Variant report

Variant	rs1375653
Chromosome Location	chr12:122388314-122388315
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	FOS	chr12:122387754-122388354	MCF10A-Er-Src	breast:	n/a	n/a
2	POLR2A	chr12:122387910-122388399	SK-N-SH	brain:	n/a	n/a
3	USF1	chr12:122387913-122388333	A549	lung:	n/a	chr12:122388126-122388137
4	POLR2A	chr12:122387962-122388354	MCF10A-Er-Src	breast:	n/a	n/a
5	POLR2A	chr12:122387785-122388440	MCF10A-Er-Src	breast:	n/a	n/a
6	TCF12	chr12:122387720-122388540	SK-N-SH	brain:	n/a	n/a
7	MYC	chr12:122387816-122388332	MCF10A-Er-Src	breast:	n/a	n/a
8	CEBPB	chr12:122387919-122388342	IMR90	lung:	n/a	n/a
9	FOS	chr12:122387797-122388439	MCF10A-Er-Src	breast:	n/a	chr12:122388408-122388419 chr12:122388411-122388421 chr12:122388412-122388420 chr12:122388411-122388421
10	FOSL2	chr12:122387744-122388495	SK-N-SH	brain:	n/a	chr12:122388408-122388419 chr12:122388411-122388421 chr12:122388412-122388420 chr12:122388411-122388421
11	PBX3	chr12:122387767-122388509	SK-N-SH	brain:	n/a	n/a
12	FOS	chr12:122387895-122388380	MCF10A-Er-Src	breast:	n/a	n/a
13	FOS	chr12:122387755-122388428	MCF10A-Er-Src	breast:	n/a	chr12:122388408-122388419 chr12:122388411-122388421 chr12:122388412-122388420 chr12:122388411-122388421
14	USF1	chr12:122387887-122388355	A549	lung:	n/a	chr12:122388126-122388137
15	USF1	chr12:122387896-122388382	A549	lung:	n/a	chr12:122388126-122388137
16	USF1	chr12:122387874-122388320	A549	lung:	n/a	chr12:122388126-122388137
17	MAFK	chr12:122387691-122388381	IMR90	lung:	n/a	n/a

Variant related genes	Relation type
WDR66	TF binding region

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

rSNPs within LD-proxies of this variant (count:46)

rs_ID	r²[population]
rs1154514	0.86[YRI][hapmap]
rs1169076	0.82[CEU][hapmap];0.87[CHB][hapmap];0.95[CHD][hapmap];0.91[GIH][hapmap];0.95[JPT][hapmap];0.86[MEX][hapmap];0.88[TSI][hapmap];0.85[AMR][1000 genomes];0.90[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs1169081	0.91[CHB][hapmap];0.95[CHD][hapmap];1.00[JPT][hapmap];0.91[ASN][1000 genomes]
rs1169083	0.80[ASN][1000 genomes]
rs1169084	0.83[CHB][hapmap];0.91[CHD][hapmap];1.00[JPT][hapmap]
rs1169091	0.87[CHB][hapmap];0.91[CHD][hapmap];1.00[JPT][hapmap]
rs1177588	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1179947	0.82[CEU][hapmap];0.87[CHB][hapmap];0.95[CHD][hapmap];0.91[GIH][hapmap];1.00[JPT][hapmap];0.87[MEX][hapmap];0.88[TSI][hapmap];0.84[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs1184893	0.87[AFR][1000 genomes];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs12578258	1.00[CHB][hapmap];0.95[CHD][hapmap];1.00[JPT][hapmap];0.99[ASN][1000 genomes]
rs12579389	0.99[ASN][1000 genomes]
rs12579730	0.81[ASN][1000 genomes]
rs1375654	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1375655	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];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs14259	0.83[ASN][1000 genomes]
rs1630699	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1667586	0.97[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1678952	1.00[CEU][hapmap];1.00[CHB][hapmap];0.94[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1678953	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];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1720030	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1720033	0.81[YRI][hapmap]
rs1720035	0.87[CEU][hapmap];0.87[MEX][hapmap];0.94[TSI][hapmap]
rs1720068	1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[YRI][hapmap];0.83[ASN][1000 genomes]
rs17852561	0.98[ASN][1000 genomes]
rs2009257	0.87[CHB][hapmap];1.00[JPT][hapmap]
rs2272133	0.87[CHB][hapmap];0.95[JPT][hapmap]
rs2272135	1.00[CHB][hapmap];0.95[CHD][hapmap];1.00[JPT][hapmap];0.83[ASN][1000 genomes]
rs2309275	0.82[CHB][hapmap];0.90[JPT][hapmap];0.92[ASN][1000 genomes]
rs2442439	0.80[ASN][1000 genomes]
rs2688409	0.83[ASN][1000 genomes]
rs2688411	0.96[AFR][1000 genomes];0.93[AMR][1000 genomes];0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2922797	0.97[AFR][1000 genomes];0.91[AMR][1000 genomes];0.89[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2948663	0.98[AFR][1000 genomes];0.91[AMR][1000 genomes];0.94[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2948664	0.98[AFR][1000 genomes];0.88[AMR][1000 genomes];0.89[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs35252940	0.99[ASN][1000 genomes]
rs508395	0.83[ASN][1000 genomes]
rs529736	0.88[ASW][hapmap];0.81[CEU][hapmap];0.83[GIH][hapmap];0.82[MEX][hapmap];0.88[MKK][hapmap];1.00[YRI][hapmap];0.86[AFR][1000 genomes];0.83[AMR][1000 genomes];0.87[ASN][1000 genomes]
rs59972569	0.99[ASN][1000 genomes]
rs658957	0.81[AMR][1000 genomes]
rs686220	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7313748	1.00[CHB][hapmap];0.95[CHD][hapmap];1.00[JPT][hapmap];0.99[ASN][1000 genomes]
rs745327	0.82[CHB][hapmap]
rs830115	0.91[ASN][1000 genomes]
rs830121	0.87[CHB][hapmap];0.93[CHD][hapmap];1.00[JPT][hapmap];0.85[ASN][1000 genomes]
rs876934	0.83[ASN][1000 genomes]
rs895960	0.87[CEU][hapmap];0.87[MEX][hapmap];0.94[TSI][hapmap]

Variant overlapped rSNPs/rCNVs (count:5 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv529868	chr12:121956483-122944265	Flanking Active TSS Enhancers Weak transcription Active TSS Genic enhancers Strong transcription ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	173 gene(s)	inside rSNPs	diseases
2	nsv916686	chr12:122240149-122714056	Enhancers Strong transcription Weak transcription Flanking Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer Genic enhancers Active TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	89 gene(s)	inside rSNPs	diseases
3	nsv899568	chr12:122254713-122456524	Active TSS Enhancers Flanking Active TSS Weak transcription Strong transcription Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	19 gene(s)	inside rSNPs	diseases
4	esv34001	chr12:122298737-122521637	Active TSS Weak transcription Flanking Active TSS Strong transcription Enhancers Genic enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	35 gene(s)	inside rSNPs	diseases
5	esv1799099	chr12:122382229-122398494	Enhancers Flanking Active TSS Strong transcription Weak transcription ZNF genes & repeats Active TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region	8 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs1375653	MSI1	cis	cerebellum	SCAN

Chromatin state (count:54 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:122363000-122393400	Weak transcription	Brain Angular Gyrus	brain
2	chr12:122363600-122392200	Weak transcription	Left Ventricle	heart
3	chr12:122363600-122398600	Weak transcription	Skeletal Muscle Male	skeletal muscle
4	chr12:122363600-122408000	Weak transcription	Right Ventricle	heart
5	chr12:122365600-122393400	Weak transcription	Brain Substantia Nigra	brain
6	chr12:122365800-122390200	Weak transcription	HUVEC	blood vessel
7	chr12:122365800-122405000	Weak transcription	Placenta Amnion	Placenta Amnion
8	chr12:122370600-122403200	Weak transcription	Fetal Kidney	kidney
9	chr12:122372200-122396400	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
10	chr12:122372800-122393600	Weak transcription	Brain Hippocampus Middle	brain
11	chr12:122374000-122402800	Weak transcription	HSMM	muscle
12	chr12:122374000-122405600	Weak transcription	Adipose Nuclei	Adipose
13	chr12:122375400-122401400	Weak transcription	Ovary	ovary
14	chr12:122375400-122402600	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
15	chr12:122375800-122393600	Weak transcription	Brain Inferior Temporal Lobe	brain
16	chr12:122375800-122415800	Weak transcription	Liver	Liver
17	chr12:122376000-122393400	Weak transcription	Brain Anterior Caudate	brain
18	chr12:122376000-122401600	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
19	chr12:122376000-122413000	Weak transcription	Aorta	Aorta
20	chr12:122377400-122406200	Weak transcription	Thymus	Thymus
21	chr12:122380600-122401600	Weak transcription	Pancreas	Pancrea
22	chr12:122380800-122405800	Weak transcription	Skeletal Muscle Female	skeletal muscle
23	chr12:122381000-122396400	Weak transcription	Stomach Smooth Muscle	stomach
24	chr12:122381000-122400000	Weak transcription	Spleen	Spleen
25	chr12:122381000-122405800	Weak transcription	Fetal Muscle Leg	muscle
26	chr12:122382200-122393600	Weak transcription	Breast Myoepithelial Primary Cells	Breast
27	chr12:122382200-122396200	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
28	chr12:122382200-122402200	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
29	chr12:122382600-122399600	Weak transcription	K562	blood
30	chr12:122383000-122391000	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
31	chr12:122384800-122388800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
32	chr12:122384800-122396400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
33	chr12:122385000-122391200	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
34	chr12:122386200-122398600	Weak transcription	Fetal Stomach	stomach
35	chr12:122387200-122388600	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
36	chr12:122387400-122388400	Enhancers	A549	lung
37	chr12:122387600-122388400	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
38	chr12:122387800-122388400	Enhancers	Muscle Satellite Cultured Cells	--
39	chr12:122387800-122388400	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
40	chr12:122387800-122388400	Enhancers	Fetal Heart	heart
41	chr12:122388000-122388400	Enhancers	ES-I3 Cell Line	embryonic stem cell
42	chr12:122388000-122388400	Active TSS	IMR90 fetal lung fibroblasts Cell Line	lung
43	chr12:122388000-122388400	Enhancers	HepG2	liver
44	chr12:122388000-122388400	Enhancers	NHLF	lung
45	chr12:122388000-122388400	Enhancers	Osteobl	bone
46	chr12:122388000-122390400	Active TSS	Foreskin Keratinocyte Primary Cells skin03	Skin
47	chr12:122388200-122388400	Genic enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
48	chr12:122388200-122388400	Active TSS	Foreskin Keratinocyte Primary Cells skin02	Skin
49	chr12:122388200-122388400	Flanking Active TSS	NH-A	brain
50	chr12:122388200-122388400	Flanking Active TSS	NHEK	skin

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