Variant report

Variant	rs9568404
Chromosome Location	chr13:50974915-50974916
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	NFIC	chr13:50974386-50974930	SK-N-SH	brain:	n/a	chr13:50974660-50974676 chr13:50974660-50974677
2	GATA3	chr13:50974214-50975074	SK-N-SH	brain:	n/a	n/a
3	PBX3	chr13:50974218-50975066	SK-N-SH	brain:	n/a	n/a
4	EP300	chr13:50974289-50974984	SK-N-SH	brain:	n/a	n/a
5	TCF12	chr13:50974169-50975947	SK-N-SH	brain:	n/a	n/a
6	GATA3	chr13:50974258-50975033	SK-N-SH	brain:	n/a	n/a
7	NFIC	chr13:50974151-50974961	SK-N-SH	brain:	n/a	chr13:50974660-50974676 chr13:50974660-50974677
8	PBX3	chr13:50974276-50974996	SK-N-SH	brain:	n/a	n/a

Variant related genes	Relation type
DLEU1	TF binding region

Extended variants
information (count: 83 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:78)

rs_ID	r²[population]
rs12428189	0.97[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs12431131	0.97[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs1327644	1.00[CEU][hapmap];0.97[AMR][1000 genomes];0.93[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs1359860	0.97[AMR][1000 genomes];0.93[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs149846	0.80[ASN][1000 genomes]
rs17074346	0.81[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs17074358	0.90[AMR][1000 genomes];0.91[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs1924372	0.89[AFR][1000 genomes];0.90[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs1924373	0.87[AFR][1000 genomes];0.86[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs201807	0.80[ASN][1000 genomes]
rs3116625	0.85[AFR][1000 genomes];0.81[ASN][1000 genomes]
rs35824953	0.85[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs471315	0.89[YRI][hapmap];0.82[AFR][1000 genomes];0.94[ASN][1000 genomes]
rs56023535	0.87[AMR][1000 genomes];0.95[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs56075206	0.93[AMR][1000 genomes];0.95[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs58633776	0.83[AMR][1000 genomes];0.93[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs60379059	0.93[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs61962133	0.90[AMR][1000 genomes];0.95[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs61962135	0.90[AMR][1000 genomes];0.90[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs61964386	0.93[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs719103	1.00[CEU][hapmap];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs7327154	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7334326	0.81[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs7983762	0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs7996632	0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs8000329	0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs8000875	0.89[AFR][1000 genomes];0.86[AMR][1000 genomes];0.90[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs8000921	0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs9316495	0.81[CEU][hapmap];0.80[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs9562962	0.89[AFR][1000 genomes];0.86[AMR][1000 genomes];0.90[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs9562963	0.84[ASN][1000 genomes]
rs9562964	0.96[AFR][1000 genomes];0.97[AMR][1000 genomes];0.94[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs9562965	0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9562966	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs9562967	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs9562968	0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs9562970	0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs9562972	0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs9562973	0.87[AMR][1000 genomes];0.95[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs9562974	0.97[AMR][1000 genomes];0.93[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs9562975	0.81[EUR][1000 genomes]
rs9562976	0.81[EUR][1000 genomes]
rs9562980	0.81[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs9562981	0.90[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs9562982	0.90[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs9568397	0.89[AFR][1000 genomes];0.86[AMR][1000 genomes];0.90[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs9568398	0.89[AFR][1000 genomes];0.86[AMR][1000 genomes];0.90[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs9568399	0.83[ASN][1000 genomes]
rs9568400	0.93[AFR][1000 genomes];0.86[AMR][1000 genomes];0.89[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs9568401	0.89[CEU][hapmap];0.89[YRI][hapmap];0.93[AFR][1000 genomes];0.86[AMR][1000 genomes];0.90[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs9568402	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs9568403	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs9568405	0.81[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs9568406	1.00[CEU][hapmap];0.89[YRI][hapmap];0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs9568407	0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs9568408	0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs9568409	0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs9568410	0.90[AMR][1000 genomes];0.95[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs9568412	0.97[AMR][1000 genomes];0.93[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs9568413	0.90[AMR][1000 genomes];0.93[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs9568414	0.90[AMR][1000 genomes];0.93[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs9568415	0.90[AMR][1000 genomes];0.93[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs9568416	0.84[ASN][1000 genomes]
rs9568417	0.81[EUR][1000 genomes]
rs9568419	0.93[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs9568422	0.90[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs9568423	0.90[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs9568424	0.90[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs9568425	0.93[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs9568427	0.87[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs9568428	0.81[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs9568429	0.90[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs9568430	0.84[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs9568431	0.84[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs9568433	0.83[CEU][hapmap]
rs9634832	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.94[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs9634833	0.80[AMR][1000 genomes]
rs9634834	0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];0.92[ASN][1000 genomes]

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	nsv1035151	chr13:50513535-51167850	Weak transcription Flanking Active TSS Strong transcription Enhancers Active TSS Transcr. at gene 5' and 3' Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA	1254 gene(s)	inside rSNPs	diseases
2	esv2753964	chr13:50545399-51421199	Flanking Active TSS Enhancers Bivalent Enhancer Weak transcription Active TSS Genic enhancers Strong transcription Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	1256 gene(s)	inside rSNPs	diseases
3	esv2753492	chr13:50550081-51461720	Enhancers Flanking Active TSS ZNF genes & repeats Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Weak transcription Strong transcription Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA	1256 gene(s)	inside rSNPs	diseases
4	esv2752608	chr13:50550099-51054499	Weak transcription Enhancers Strong transcription Active TSS Genic enhancers Flanking Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA	1249 gene(s)	inside rSNPs	diseases
5	nsv832609	chr13:50946577-51065968	Enhancers Flanking Active TSS Weak transcription Active TSS ZNF genes & repeats Strong transcription Bivalent Enhancer Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:62 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr13:50965200-50977000	Weak transcription	Esophagus	oesophagus
2	chr13:50966600-50979800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
3	chr13:50968200-50975600	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
4	chr13:50968200-50985400	Weak transcription	ES-I3 Cell Line	embryonic stem cell
5	chr13:50968200-50986600	Weak transcription	HUES48 Cell Line	embryonic stem cell
6	chr13:50970600-50975400	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
7	chr13:50972000-50977200	Weak transcription	Gastric	stomach
8	chr13:50972200-50985400	Weak transcription	HUES6 Cell Line	embryonic stem cell
9	chr13:50973200-50976200	Enhancers	Fetal Muscle Leg	muscle
10	chr13:50973200-50979200	Enhancers	Cortex derived primary cultured neurospheres	brain
11	chr13:50974000-50975800	Enhancers	Colon Smooth Muscle	Colon
12	chr13:50974000-50975800	Enhancers	Fetal Adrenal Gland	Adrenal Gland
13	chr13:50974000-50975800	Enhancers	Rectal Smooth Muscle	rectum
14	chr13:50974200-50975200	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
15	chr13:50974200-50975200	Enhancers	HSMMtube	muscle
16	chr13:50974200-50975400	Enhancers	Right Ventricle	heart
17	chr13:50974200-50975400	Enhancers	NHDF-Ad	bronchial
18	chr13:50974200-50975600	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
19	chr13:50974200-50975600	Enhancers	Duodenum Smooth Muscle	Duodenum
20	chr13:50974200-50975600	Enhancers	Fetal Lung	lung
21	chr13:50974200-50975600	Enhancers	Osteobl	bone
22	chr13:50974200-50975800	Enhancers	Fetal Brain Male	brain
23	chr13:50974200-50975800	Enhancers	Fetal Stomach	stomach
24	chr13:50974200-50976000	Flanking Active TSS	Brain Hippocampus Middle	brain
25	chr13:50974200-50976400	Enhancers	NHLF	lung
26	chr13:50974200-50976600	Enhancers	Foreskin Melanocyte Primary Cells skin01	Skin
27	chr13:50974200-50976800	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
28	chr13:50974200-50976800	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
29	chr13:50974200-50976800	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
30	chr13:50974200-50976800	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
31	chr13:50974200-50976800	Enhancers	NH-A	brain
32	chr13:50974200-50977000	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
33	chr13:50974200-50977000	Enhancers	Brain Germinal Matrix	brain
34	chr13:50974400-50975600	Enhancers	HSMM	muscle
35	chr13:50974400-50976800	Enhancers	Muscle Satellite Cultured Cells	--
36	chr13:50974400-50977400	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
37	chr13:50974400-50977400	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
38	chr13:50974400-50977800	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
39	chr13:50974600-50975400	Enhancers	Lung	lung
40	chr13:50974600-50975600	Enhancers	Fetal Thymus	thymus
41	chr13:50974600-50975800	Enhancers	Left Ventricle	heart
42	chr13:50974600-50975800	Enhancers	Right Atrium	heart
43	chr13:50974600-50975800	Strong transcription	HepG2	liver
44	chr13:50974600-50976000	Enhancers	Fetal Brain Female	brain
45	chr13:50974600-50976200	Enhancers	Breast Myoepithelial Primary Cells	Breast
46	chr13:50974600-50976200	Enhancers	Foreskin Fibroblast Primary Cells skin02	Skin
47	chr13:50974600-50976200	Enhancers	NHEK	skin
48	chr13:50974600-50976600	Enhancers	Brain Dorsolateral Prefrontal Cortex	brain
49	chr13:50974600-50977600	Enhancers	Hela-S3	cervix
50	chr13:50974800-50975000	Enhancers	Brain Anterior Caudate	brain

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