Variant report

Variant	rs1197288
Chromosome Location	chr3:133093736-133093737
allele	C/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	EP300	chr3:133093535-133093859	SK-N-SH_RA	brain:	n/a	n/a
2	PBX3	chr3:133093518-133093959	SK-N-SH	brain:	n/a	n/a
3	EP300	chr3:133093575-133093863	SK-N-SH_RA	brain:	n/a	n/a
4	POLR2A	chr3:133093508-133093898	H1-neurons	neurons:	n/a	n/a
5	PBX3	chr3:133093550-133093985	SK-N-SH	brain:	n/a	n/a
6	FOS	chr3:133093720-133093788	MCF10A-Er-Src	breast:	n/a	n/a
7	CTCF	chr3:133093680-133093830	SK-N-SH_RA	brain:	n/a	n/a
8	POLR2A	chr3:133093561-133093950	H1-neurons	neurons:	n/a	n/a
9	RAD21	chr3:133093586-133093919	SK-N-SH_RA	brain:	n/a	chr3:133093727-133093737 chr3:133093725-133093737
10	EBF1	chr3:133093605-133093834	GM12878	blood:	n/a	chr3:133093728-133093739

Variant related genes	Relation type
TMEM108	TF binding region

Extended variants
information (count: 47 )
Associated
traits (count: 0)

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

rs_ID	r²[population]
rs1109858	0.82[JPT][hapmap]
rs1114630	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1197287	1.00[CEU][hapmap];0.91[CHB][hapmap];0.91[JPT][hapmap];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1197293	0.81[CHB][hapmap];0.82[JPT][hapmap];1.00[YRI][hapmap];0.89[AFR][1000 genomes];0.82[AMR][1000 genomes];0.85[ASN][1000 genomes]
rs1197296	0.95[CHB][hapmap];1.00[JPT][hapmap];0.85[AMR][1000 genomes];0.97[ASN][1000 genomes]
rs1197297	0.87[CHB][hapmap];0.95[JPT][hapmap];0.92[ASN][1000 genomes]
rs1197298	0.91[CHB][hapmap];1.00[JPT][hapmap];0.80[AMR][1000 genomes];0.99[ASN][1000 genomes]
rs1197299	0.95[CHB][hapmap];1.00[JPT][hapmap];0.99[ASN][1000 genomes]
rs1197301	0.85[AMR][1000 genomes];0.90[ASN][1000 genomes]
rs1197302	0.91[CHB][hapmap];1.00[JPT][hapmap];0.80[AMR][1000 genomes];0.94[ASN][1000 genomes]
rs1197304	0.95[CHB][hapmap];1.00[JPT][hapmap];0.93[AMR][1000 genomes];0.84[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1197305	0.95[CHB][hapmap];1.00[JPT][hapmap];0.85[AMR][1000 genomes];0.99[ASN][1000 genomes]
rs1197306	0.91[CHB][hapmap];1.00[JPT][hapmap];0.99[ASN][1000 genomes]
rs1197308	0.83[JPT][hapmap]
rs1197309	0.91[CHB][hapmap];1.00[JPT][hapmap];0.94[AMR][1000 genomes];0.84[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1197313	0.95[CHB][hapmap];1.00[JPT][hapmap];0.87[AMR][1000 genomes];0.99[ASN][1000 genomes]
rs1197314	0.86[CHB][hapmap];1.00[JPT][hapmap];0.96[ASN][1000 genomes]
rs1201671	0.91[CHB][hapmap];1.00[JPT][hapmap];0.90[AMR][1000 genomes];0.94[ASN][1000 genomes]
rs1201673	0.87[CHB][hapmap];0.95[JPT][hapmap];0.93[ASN][1000 genomes]
rs12631678	0.87[CHB][hapmap];0.95[JPT][hapmap];0.91[ASN][1000 genomes]
rs13318906	0.87[YRI][hapmap]
rs1619552	0.91[CHB][hapmap];1.00[JPT][hapmap];0.81[AMR][1000 genomes];0.97[ASN][1000 genomes]
rs1619622	0.91[CHB][hapmap];1.00[JPT][hapmap];0.81[AMR][1000 genomes];0.97[ASN][1000 genomes]
rs1708376	0.87[AMR][1000 genomes];0.97[ASN][1000 genomes]
rs1708377	0.91[CHB][hapmap];1.00[JPT][hapmap];0.89[AMR][1000 genomes];0.94[ASN][1000 genomes]
rs1708384	0.83[AMR][1000 genomes];0.99[ASN][1000 genomes]
rs1708385	0.83[CHB][hapmap];0.95[JPT][hapmap];0.92[ASN][1000 genomes]
rs1795101	0.83[JPT][hapmap]
rs1795104	0.92[ASN][1000 genomes]
rs1795107	0.91[CHB][hapmap];1.00[JPT][hapmap];0.82[AMR][1000 genomes];0.99[ASN][1000 genomes]
rs2089987	0.95[JPT][hapmap];0.90[ASN][1000 genomes]
rs2670179	0.91[CHB][hapmap];1.00[JPT][hapmap];0.87[YRI][hapmap];0.93[AMR][1000 genomes];0.94[ASN][1000 genomes]
rs2699880	0.95[JPT][hapmap];0.88[ASN][1000 genomes]
rs2699882	0.91[CHB][hapmap];1.00[JPT][hapmap];0.90[AMR][1000 genomes];0.94[ASN][1000 genomes]
rs3732572	0.83[CHB][hapmap];0.95[JPT][hapmap];0.91[ASN][1000 genomes]
rs4854583	0.90[ASN][1000 genomes]
rs4854719	0.95[CHB][hapmap];0.95[JPT][hapmap];0.87[AMR][1000 genomes];0.99[ASN][1000 genomes]
rs4854720	0.95[JPT][hapmap];0.90[ASN][1000 genomes]
rs56181416	0.87[ASN][1000 genomes]
rs656721	0.95[JPT][hapmap]
rs6780144	0.92[ASN][1000 genomes]
rs6802663	0.83[CHB][hapmap];0.95[JPT][hapmap];0.83[AMR][1000 genomes];0.88[ASN][1000 genomes]
rs938231	0.89[AFR][1000 genomes];0.84[AMR][1000 genomes];0.87[ASN][1000 genomes]
rs9850193	0.95[JPT][hapmap];0.90[ASN][1000 genomes]
rs9853752	0.96[ASN][1000 genomes]
rs9853757	0.96[ASN][1000 genomes]

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	nsv877503	chr3:133035774-133104631	Bivalent/Poised TSS Weak transcription Enhancers Bivalent Enhancer Flanking Active TSS Strong transcription ZNF genes & repeats Genic enhancers Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:33 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:133080800-133098600	Weak transcription	Breast Myoepithelial Primary Cells	Breast
2	chr3:133083200-133099200	Weak transcription	Lung	lung
3	chr3:133088000-133093800	Weak transcription	HSMMtube	muscle
4	chr3:133089200-133094800	Weak transcription	Fetal Lung	lung
5	chr3:133089600-133093800	Weak transcription	Brain Substantia Nigra	brain
6	chr3:133089800-133093800	Weak transcription	Brain Inferior Temporal Lobe	brain
7	chr3:133090200-133093800	Weak transcription	Brain Hippocampus Middle	brain
8	chr3:133090200-133093800	Weak transcription	Fetal Brain Female	brain
9	chr3:133090800-133093800	Weak transcription	Brain Cingulate Gyrus	brain
10	chr3:133091800-133093800	Weak transcription	iPS-15b Cell Line	embryonic stem cell
11	chr3:133091800-133094000	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
12	chr3:133092400-133096400	Enhancers	Cortex derived primary cultured neurospheres	brain
13	chr3:133092600-133093800	Enhancers	Brain Germinal Matrix	brain
14	chr3:133092600-133094400	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
15	chr3:133092600-133094400	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
16	chr3:133092600-133096400	Enhancers	Fetal Brain Male	brain
17	chr3:133092800-133095000	Enhancers	HUES64 Cell Line	embryonic stem cell
18	chr3:133093000-133093800	Enhancers	iPS-20b Cell Line	embryonic stem cell
19	chr3:133093000-133094800	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
20	chr3:133093000-133094800	Enhancers	iPS-18 Cell Line	embryonic stem cell
21	chr3:133093000-133095200	Enhancers	HUES48 Cell Line	embryonic stem cell
22	chr3:133093000-133102400	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
23	chr3:133093400-133093800	Weak transcription	HSMM	muscle
24	chr3:133093400-133094400	Flanking Active TSS	Ganglion Eminence derived primary cultured neurospheres	brain
25	chr3:133093600-133093800	Enhancers	Foreskin Melanocyte Primary Cells skin01	Skin
26	chr3:133093600-133094000	Enhancers	Brain Dorsolateral Prefrontal Cortex	brain
27	chr3:133093600-133094200	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
28	chr3:133093600-133094200	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
29	chr3:133093600-133094400	Enhancers	Brain Angular Gyrus	brain
30	chr3:133093600-133094400	Enhancers	Brain Anterior Caudate	brain
31	chr3:133093600-133094800	Enhancers	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
32	chr3:133093600-133094800	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
33	chr3:133093600-133095000	Enhancers	HUES6 Cell Line	embryonic stem cell

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