Variant report

Variant	rs1696326
Chromosome Location	chr12:123311981-123311982
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr12:123303686..123306073-chr12:123311206..123312843,2	MCF-7	breast:
2	chr12:123311180..123313487-chr12:123316149..123318304,2	K562	blood:
3	chr12:123311285..123313219-chr12:123325523..123328002,2	MCF-7	breast:
4	chr12:123310638..123313614-chr12:123319077..123320937,3	MCF-7	breast:
5	chr12:123310760..123313815-chr12:123319120..123321781,3	K562	blood:

Variant related genes	Relation type
ENSG00000130787	Chromatin interaction

Extended variants
information (count: 86 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:83)

rs_ID	r²[population]
rs10773627	0.86[CHB][hapmap];0.89[CHD][hapmap];0.94[JPT][hapmap];0.90[ASN][1000 genomes]
rs10773657	0.90[ASN][1000 genomes]
rs10847826	0.90[ASN][1000 genomes]
rs10847869	0.90[ASN][1000 genomes]
rs11059711	0.92[GIH][hapmap]
rs11060064	1.00[CEU][hapmap];0.95[CHB][hapmap];0.97[CHD][hapmap];0.84[GIH][hapmap];0.94[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.81[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs11060065	1.00[CEU][hapmap];0.95[CHB][hapmap];0.97[CHD][hapmap];0.84[GIH][hapmap];0.94[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.81[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs11060208	0.90[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs11060209	0.90[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11060762	1.00[MEX][hapmap]
rs12255	0.86[CHB][hapmap];0.86[CHD][hapmap];0.94[JPT][hapmap]
rs12297553	0.81[EUR][1000 genomes]
rs12298151	0.87[ASN][1000 genomes]
rs12298664	0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12299742	0.86[AMR][1000 genomes];0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12303328	1.00[CEU][hapmap]
rs12310386	0.92[GIH][hapmap]
rs12313006	1.00[CHB][hapmap];0.92[CHD][hapmap];0.94[JPT][hapmap];0.83[ASN][1000 genomes]
rs12314494	0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12314544	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12314976	1.00[CEU][hapmap]
rs12319654	0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12321131	0.81[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs12426809	0.90[ASN][1000 genomes]
rs1532835	0.88[ASN][1000 genomes]
rs1587856	0.80[ASN][1000 genomes]
rs1671685	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1696349	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1799618	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1979236	0.86[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1979237	0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2100500	1.00[ASN][1000 genomes]
rs2135014	0.82[CHB][hapmap];0.89[CHD][hapmap];0.89[JPT][hapmap];0.88[ASN][1000 genomes]
rs2271050	0.82[CHB][hapmap];0.89[CHD][hapmap];0.82[JPT][hapmap]
rs2271051	1.00[CHB][hapmap];0.97[CHD][hapmap];1.00[JPT][hapmap];0.85[ASN][1000 genomes]
rs2292131	0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2292132	0.88[ASN][1000 genomes]
rs2292134	0.82[CHB][hapmap];0.94[JPT][hapmap];0.86[ASN][1000 genomes]
rs2292135	0.84[ASN][1000 genomes]
rs2292136	0.90[CHB][hapmap];0.94[JPT][hapmap];0.82[ASN][1000 genomes]
rs2292138	0.80[ASN][1000 genomes]
rs2292139	0.86[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs2343108	0.88[ASN][1000 genomes]
rs2343109	0.80[ASN][1000 genomes]
rs2343685	0.90[ASN][1000 genomes]
rs2649908	0.88[AFR][1000 genomes];1.00[AMR][1000 genomes];0.90[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2649909	0.98[AFR][1000 genomes];0.95[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2880678	0.90[ASN][1000 genomes]
rs3782289	1.00[MEX][hapmap]
rs3817094	0.87[ASN][1000 genomes]
rs3817095	0.92[GIH][hapmap]
rs3825143	0.86[CHB][hapmap];0.86[CHD][hapmap];0.94[JPT][hapmap]
rs3852536	0.86[ASN][1000 genomes]
rs3852537	0.86[CHB][hapmap];0.82[JPT][hapmap]
rs4759355	0.91[CHB][hapmap];0.89[CHD][hapmap];0.94[JPT][hapmap];0.94[ASN][1000 genomes]
rs4759382	0.86[CHB][hapmap];0.86[CHD][hapmap];0.94[JPT][hapmap]
rs4759389	0.86[CHB][hapmap];0.94[JPT][hapmap];0.90[ASN][1000 genomes]
rs4759392	0.81[ASN][1000 genomes]
rs4759393	0.81[CHB][hapmap];0.87[CHD][hapmap]
rs56272219	1.00[ASN][1000 genomes]
rs58182048	0.81[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs59192320	0.85[ASN][1000 genomes]
rs59922385	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs60308342	1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7138398	0.91[CHB][hapmap];0.94[JPT][hapmap];0.80[ASN][1000 genomes]
rs7294991	0.86[CHB][hapmap];0.89[CHD][hapmap];0.89[JPT][hapmap];0.81[ASN][1000 genomes]
rs7303024	1.00[ASN][1000 genomes]
rs7309225	0.86[CHB][hapmap];0.89[CHD][hapmap];0.89[JPT][hapmap];0.81[ASN][1000 genomes]
rs73421642	1.00[ASN][1000 genomes]
rs735378	0.86[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7398546	0.84[ASN][1000 genomes]
rs754080	0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs839360	1.00[CEU][hapmap];0.81[CHB][hapmap]
rs897385	0.80[ASN][1000 genomes]
rs897386	0.89[CHB][hapmap];0.94[JPT][hapmap];0.80[ASN][1000 genomes]
rs897391	0.86[CHB][hapmap];0.89[CHD][hapmap];0.94[JPT][hapmap];0.90[ASN][1000 genomes]
rs897392	0.90[ASN][1000 genomes]
rs897393	0.86[CHB][hapmap];0.89[CHD][hapmap];0.94[JPT][hapmap];0.90[ASN][1000 genomes]
rs921808	0.86[CHB][hapmap];0.89[CHD][hapmap];0.94[JPT][hapmap];0.88[ASN][1000 genomes]
rs936083	0.82[ASN][1000 genomes]
rs937520	0.81[AFR][1000 genomes];1.00[AMR][1000 genomes];0.90[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs937766	0.88[ASN][1000 genomes]
rs9788290	0.81[EUR][1000 genomes];0.86[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:3 , 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

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs1696326	HIP1R	cis	lymphoblastoid	seeQTL
rs1696326	OGFOD2	cis	lymphoblastoid	seeQTL
rs1696326	VPS37B	cis	lymphoblastoid	seeQTL

Chromatin state (count:44 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:123302200-123312000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
2	chr12:123304400-123312000	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
3	chr12:123305800-123318800	Weak transcription	Pancreas	Pancrea
4	chr12:123310400-123312000	Active TSS	Breast Myoepithelial Primary Cells	Breast
5	chr12:123310400-123312000	Active TSS	HMEC	breast
6	chr12:123310400-123312200	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
7	chr12:123310400-123319200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
8	chr12:123310600-123312000	Active TSS	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
9	chr12:123310600-123312000	Active TSS	Brain Hippocampus Middle	brain
10	chr12:123310600-123312200	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
11	chr12:123310600-123312200	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
12	chr12:123311000-123315200	Weak transcription	K562	blood
13	chr12:123311000-123318800	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
14	chr12:123311200-123312000	Weak transcription	Primary B cells from peripheral blood	blood
15	chr12:123311200-123312000	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
16	chr12:123311200-123312000	Weak transcription	Brain Cingulate Gyrus	brain
17	chr12:123311200-123312000	Weak transcription	Brain Substantia Nigra	brain
18	chr12:123311200-123312200	Flanking Active TSS	Ganglion Eminence derived primary cultured neurospheres	brain
19	chr12:123311200-123312200	Enhancers	Liver	Liver
20	chr12:123311200-123312200	Enhancers	Fetal Intestine Large	intestine
21	chr12:123311200-123312200	Enhancers	Fetal Kidney	kidney
22	chr12:123311200-123312200	Enhancers	Rectal Mucosa Donor 31	rectum
23	chr12:123311200-123312600	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
24	chr12:123311200-123312600	Enhancers	Stomach Mucosa	stomach
25	chr12:123311200-123313400	Weak transcription	Fetal Heart	heart
26	chr12:123311200-123315200	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
27	chr12:123311200-123318200	Weak transcription	Fetal Brain Female	brain
28	chr12:123311200-123319000	Weak transcription	Aorta	Aorta
29	chr12:123311400-123312000	Weak transcription	Brain Inferior Temporal Lobe	brain
30	chr12:123311400-123312000	Active TSS	HepG2	liver
31	chr12:123311400-123312200	Bivalent Enhancer	HUVEC	blood vessel
32	chr12:123311400-123313600	Weak transcription	Pancreatic Islets	Pancreatic Islet
33	chr12:123311400-123315400	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
34	chr12:123311400-123315600	Weak transcription	Muscle Satellite Cultured Cells	--
35	chr12:123311400-123318800	Weak transcription	Duodenum Mucosa	Duodenum
36	chr12:123311600-123312200	Enhancers	NHEK	skin
37	chr12:123311600-123312400	Enhancers	Cortex derived primary cultured neurospheres	brain
38	chr12:123311600-123312400	Enhancers	Brain Anterior Caudate	brain
39	chr12:123311600-123312400	Enhancers	Fetal Intestine Small	intestine
40	chr12:123311600-123312400	Enhancers	A549	lung
41	chr12:123311600-123315200	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
42	chr12:123311600-123315600	Weak transcription	NHLF	lung
43	chr12:123311600-123318800	Weak transcription	NHDF-Ad	bronchial
44	chr12:123311800-123312000	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived

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