Variant report

Variant	rs1233046
Chromosome Location	chr12:48103324-48103325
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:3)
CpG islands
(count:0)
Chromatin interactive
region (count:5)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:3 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	RUNX3	chr12:48102945-48103792	GM12878	blood:	n/a	n/a
2	RUNX3	chr12:48102926-48103823	GM12878	blood:	n/a	n/a
3	MEF2A	chr12:48103212-48103928	GM12878	blood:	n/a	n/a

No data

(count:5 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr12:48098316..48105030-chr12:48164986..48170762,10	K562	blood:
2	chr12:48102656..48104462-chr12:48112681..48114744,2	MCF-7	breast:
3	chr12:48101224..48103938-chr12:48201884..48203806,2	MCF-7	breast:
4	chr12:48097267..48105309-chr12:48111877..48120917,8	MCF-7	breast:
5	chr12:48101516..48103781-chr12:48167915..48169892,2	K562	blood:

No data

Variant related genes	Relation type
RPAP3	TF binding region
ENSG00000211584	Chromatin interaction
ENSG00000257433	Chromatin interaction
ENSG00000111405	Chromatin interaction

Extended variants
information (count: 51 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:49)

rs_ID	r²[population]
rs10875679	0.89[AFR][1000 genomes];0.92[AMR][1000 genomes];0.95[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs1153975	0.85[AMR][1000 genomes]
rs11609044	0.86[AMR][1000 genomes];0.89[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs11615078	0.84[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs1232985	0.92[CEU][hapmap];0.95[CHB][hapmap];0.95[CHD][hapmap];0.92[GIH][hapmap];0.90[JPT][hapmap];1.00[TSI][hapmap]
rs1232987	0.90[CHB][hapmap];0.89[JPT][hapmap]
rs1233042	0.90[ASN][1000 genomes]
rs1233044	0.89[ASN][1000 genomes]
rs1233045	0.92[AMR][1000 genomes];0.95[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs1233047	1.00[CEU][hapmap];0.95[CHB][hapmap];0.89[JPT][hapmap];1.00[YRI][hapmap];0.89[AMR][1000 genomes];0.92[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs1233049	0.92[AMR][1000 genomes];0.91[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs1233050	0.92[AMR][1000 genomes];0.91[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs1233052	1.00[ASW][hapmap];1.00[CEU][hapmap];0.95[CHB][hapmap];0.95[CHD][hapmap];0.92[GIH][hapmap];0.95[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];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1233053	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs1233055	1.00[ASW][hapmap];1.00[CEU][hapmap];0.95[CHB][hapmap];0.95[CHD][hapmap];0.92[GIH][hapmap];0.90[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];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs1233061	0.92[AMR][1000 genomes];0.85[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs1234820	0.85[AFR][1000 genomes];0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs1235151	1.00[AFR][1000 genomes];0.92[AMR][1000 genomes];0.95[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs12580458	0.81[JPT][hapmap];0.83[AFR][1000 genomes];0.86[AMR][1000 genomes];0.91[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs2022526	0.92[CEU][hapmap];0.95[CHB][hapmap];0.90[JPT][hapmap];0.85[AMR][1000 genomes]
rs2022527	0.85[AMR][1000 genomes]
rs2074535	0.89[EUR][1000 genomes]
rs2155794	0.95[CHB][hapmap];0.90[JPT][hapmap]
rs2155795	1.00[ASW][hapmap];0.92[CEU][hapmap];0.95[CHB][hapmap];0.95[CHD][hapmap];0.92[GIH][hapmap];0.90[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.85[AMR][1000 genomes]
rs2524317	1.00[CHB][hapmap];0.89[CHD][hapmap];0.85[JPT][hapmap];0.95[ASN][1000 genomes]
rs2525448	0.85[AMR][1000 genomes]
rs2525449	0.85[AMR][1000 genomes]
rs2847433	0.92[AMR][1000 genomes];0.93[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs5006306	0.91[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs590089	0.85[AMR][1000 genomes]
rs605026	0.85[AMR][1000 genomes]
rs611208	0.85[AMR][1000 genomes]
rs612096	0.85[AMR][1000 genomes]
rs61917588	0.92[AMR][1000 genomes];0.85[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs61917615	0.86[AMR][1000 genomes];0.91[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs622728	0.85[AMR][1000 genomes]
rs623947	0.85[AMR][1000 genomes]
rs628070	0.89[AMR][1000 genomes];0.84[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs652457	0.85[AMR][1000 genomes]
rs652543	0.85[AMR][1000 genomes]
rs652898	0.85[AMR][1000 genomes]
rs663945	0.85[AMR][1000 genomes]
rs666154	0.85[AMR][1000 genomes]
rs667610	0.85[AMR][1000 genomes]
rs681100	0.85[AMR][1000 genomes];0.80[ASN][1000 genomes]
rs682782	0.85[AMR][1000 genomes]
rs688815	0.92[AMR][1000 genomes];0.85[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs948392	1.00[CEU][hapmap];0.94[CHB][hapmap];0.92[AMR][1000 genomes];0.91[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs948394	0.92[AMR][1000 genomes];0.93[EUR][1000 genomes];0.89[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:2 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv2751101	chr12:47940858-48126885	Active TSS Enhancers Weak transcription Strong transcription Flanking Active TSS ZNF genes & repeats Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	30 gene(s)	inside rSNPs	diseases
2	esv1813565	chr12:48097697-48177858	Enhancers Weak transcription Flanking Active TSS Strong transcription Active TSS Genic enhancers Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	39 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs1233046	C1QL4	cis	cerebellum	SCAN

Chromatin state (count:63 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:48100000-48109200	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
2	chr12:48100000-48111200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
3	chr12:48100400-48105400	Weak transcription	Esophagus	oesophagus
4	chr12:48100600-48103600	Weak transcription	Placenta	Placenta
5	chr12:48100600-48106200	Weak transcription	Placenta Amnion	Placenta Amnion
6	chr12:48100600-48106800	Weak transcription	iPS-18 Cell Line	embryonic stem cell
7	chr12:48100600-48108800	Weak transcription	Fetal Muscle Trunk	muscle
8	chr12:48100600-48109000	Weak transcription	Aorta	Aorta
9	chr12:48100600-48109000	Weak transcription	Lung	lung
10	chr12:48100800-48104800	Flanking Active TSS	Monocytes-CD14+_RO01746	blood
11	chr12:48100800-48106800	Weak transcription	Fetal Stomach	stomach
12	chr12:48100800-48108800	Weak transcription	Brain Hippocampus Middle	brain
13	chr12:48100800-48108800	Weak transcription	Right Ventricle	heart
14	chr12:48100800-48109400	Weak transcription	HSMM	muscle
15	chr12:48101000-48103400	Enhancers	Primary T helper cells fromperipheralblood	blood
16	chr12:48101000-48103600	Flanking Active TSS	GM12878-XiMat	blood
17	chr12:48101000-48104000	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
18	chr12:48101000-48105200	Enhancers	Primary B cells from peripheral blood	blood
19	chr12:48101000-48108800	Weak transcription	Brain Angular Gyrus	brain
20	chr12:48101000-48108800	Weak transcription	Brain Cingulate Gyrus	brain
21	chr12:48101000-48108800	Weak transcription	Brain Substantia Nigra	brain
22	chr12:48101000-48108800	Weak transcription	Fetal Lung	lung
23	chr12:48101000-48108800	Weak transcription	Fetal Muscle Leg	muscle
24	chr12:48101000-48109000	Weak transcription	Fetal Heart	heart
25	chr12:48101000-48109200	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
26	chr12:48101000-48109200	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
27	chr12:48101200-48105400	Enhancers	Primary monocytes fromperipheralblood	blood
28	chr12:48101200-48109200	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
29	chr12:48101400-48104600	Enhancers	Primary neutrophils fromperipheralblood	blood
30	chr12:48101400-48104800	Enhancers	Primary B cells from cord blood	blood
31	chr12:48101400-48108000	Weak transcription	Skeletal Muscle Female	skeletal muscle
32	chr12:48101400-48108800	Weak transcription	Brain Inferior Temporal Lobe	brain
33	chr12:48101400-48108800	Weak transcription	Skeletal Muscle Male	skeletal muscle
34	chr12:48101400-48109600	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
35	chr12:48101400-48111000	Weak transcription	Colonic Mucosa	Colon
36	chr12:48101400-48111200	Weak transcription	Small Intestine	intestine
37	chr12:48101800-48111200	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
38	chr12:48102000-48103400	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
39	chr12:48102000-48104800	Enhancers	Primary hematopoietic stem cells	blood
40	chr12:48102000-48109200	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
41	chr12:48102200-48103400	Enhancers	Primary T helper naive cells from peripheral blood	blood
42	chr12:48102200-48103400	Enhancers	Primary T helper naive cells fromperipheralblood	blood
43	chr12:48102200-48103400	Enhancers	Primary mononuclear cells fromperipheralblood	Blood
44	chr12:48102200-48103800	Enhancers	Primary T helper cells PMA-I stimulated	--
45	chr12:48102200-48103800	Enhancers	K562	blood
46	chr12:48102200-48104600	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
47	chr12:48102200-48104600	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
48	chr12:48102200-48108200	Weak transcription	Breast Myoepithelial Primary Cells	Breast
49	chr12:48102200-48108200	Weak transcription	Duodenum Smooth Muscle	Duodenum
50	chr12:48102200-48108800	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin

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