Variant report

Variant	rs13063312
Chromosome Location	chr3:48661985-48661986
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	FOXA1	chr3:48661341-48662008	HepG2	liver:	n/a	n/a
2	POLR2A	chr3:48661836-48661988	HepG2	liver:	n/a	n/a
3	POLR2A	chr3:48661018-48662177	HepG2	liver:	n/a	n/a
4	MAX	chr3:48661082-48662249	HepG2	liver:	n/a	chr3:48661429-48661439 chr3:48661941-48661957 chr3:48661590-48661599 chr3:48661401-48661411 chr3:48661588-48661601 chr3:48661590-48661599
5	POLR2A	chr3:48661493-48662566	PFSK-1	brain:	n/a	n/a
6	POLR2A	chr3:48661821-48662159	H1-hESC	embryonic stem cell:	n/a	n/a
7	MYBL2	chr3:48661009-48661989	HepG2	liver:	n/a	n/a
8	POLR2A	chr3:48660022-48663466	HepG2	liver:	n/a	n/a
9	HEY1	chr3:48661208-48662484	HepG2	liver:	n/a	n/a
10	POLR2A	chr3:48660932-48662551	H1-hESC	embryonic stem cell:	n/a	n/a
11	POLR2A	chr3:48661204-48662137	HepG2	liver:	n/a	n/a
12	FOXA1	chr3:48661186-48662026	HepG2	liver:	n/a	n/a
13	POLR2A	chr3:48661185-48662161	HepG2	liver:	n/a	n/a
14	POLR2A	chr3:48661469-48662257	H1-hESC	embryonic stem cell:	n/a	n/a
15	CTCF	chr3:48661920-48662070	HepG2	liver:	n/a	n/a
16	FOXA1	chr3:48661370-48662025	HepG2	liver:	n/a	n/a
17	FOXA2	chr3:48661297-48662223	HepG2	liver:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr3:48661665..48664371-chr3:48687435..48689598,2	MCF-7	breast:
2	chr3:48645833..48648564-chr3:48660520..48662280,2	K562	blood:
3	chr3:48660415..48662827-chr3:48667467..48669112,2	K562	blood:
4	chr3:48656876..48658488-chr3:48660227..48663106,2	MCF-7	breast:
5	chr3:48645535..48647761-chr3:48661454..48663479,2	MCF-7	breast:
6	chr3:48659034..48660590-chr3:48661591..48664038,3	K562	blood:

Variant related genes	Relation type
TMEM89	TF binding region
ENSG00000010256	Chromatin interaction
ENSG00000183396	Chromatin interaction
ENSG00000225697	Chromatin interaction

Extended variants
information (count: 88 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:81)

rs_ID	r²[population]
rs1003649	0.83[GIH][hapmap]
rs10470687	0.85[CHD][hapmap];0.83[GIH][hapmap];1.00[JPT][hapmap]
rs11706983	1.00[GIH][hapmap];0.91[TSI][hapmap]
rs11708786	1.00[GIH][hapmap];0.81[TSI][hapmap]
rs11713694	0.83[GIH][hapmap]
rs11719291	1.00[GIH][hapmap];0.91[TSI][hapmap]
rs12107252	0.90[CEU][hapmap];0.89[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.87[TSI][hapmap];0.86[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs12107418	0.90[CEU][hapmap];0.85[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.87[TSI][hapmap];0.87[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs12715429	0.87[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs13060933	0.85[CHD][hapmap];0.83[GIH][hapmap];1.00[JPT][hapmap]
rs13062576	0.82[CHB][hapmap]
rs13070798	0.90[CEU][hapmap];0.89[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.95[TSI][hapmap];0.87[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs13074318	0.83[GIH][hapmap]
rs13076269	0.90[AMR][1000 genomes];0.92[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs13091944	1.00[JPT][hapmap]
rs13096357	0.90[AMR][1000 genomes];0.99[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs13319651	0.89[CHD][hapmap];0.83[GIH][hapmap];1.00[JPT][hapmap]
rs13324119	0.87[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs13324142	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];0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs13434258	1.00[GIH][hapmap];0.91[TSI][hapmap]
rs17080289	0.90[CHD][hapmap];1.00[GIH][hapmap];0.81[ASN][1000 genomes]
rs2006871	0.89[CHD][hapmap];0.83[GIH][hapmap];1.00[JPT][hapmap]
rs2276850	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];0.88[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2276852	1.00[CEU][hapmap];0.95[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.92[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2286651	0.93[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2286652	1.00[ASW][hapmap];0.90[CEU][hapmap];0.85[CHB][hapmap];0.89[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.81[LWK][hapmap];0.87[MKK][hapmap];1.00[TSI][hapmap];0.81[YRI][hapmap];0.93[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2302295	0.88[CEU][hapmap];1.00[JPT][hapmap];0.91[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2310996	1.00[CEU][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.83[TSI][hapmap];0.93[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2310997	0.94[AFR][1000 genomes];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs28452701	0.87[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2854394	0.85[CHD][hapmap];0.83[GIH][hapmap];1.00[JPT][hapmap]
rs34037363	0.83[GIH][hapmap]
rs34096717	0.87[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs34368826	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34638686	0.86[AMR][1000 genomes];0.92[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs35064573	1.00[GIH][hapmap];0.91[TSI][hapmap]
rs35343040	0.83[ASN][1000 genomes]
rs35796820	0.81[ASN][1000 genomes]
rs3733086	0.86[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs3806694	1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[YRI][hapmap];0.97[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3821875	0.81[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs3821876	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];0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs3895736	0.85[LWK][hapmap];0.85[MKK][hapmap]
rs3969942	0.80[CHD][hapmap];0.83[GIH][hapmap]
rs57334642	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6768448	0.82[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs6773261	1.00[CEU][hapmap];1.00[JPT][hapmap];0.90[AMR][1000 genomes];0.99[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs6781283	0.85[CHD][hapmap];0.83[GIH][hapmap];1.00[JPT][hapmap]
rs6792156	0.90[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.84[ASN][1000 genomes]
rs6792525	0.89[CHD][hapmap];0.83[GIH][hapmap];1.00[JPT][hapmap]
rs68042649	0.82[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs6806059	0.85[CHD][hapmap];0.83[GIH][hapmap];1.00[JPT][hapmap]
rs73078349	0.82[EUR][1000 genomes]
rs740787	1.00[CEU][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.83[TSI][hapmap];0.93[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7428949	1.00[JPT][hapmap]
rs7620853	1.00[CEU][hapmap];1.00[JPT][hapmap];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7631574	1.00[CEU][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.87[TSI][hapmap];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs9809222	0.82[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs9810549	0.89[CHD][hapmap];0.83[GIH][hapmap];1.00[JPT][hapmap]
rs9810991	0.89[CHD][hapmap];0.83[GIH][hapmap]
rs9811318	0.90[CEU][hapmap];0.89[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.87[TSI][hapmap];0.82[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs9812200	0.90[CEU][hapmap];0.89[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.87[TSI][hapmap];0.85[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs9812977	0.81[ASN][1000 genomes]
rs9821797	0.90[CEU][hapmap];1.00[JPT][hapmap];0.82[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs9830581	0.84[ASW][hapmap];0.84[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.83[ASN][1000 genomes]
rs9836462	0.90[CEU][hapmap];0.95[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.87[TSI][hapmap];0.82[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs9837687	0.85[CHD][hapmap];0.83[GIH][hapmap];1.00[JPT][hapmap]
rs9841602	0.90[CEU][hapmap];0.89[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.87[TSI][hapmap];0.82[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs9843316	0.90[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.83[ASN][1000 genomes]
rs9850102	0.85[CHD][hapmap];0.83[GIH][hapmap];1.00[JPT][hapmap]
rs9851771	0.83[GIH][hapmap]
rs9868809	1.00[ASW][hapmap];0.90[CEU][hapmap];0.89[CHD][hapmap];0.83[GIH][hapmap];0.92[LWK][hapmap];0.88[MEX][hapmap];0.97[MKK][hapmap];0.90[TSI][hapmap];0.89[YRI][hapmap];0.92[AFR][1000 genomes];0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs9869698	0.85[CHD][hapmap];0.83[GIH][hapmap];1.00[JPT][hapmap]
rs9871180	0.89[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap]
rs9873726	0.86[CEU][hapmap];1.00[JPT][hapmap];0.82[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs9875911	0.83[GIH][hapmap]
rs9878063	0.94[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs9878950	0.85[CHD][hapmap];0.83[GIH][hapmap];1.00[JPT][hapmap]
rs9881877	0.85[CHD][hapmap];1.00[GIH][hapmap]
rs9882549	1.00[GIH][hapmap];0.81[TSI][hapmap]
rs9882962	0.80[CHD][hapmap];0.83[GIH][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	nsv1008232	chr3:48517121-48702416	Transcr. at gene 5' and 3' Active TSS Genic enhancers Enhancers Strong transcription Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Weak transcription ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	50 gene(s)	inside rSNPs	diseases
2	nsv523981	chr3:48520289-48721040	Weak transcription Enhancers Strong transcription Flanking Active TSS ZNF genes & repeats Active TSS Bivalent Enhancer Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	52 gene(s)	inside rSNPs	diseases
3	nsv834685	chr3:48565009-48745774	Strong transcription Active TSS Genic enhancers Weak transcription Enhancers Flanking Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	55 gene(s)	inside rSNPs	diseases
4	nsv876762	chr3:48591481-48731487	Strong transcription Enhancers Flanking Bivalent TSS/Enh Weak transcription Genic enhancers Flanking Active TSS Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	53 gene(s)	inside rSNPs	diseases
5	nsv818138	chr3:48610925-48731487	Strong transcription Weak transcription Enhancers Flanking Active TSS Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Active TSS 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	49 gene(s)	inside rSNPs	diseases
6	nsv590246	chr3:48628014-48721040	Flanking Active TSS Weak transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Genic enhancers Enhancers Strong transcription Active TSS 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	47 gene(s)	inside rSNPs	diseases
7	nsv590247	chr3:48661985-48801929	Transcr. at gene 5' and 3' Strong transcription Active TSS Genic enhancers Enhancers Flanking Active TSS Weak transcription Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	53 gene(s)	inside rSNPs	diseases

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs13063312	WDR6	cis	Esophagus Mucosa	GTEx
rs13063312	WDR6	cis	Skin Sun Exposed Lower leg	GTEx
rs13063312	SLC26A6	cis	lung	GTEx
rs13063312	WDR6	cis	lymphoblastoid	seeQTL

Chromatin state (count:114 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:48649000-48672000	Weak transcription	Fetal Brain Male	brain
2	chr3:48651800-48662400	Weak transcription	NHLF	lung
3	chr3:48655200-48662200	Weak transcription	Skeletal Muscle Male	skeletal muscle
4	chr3:48655400-48662800	Weak transcription	Esophagus	oesophagus
5	chr3:48655400-48662800	Weak transcription	Fetal Brain Female	brain
6	chr3:48655600-48662200	Weak transcription	Fetal Stomach	stomach
7	chr3:48655600-48663000	Weak transcription	Cortex derived primary cultured neurospheres	brain
8	chr3:48656000-48662400	Weak transcription	iPS-18 Cell Line	embryonic stem cell
9	chr3:48656000-48664000	Weak transcription	Brain Germinal Matrix	brain
10	chr3:48656200-48662600	Weak transcription	Placenta Amnion	Placenta Amnion
11	chr3:48656400-48663000	Weak transcription	HSMM	muscle
12	chr3:48656400-48663200	Weak transcription	Hela-S3	cervix
13	chr3:48656400-48664400	Weak transcription	HMEC	breast
14	chr3:48656400-48671400	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
15	chr3:48656600-48662200	Weak transcription	Osteobl	bone
16	chr3:48656600-48662600	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
17	chr3:48656600-48662800	Weak transcription	H9 Cell Line	embryonic stem cell
18	chr3:48656800-48662400	Weak transcription	iPS-20b Cell Line	embryonic stem cell
19	chr3:48656800-48662600	Weak transcription	HUES64 Cell Line	embryonic stem cell
20	chr3:48657200-48664600	Strong transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
21	chr3:48657400-48662600	Weak transcription	Liver	Liver
22	chr3:48657600-48662200	Weak transcription	Fetal Muscle Trunk	muscle
23	chr3:48657600-48662400	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
24	chr3:48657800-48664200	Weak transcription	Pancreas	Pancrea
25	chr3:48657800-48670000	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
26	chr3:48658200-48668000	Strong transcription	Foreskin Fibroblast Primary Cells skin01	Skin
27	chr3:48658400-48662200	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
28	chr3:48658400-48662400	Weak transcription	HUES48 Cell Line	embryonic stem cell
29	chr3:48658600-48662800	Weak transcription	Lung	lung
30	chr3:48658800-48662400	Weak transcription	Primary monocytes fromperipheralblood	blood
31	chr3:48659000-48662400	Weak transcription	Stomach Smooth Muscle	stomach
32	chr3:48659000-48663600	Weak transcription	Rectal Smooth Muscle	rectum
33	chr3:48659000-48671200	Strong transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
34	chr3:48659200-48662000	Enhancers	Primary neutrophils fromperipheralblood	blood
35	chr3:48659400-48662400	Weak transcription	Gastric	stomach
36	chr3:48659600-48663200	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
37	chr3:48659800-48662000	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
38	chr3:48659800-48662400	Weak transcription	Fetal Muscle Leg	muscle
39	chr3:48659800-48663000	Weak transcription	Left Ventricle	heart
40	chr3:48660000-48663600	Weak transcription	Ovary	ovary
41	chr3:48660000-48671200	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
42	chr3:48660200-48662000	Weak transcription	Brain Hippocampus Middle	brain
43	chr3:48660200-48663200	Weak transcription	Right Ventricle	heart
44	chr3:48660400-48662400	Weak transcription	Skeletal Muscle Female	skeletal muscle
45	chr3:48660400-48663000	Weak transcription	Brain Inferior Temporal Lobe	brain
46	chr3:48660400-48665000	Weak transcription	NHDF-Ad	bronchial
47	chr3:48660400-48667800	Weak transcription	A549	lung
48	chr3:48660600-48662400	Weak transcription	Brain Cingulate Gyrus	brain
49	chr3:48660600-48662600	Weak transcription	Adipose Nuclei	Adipose
50	chr3:48660600-48663600	Weak transcription	GM12878-XiMat	blood

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