Variant report

Variant	rs3741470
Chromosome Location	chr12:117581158-117581159
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr12:117461340..117464538-chr12:117578917..117582364,3	MCF-7	breast:
2	chr12:117564140..117566013-chr12:117581148..117583072,2	MCF-7	breast:
3	chr12:117575984..117579086-chr12:117579299..117582176,4	MCF-7	breast:
4	chr12:117578702..117581617-chr12:117599263..117601278,2	MCF-7	breast:
5	chr12:117580874..117582720-chr12:117585893..117588244,3	MCF-7	breast:
6	chr12:117579571..117583522-chr12:117585472..117588878,4	K562	blood:

Extended variants
information (count: 116 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:114)

rs_ID	r²[population]
rs10161089	0.93[CEU][hapmap];0.86[CHB][hapmap];0.81[JPT][hapmap];0.86[AMR][1000 genomes];0.92[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs10161283	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.89[TSI][hapmap];0.91[AMR][1000 genomes];0.89[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10850775	1.00[YRI][hapmap];0.84[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs10850776	0.98[AMR][1000 genomes];0.94[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs10850777	0.91[CHB][hapmap];0.89[ASN][1000 genomes]
rs10850782	0.83[CHB][hapmap];0.87[ASN][1000 genomes]
rs10850784	0.91[AMR][1000 genomes];0.92[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs10850785	0.90[AMR][1000 genomes];0.95[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs10850786	0.87[ASN][1000 genomes]
rs10850788	0.91[ASN][1000 genomes]
rs10850789	1.00[CEU][hapmap];0.87[CHB][hapmap];0.86[AMR][1000 genomes];0.92[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs10850790	0.94[CHB][hapmap];0.88[ASN][1000 genomes]
rs10850791	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10850792	0.86[AMR][1000 genomes];0.92[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs10850793	0.86[AMR][1000 genomes];0.82[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs10850794	0.93[CEU][hapmap];0.84[CHB][hapmap];0.81[JPT][hapmap];0.86[AMR][1000 genomes];0.92[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs10850795	1.00[CEU][hapmap];0.87[CHB][hapmap];0.95[CHD][hapmap];1.00[GIH][hapmap];0.82[MEX][hapmap];0.97[TSI][hapmap];0.86[AMR][1000 genomes];0.92[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs10850798	1.00[CEU][hapmap];1.00[YRI][hapmap];0.86[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs10850799	0.87[CHB][hapmap];0.86[ASN][1000 genomes]
rs11068360	0.94[ASN][1000 genomes]
rs11068361	0.89[AFR][1000 genomes];0.85[AMR][1000 genomes];0.89[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs11068363	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11068364	0.90[AMR][1000 genomes];0.99[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs11068365	0.84[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs11068366	0.84[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs11068367	0.84[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs11068368	1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs11068369	0.89[ASN][1000 genomes]
rs11068370	0.89[ASN][1000 genomes]
rs11068371	0.89[ASN][1000 genomes]
rs11068372	1.00[AMR][1000 genomes];0.92[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs11068373	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.84[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11068374	1.00[CEU][hapmap];1.00[YRI][hapmap];0.95[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs11068377	0.93[CEU][hapmap];0.83[CHB][hapmap];0.93[AMR][1000 genomes];0.95[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs11068378	1.00[YRI][hapmap];0.91[ASN][1000 genomes]
rs11068382	0.85[AMR][1000 genomes];0.93[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs11068384	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.97[TSI][hapmap];0.95[AMR][1000 genomes];0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs11068385	0.90[AMR][1000 genomes];0.95[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs11068386	0.90[AMR][1000 genomes];0.95[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs11068387	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[AMR][1000 genomes];0.92[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11068389	0.85[AMR][1000 genomes];0.92[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs11068390	0.80[AMR][1000 genomes];0.90[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs11068391	0.86[AMR][1000 genomes];0.90[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs11068392	0.86[AMR][1000 genomes];0.92[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs11068397	0.91[AMR][1000 genomes];0.90[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs11068409	0.84[AMR][1000 genomes];0.85[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs12296271	0.86[AMR][1000 genomes];0.95[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs12302515	1.00[CEU][hapmap];0.86[CHB][hapmap];0.81[JPT][hapmap];0.86[AMR][1000 genomes];0.95[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs12304192	0.86[AMR][1000 genomes];0.95[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs12304378	0.85[AMR][1000 genomes];0.91[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs12304875	0.89[ASN][1000 genomes]
rs12310778	0.89[ASN][1000 genomes]
rs12310794	0.80[AMR][1000 genomes];0.92[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs12311466	0.91[AMR][1000 genomes];0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12322298	0.86[CHB][hapmap];0.89[ASN][1000 genomes]
rs12322527	0.95[AMR][1000 genomes];0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12367404	0.90[AMR][1000 genomes];0.93[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs12368232	1.00[CEU][hapmap];0.87[CHB][hapmap];0.81[JPT][hapmap];0.90[AMR][1000 genomes];0.95[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs12370592	0.86[AMR][1000 genomes];0.91[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs12372085	0.91[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs12422378	0.89[ASN][1000 genomes]
rs12422760	0.86[AMR][1000 genomes];0.92[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs12425763	0.90[AMR][1000 genomes];0.88[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs12426884	0.91[AMR][1000 genomes];0.89[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1344250	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.84[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1472522	0.87[CHB][hapmap];0.89[ASN][1000 genomes]
rs2036311	0.87[CHB][hapmap];0.95[CHD][hapmap];0.87[ASN][1000 genomes]
rs2036312	0.82[CHB][hapmap];0.95[CHD][hapmap];0.88[ASN][1000 genomes]
rs2062518	0.87[ASN][1000 genomes]
rs2062530	0.87[CHB][hapmap];0.89[ASN][1000 genomes]
rs2133678	1.00[CEU][hapmap];1.00[GIH][hapmap];1.00[LWK][hapmap];0.93[MEX][hapmap];0.80[MKK][hapmap];0.97[TSI][hapmap];1.00[YRI][hapmap];0.86[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs2221165	0.86[ASW][hapmap];1.00[CEU][hapmap];0.87[CHB][hapmap];0.95[CHD][hapmap];1.00[GIH][hapmap];0.82[MEX][hapmap];0.97[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.84[AFR][1000 genomes];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2270790	1.00[CEU][hapmap];0.87[CHB][hapmap];0.90[AMR][1000 genomes];0.94[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2270791	1.00[CEU][hapmap];0.87[CHB][hapmap];0.90[AMR][1000 genomes];0.95[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2279765	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.95[AMR][1000 genomes];0.95[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2840100	0.87[CHB][hapmap];0.89[ASN][1000 genomes]
rs3741472	0.90[ASN][1000 genomes]
rs3817015	1.00[CEU][hapmap];0.87[CHB][hapmap];0.95[CHD][hapmap];1.00[GIH][hapmap];0.82[MEX][hapmap];0.97[TSI][hapmap];0.86[AMR][1000 genomes];0.95[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs4238053	0.87[ASN][1000 genomes]
rs4767503	0.88[ASN][1000 genomes]
rs4767504	0.89[ASN][1000 genomes]
rs4767506	0.88[ASN][1000 genomes]
rs4767507	0.89[ASN][1000 genomes]
rs4767511	0.87[CHB][hapmap];0.93[CHD][hapmap];0.87[ASN][1000 genomes]
rs4767518	0.86[ASN][1000 genomes]
rs4992936	1.00[YRI][hapmap];0.89[AFR][1000 genomes];0.87[AMR][1000 genomes];0.89[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs57559958	0.90[AMR][1000 genomes];0.95[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs58346019	0.86[AMR][1000 genomes];0.92[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs59583452	0.86[AMR][1000 genomes];0.92[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs60439829	0.86[AMR][1000 genomes];0.89[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs61572753	0.86[AMR][1000 genomes];0.92[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs61626101	0.85[AMR][1000 genomes];0.92[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs67383912	0.88[ASN][1000 genomes]
rs67983226	0.90[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs7300763	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.97[TSI][hapmap];0.95[AMR][1000 genomes];0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7302633	0.85[ASN][1000 genomes]
rs7306379	0.89[AFR][1000 genomes];0.85[AMR][1000 genomes];0.89[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs7307866	0.80[AMR][1000 genomes]
rs7315039	1.00[CEU][hapmap];0.90[CHB][hapmap];0.90[AMR][1000 genomes];0.95[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs73206024	0.89[AFR][1000 genomes];0.91[AMR][1000 genomes];0.89[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs73206026	0.89[AFR][1000 genomes];0.91[AMR][1000 genomes];0.88[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs73206027	0.89[AFR][1000 genomes];0.91[AMR][1000 genomes];0.88[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs73206028	0.89[AFR][1000 genomes];0.91[AMR][1000 genomes];0.89[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs73206032	0.86[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73206033	1.00[AFR][1000 genomes];0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs73206063	0.88[AMR][1000 genomes];0.89[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs73393645	0.91[AMR][1000 genomes];0.89[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7489177	0.84[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7974581	0.84[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs868757	1.00[CEU][hapmap];0.87[CHB][hapmap];0.95[CHD][hapmap];0.97[GIH][hapmap];0.82[MEX][hapmap];0.97[TSI][hapmap];0.86[AMR][1000 genomes];0.95[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs875036	0.84[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs884282	0.87[CHB][hapmap];0.89[ASN][1000 genomes]
rs884283	0.94[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.89[AFR][1000 genomes];0.93[AMR][1000 genomes];0.89[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs904656	0.86[AMR][1000 genomes];0.95[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	nsv832526	chr12:117530234-117723821	Strong transcription Enhancers Active TSS Weak transcription Bivalent Enhancer Flanking Active TSS Bivalent/Poised TSS Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	14 gene(s)	inside rSNPs	diseases
2	nsv899542	chr12:117549739-117623136	Weak transcription Genic enhancers Enhancers Strong transcription Active TSS ZNF genes & repeats Flanking Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	6 gene(s)	inside rSNPs	n/a

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs3741470	FBXO21	cis	Heart Left Ventricle	GTEx
rs3741470	FBXO21	cis	Muscle Skeletal	GTEx
rs3741470	SDS	cis	cerebellum	SCAN

Chromatin state (count:123 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:117559800-117582200	Weak transcription	Brain Angular Gyrus	brain
2	chr12:117566400-117582200	Weak transcription	H9 Cell Line	embryonic stem cell
3	chr12:117566800-117582200	Weak transcription	Brain Substantia Nigra	brain
4	chr12:117566800-117583400	Weak transcription	Fetal Kidney	kidney
5	chr12:117568400-117582200	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
6	chr12:117568400-117582200	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
7	chr12:117568600-117583200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
8	chr12:117568600-117588400	Weak transcription	ES-I3 Cell Line	embryonic stem cell
9	chr12:117571800-117583400	Weak transcription	Colon Smooth Muscle	Colon
10	chr12:117572000-117582000	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
11	chr12:117572200-117581200	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
12	chr12:117572200-117581600	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
13	chr12:117572200-117582200	Weak transcription	Aorta	Aorta
14	chr12:117572200-117586400	Weak transcription	NHDF-Ad	bronchial
15	chr12:117572200-117586800	Weak transcription	Primary neutrophils fromperipheralblood	blood
16	chr12:117572400-117581400	Weak transcription	Monocytes-CD14+_RO01746	blood
17	chr12:117572400-117583800	Weak transcription	Primary T helper naive cells from peripheral blood	blood
18	chr12:117572400-117584000	Weak transcription	Primary T killer memory cells from peripheral blood	blood
19	chr12:117572400-117596000	Weak transcription	Fetal Brain Male	brain
20	chr12:117572600-117581200	Weak transcription	Primary monocytes fromperipheralblood	blood
21	chr12:117572800-117581200	Weak transcription	Primary hematopoietic stem cells	blood
22	chr12:117572800-117581800	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
23	chr12:117573000-117581800	Weak transcription	Fetal Thymus	thymus
24	chr12:117573000-117588400	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
25	chr12:117573200-117582000	Weak transcription	Primary T helper cells PMA-I stimulated	--
26	chr12:117573400-117581600	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
27	chr12:117574000-117582400	Weak transcription	Primary hematopoietic stem cells short term culture	blood
28	chr12:117574600-117583400	Weak transcription	HMEC	breast
29	chr12:117577400-117582000	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
30	chr12:117577600-117582000	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
31	chr12:117577600-117582000	Weak transcription	HUVEC	blood vessel
32	chr12:117578200-117582000	Weak transcription	NHLF	lung
33	chr12:117578200-117617200	Strong transcription	Fetal Stomach	stomach
34	chr12:117578400-117582200	Weak transcription	Brain Anterior Caudate	brain
35	chr12:117578600-117581200	Weak transcription	HUES6 Cell Line	embryonic stem cell
36	chr12:117578600-117591400	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
37	chr12:117578800-117581200	Weak transcription	Duodenum Smooth Muscle	Duodenum
38	chr12:117578800-117581200	Enhancers	GM12878-XiMat	blood
39	chr12:117578800-117581800	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
40	chr12:117578800-117582200	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
41	chr12:117578800-117582200	Weak transcription	Rectal Mucosa Donor 31	rectum
42	chr12:117578800-117583400	Weak transcription	Brain Hippocampus Middle	brain
43	chr12:117578800-117583400	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
44	chr12:117578800-117588400	Strong transcription	Stomach Smooth Muscle	stomach
45	chr12:117578800-117588600	Strong transcription	Fetal Brain Female	brain
46	chr12:117578800-117588600	Weak transcription	Fetal Heart	heart
47	chr12:117579000-117581200	Weak transcription	Duodenum Mucosa	Duodenum
48	chr12:117579000-117581400	Weak transcription	iPS-18 Cell Line	embryonic stem cell
49	chr12:117579000-117581800	Weak transcription	Cortex derived primary cultured neurospheres	brain
50	chr12:117579000-117582000	Weak transcription	Brain Cingulate Gyrus	brain

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