316200-123318800	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
30	chr12:123316200-123318800	Weak transcription	HMEC	breast
31	chr12:123316400-123319200	Weak transcription	Gastric	stomach

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links