Variant report

Variant	rs11164838
Chromosome Location	chr1:93395378-93395379
allele	C/T
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	FOXM1	chr1:93394773-93395486	GM12878	blood:	n/a	chr1:93395161-93395169
2	SPI1	chr1:93394690-93395561	GM12878	blood:	n/a	chr1:93395181-93395190
3	IKZF1	chr1:93394925-93395503	GM12878	blood:	n/a	n/a
4	CEBPB	chr1:93394902-93395667	GM12878	blood:	n/a	chr1:93395048-93395059
5	MTA3	chr1:93394804-93395554	GM12878	blood:	n/a	n/a
6	MEF2A	chr1:93395014-93395496	GM12878	blood:	n/a	chr1:93395201-93395212 chr1:93395194-93395215 chr1:93395194-93395215 chr1:93395201-93395210
7	EP300	chr1:93394850-93395503	GM12878	blood:	n/a	chr1:93395181-93395195
8	CREB1	chr1:93394948-93395532	GM12878	blood:	n/a	n/a
9	MEF2A	chr1:93394968-93395536	GM12878	blood:	n/a	chr1:93395201-93395212 chr1:93395194-93395215 chr1:93395194-93395215 chr1:93395201-93395210
10	NFIC	chr1:93394889-93395504	GM12878	blood:	n/a	n/a
11	FOS	chr1:93395242-93395428	MCF10A-Er-Src	breast:	n/a	n/a
12	BATF	chr1:93394939-93395476	GM12878	blood:	n/a	chr1:93395296-93395309
13	CUX1	chr1:93394853-93395515	GM12878	blood:	n/a	n/a
14	NFATC1	chr1:93394771-93395620	GM12878	blood:	n/a	n/a
15	RUNX3	chr1:93394946-93395518	GM12878	blood:	n/a	n/a
16	ATF2	chr1:93394878-93395592	GM12878	blood:	n/a	n/a
17	MEF2C	chr1:93394905-93395551	GM12878	blood:	n/a	chr1:93395201-93395212 chr1:93395194-93395215 chr1:93395194-93395215 chr1:93395201-93395210
18	ATF2	chr1:93394846-93395628	GM12878	blood:	n/a	n/a
19	STAT5A	chr1:93395012-93395408	GM12878	blood:	n/a	n/a
20	FOS	chr1:93395195-93395425	MCF10A-Er-Src	breast:	n/a	n/a
21	MAZ	chr1:93395282-93395679	GM12878	blood:	n/a	n/a
22	NFIC	chr1:93394629-93395637	GM12878	blood:	n/a	n/a
23	PML	chr1:93394747-93395536	GM12878	blood:	n/a	n/a
24	CEBPB	chr1:93395198-93395436	IMR90	lung:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr1:93386478..93390849-chr1:93391489..93395394,4	K562	blood:
2	chr1:93386924..93390849-chr1:93391965..93395394,6	K562	blood:
3	chr1:93393287..93395387-chr1:93397331..93399840,2	K562	blood:
4	chr1:93394068..93396228-chr1:93397611..93399427,2	K562	blood:

Variant related genes	Relation type
ENSG00000229052	TF binding region

Extended variants
information (count: 25 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:24)

rs_ID	r²[population]
rs1011663	0.81[JPT][hapmap]
rs10874752	0.88[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[ASN][1000 genomes]
rs11164826	0.81[EUR][1000 genomes]
rs11164827	1.00[CEU][hapmap];0.94[CHB][hapmap];0.94[JPT][hapmap];0.83[EUR][1000 genomes]
rs11164848	0.80[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs11164849	0.81[ASN][1000 genomes]
rs11164850	0.81[JPT][hapmap]
rs11164851	0.81[JPT][hapmap]
rs11164854	0.81[JPT][hapmap]
rs12092304	0.80[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs12747275	0.82[ASN][1000 genomes]
rs3943283	0.81[JPT][hapmap]
rs4847386	0.84[CEU][hapmap];1.00[CHB][hapmap];0.84[CHD][hapmap];0.91[GIH][hapmap];1.00[JPT][hapmap];0.96[MEX][hapmap];0.87[TSI][hapmap];0.80[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs514235	0.88[CHB][hapmap];0.87[GIH][hapmap];0.94[JPT][hapmap];0.87[TSI][hapmap]
rs521428	0.88[CHB][hapmap];0.82[GIH][hapmap];0.94[JPT][hapmap];0.87[MEX][hapmap];0.82[TSI][hapmap]
rs567613	0.88[CHB][hapmap];0.87[JPT][hapmap]
rs641462	0.86[CHB][hapmap];0.93[JPT][hapmap]
rs660870	0.88[CHB][hapmap];0.87[JPT][hapmap];0.83[MEX][hapmap];0.87[TSI][hapmap]
rs6671268	0.88[CHB][hapmap];0.87[GIH][hapmap];0.94[JPT][hapmap];0.87[MEX][hapmap];0.87[TSI][hapmap]
rs6681240	0.81[ASN][1000 genomes]
rs6681345	0.83[ASN][1000 genomes]
rs7524934	0.81[JPT][hapmap]
rs753391	0.83[CEU][hapmap]
rs770883	0.81[JPT][hapmap]

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

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1008602	chr1:93176811-93640808	Enhancers Weak transcription Strong transcription Active TSS Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	51 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs11164838	MTF2	cis	Skin Sun Exposed Lower leg	GTEx
rs11164838	CDC73	trans	cerebellum	SCAN

Chromatin state (count:67 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:93366400-93409200	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
2	chr1:93376000-93395400	Weak transcription	Breast Myoepithelial Primary Cells	Breast
3	chr1:93376000-93400400	Weak transcription	Primary T cells fromperipheralblood	blood
4	chr1:93376800-93395400	Weak transcription	Primary T helper cells fromperipheralblood	blood
5	chr1:93377000-93401400	Weak transcription	Dnd41	blood
6	chr1:93381000-93395400	Weak transcription	Thymus	Thymus
7	chr1:93383000-93395800	Weak transcription	Primary T helper naive cells from peripheral blood	blood
8	chr1:93383400-93396800	Weak transcription	Fetal Stomach	stomach
9	chr1:93384800-93399200	Weak transcription	Fetal Intestine Small	intestine
10	chr1:93387200-93400400	Weak transcription	Left Ventricle	heart
11	chr1:93388200-93398200	Weak transcription	Colon Smooth Muscle	Colon
12	chr1:93388200-93408800	Weak transcription	Pancreas	Pancrea
13	chr1:93389600-93398400	Weak transcription	HMEC	breast
14	chr1:93390200-93399200	Weak transcription	Adipose Nuclei	Adipose
15	chr1:93390400-93402200	Weak transcription	Sigmoid Colon	Sigmoid Colon
16	chr1:93390600-93395400	Weak transcription	A549	lung
17	chr1:93390600-93399200	Weak transcription	Fetal Heart	heart
18	chr1:93391000-93395400	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
19	chr1:93391200-93408800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
20	chr1:93392000-93401200	Enhancers	Primary B cells from peripheral blood	blood
21	chr1:93393000-93395600	Enhancers	Monocytes-CD14+_RO01746	blood
22	chr1:93393000-93395800	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
23	chr1:93393000-93399200	Weak transcription	Fetal Brain Male	brain
24	chr1:93393600-93395400	Enhancers	Primary T cells from cord blood	blood
25	chr1:93394200-93395800	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
26	chr1:93394200-93395800	Enhancers	Placenta	Placenta
27	chr1:93394600-93396200	Enhancers	Brain Angular Gyrus	brain
28	chr1:93394600-93397400	Enhancers	Primary T helper cells PMA-I stimulated	--
29	chr1:93394800-93395400	Enhancers	Stomach Mucosa	stomach
30	chr1:93394800-93395600	Enhancers	Primary T killer naive cells fromperipheralblood	blood
31	chr1:93394800-93395600	Enhancers	Fetal Thymus	thymus
32	chr1:93394800-93395800	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
33	chr1:93394800-93395800	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
34	chr1:93394800-93395800	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
35	chr1:93394800-93395800	Enhancers	Primary monocytes fromperipheralblood	blood
36	chr1:93394800-93395800	Enhancers	Muscle Satellite Cultured Cells	--
37	chr1:93394800-93395800	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
38	chr1:93394800-93395800	Enhancers	Brain Cingulate Gyrus	brain
39	chr1:93394800-93395800	Enhancers	Brain Hippocampus Middle	brain
40	chr1:93394800-93395800	Enhancers	Brain Inferior Temporal Lobe	brain
41	chr1:93394800-93395800	Enhancers	Brain Dorsolateral Prefrontal Cortex	brain
42	chr1:93394800-93395800	Enhancers	Brain Substantia Nigra	brain
43	chr1:93394800-93396000	Enhancers	NHDF-Ad	bronchial
44	chr1:93394800-93396000	Enhancers	Osteobl	bone
45	chr1:93394800-93396200	Flanking Active TSS	GM12878-XiMat	blood
46	chr1:93395000-93395400	Enhancers	ES-I3 Cell Line	embryonic stem cell
47	chr1:93395000-93395600	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
48	chr1:93395000-93395600	Weak transcription	Gastric	stomach
49	chr1:93395000-93395600	Weak transcription	Psoas Muscle	Psoas
50	chr1:93395000-93395600	Enhancers	NH-A	brain

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