Variant report

Variant	rs2000478
Chromosome Location	chr11:58986670-58986671
allele	G/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	IKZF1	chr11:58986477-58986790	GM12878	blood:	n/a	n/a
2	NFIC	chr11:58986335-58987004	GM12878	blood:	n/a	n/a
3	RELA	chr11:58986372-58986863	GM12891	blood:	n/a	n/a
4	BATF	chr11:58986379-58986914	GM12878	blood:	n/a	n/a
5	NFIC	chr11:58986218-58986809	GM12878	blood:	n/a	n/a

Variant related genes	Relation type
RN7SL42P	TF binding region

Extended variants
information (count: 29 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:23)

rs_ID	r²[population]
rs11600401	0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs11606140	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11607278	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[YRI][hapmap];0.87[AMR][1000 genomes];0.92[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs11607673	0.84[AMR][1000 genomes];0.89[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs12419479	0.88[CEU][hapmap];0.89[CHB][hapmap];0.95[JPT][hapmap];0.92[AMR][1000 genomes];0.95[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2211912	0.96[CEU][hapmap];0.90[JPT][hapmap];0.84[EUR][1000 genomes]
rs34697089	0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs3944255	0.93[AMR][1000 genomes];0.93[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs4369428	0.82[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4939269	0.89[CEU][hapmap];0.80[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs5029315	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[YRI][hapmap];0.85[AMR][1000 genomes];0.94[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs610123	1.00[CEU][hapmap];0.90[JPT][hapmap]
rs61903328	0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs656163	0.89[CEU][hapmap];0.85[JPT][hapmap]
rs6591509	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[YRI][hapmap];0.87[AFR][1000 genomes];0.90[AMR][1000 genomes];0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7113633	0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7113936	0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7131079	0.92[CEU][hapmap];0.89[CHB][hapmap];0.95[JPT][hapmap];0.88[AMR][1000 genomes];0.94[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs7928981	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7942710	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7944135	1.00[CEU][hapmap];0.95[JPT][hapmap];0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs7944319	0.90[AMR][1000 genomes];0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7952377	0.80[AFR][1000 genomes];0.99[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:6 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1050013	chr11:58394598-59221090	Active TSS Weak transcription Flanking Active TSS Enhancers Bivalent Enhancer ZNF genes & repeats Genic enhancers Strong transcription Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	67 gene(s)	inside rSNPs	diseases
2	nsv948365	chr11:58515163-59156405	Weak transcription Flanking Bivalent TSS/Enh Active TSS Flanking Active TSS Strong transcription Genic enhancers Enhancers Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	59 gene(s)	inside rSNPs	diseases
3	esv2758272	chr11:58700092-59008673	Bivalent/Poised TSS Active TSS Weak transcription Enhancers Strong transcription Flanking Active TSS ZNF genes & repeats Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	44 gene(s)	inside rSNPs	diseases
4	esv2759830	chr11:58700092-59008673	Active TSS Weak transcription Enhancers Flanking Active TSS Bivalent/Poised TSS ZNF genes & repeats Strong transcription Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	44 gene(s)	inside rSNPs	diseases
5	esv1821250	chr11:58925860-59059179	Enhancers Flanking Active TSS Weak transcription Genic enhancers Strong transcription Flanking Bivalent TSS/Enh Active TSS Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	18 gene(s)	inside rSNPs	diseases
6	esv3351601	chr11:58979308-59052763	Enhancers Bivalent/Poised TSS Weak transcription Active TSS Flanking Active TSS Bivalent Enhancer ZNF genes & repeats Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs2000478	DTX4	cis	Esophagus Muscularis	GTEx

Chromatin state (count:36 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr11:58976000-58989400	Weak transcription	Stomach Mucosa	stomach
2	chr11:58979200-58989600	Weak transcription	Sigmoid Colon	Sigmoid Colon
3	chr11:58980400-58991200	Weak transcription	Fetal Muscle Leg	muscle
4	chr11:58981000-58991600	Weak transcription	Spleen	Spleen
5	chr11:58984200-58988200	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
6	chr11:58984400-58990600	Enhancers	Primary monocytes fromperipheralblood	blood
7	chr11:58984600-58988400	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
8	chr11:58984600-58990600	Weak transcription	Placenta	Placenta
9	chr11:58984600-58990600	Weak transcription	Fetal Thymus	thymus
10	chr11:58984800-58987200	Weak transcription	Muscle Satellite Cultured Cells	--
11	chr11:58984800-58988200	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
12	chr11:58984800-58988200	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
13	chr11:58984800-58988200	Weak transcription	Duodenum Smooth Muscle	Duodenum
14	chr11:58984800-58988600	Weak transcription	Hela-S3	cervix
15	chr11:58985000-58987200	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
16	chr11:58985000-58988600	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
17	chr11:58985000-58988600	Weak transcription	Colon Smooth Muscle	Colon
18	chr11:58985000-58989600	Weak transcription	Duodenum Mucosa	Duodenum
19	chr11:58985000-58990600	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
20	chr11:58985000-58991600	Weak transcription	Rectal Mucosa Donor 29	rectum
21	chr11:58985000-58993200	Enhancers	Primary B cells from peripheral blood	blood
22	chr11:58985200-58988200	Weak transcription	Primary hematopoietic stem cells	blood
23	chr11:58985200-58989600	Enhancers	Primary neutrophils fromperipheralblood	blood
24	chr11:58985200-58990000	Enhancers	Primary B cells from cord blood	blood
25	chr11:58985600-58986800	Flanking Active TSS	GM12878-XiMat	blood
26	chr11:58985600-58986800	Flanking Active TSS	Monocytes-CD14+_RO01746	blood
27	chr11:58985600-58987200	Weak transcription	NHLF	lung
28	chr11:58985800-58987200	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
29	chr11:58985800-58987800	Weak transcription	Adipose Nuclei	Adipose
30	chr11:58986000-58987000	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
31	chr11:58986000-58987400	Weak transcription	NHDF-Ad	bronchial
32	chr11:58986000-58988200	Weak transcription	Fetal Stomach	stomach
33	chr11:58986000-58989600	Weak transcription	Primary hematopoietic stem cells short term culture	blood
34	chr11:58986000-58991200	Weak transcription	Rectal Smooth Muscle	rectum
35	chr11:58986400-58988800	Weak transcription	Rectal Mucosa Donor 31	rectum
36	chr11:58986600-58986800	Enhancers	Gastric	stomach

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