Variant report

Variant	rs5029315
Chromosome Location	chr11:58977768-58977769
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 28 )
Associated
traits (count: 1 )

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

rs_ID	r²[population]
rs11600401	0.84[AMR][1000 genomes];0.92[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs11606140	0.85[AMR][1000 genomes];0.93[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs11607278	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[YRI][hapmap];0.94[AFR][1000 genomes];0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11607673	0.90[AMR][1000 genomes];0.93[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs12419479	0.85[CEU][hapmap];0.89[CHB][hapmap];0.95[JPT][hapmap];0.89[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs2000478	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]
rs2211912	1.00[CEU][hapmap];0.90[JPT][hapmap];0.85[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs34697089	0.86[AMR][1000 genomes];0.92[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs3944255	0.81[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs4369428	0.86[AMR][1000 genomes];0.92[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs4939269	0.92[CEU][hapmap];0.82[EUR][1000 genomes]
rs610123	0.96[CEU][hapmap];0.95[JPT][hapmap];0.83[YRI][hapmap];0.80[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs61903328	0.90[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs656163	0.92[CEU][hapmap];0.84[JPT][hapmap]
rs6591509	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[YRI][hapmap];0.87[AFR][1000 genomes];0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7113633	0.86[AMR][1000 genomes];0.92[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs7113936	0.86[AMR][1000 genomes];0.93[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7131079	0.89[CEU][hapmap];0.89[CHB][hapmap];0.95[JPT][hapmap];0.88[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs7928981	0.85[AMR][1000 genomes];0.92[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7942710	0.85[AMR][1000 genomes];0.92[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs7944135	0.96[CEU][hapmap];0.95[JPT][hapmap];0.92[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs7944319	0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7952377	0.86[AMR][1000 genomes];0.91[EUR][1000 genomes];0.90[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	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

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs5029315	DTX4	cis	Esophagus Muscularis	GTEx

Chromatin state (count:61 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr11:58950000-58978400	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
2	chr11:58965800-58978000	Weak transcription	Left Ventricle	heart
3	chr11:58973400-58978200	Weak transcription	Esophagus	oesophagus
4	chr11:58973400-58983200	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
5	chr11:58973600-58982000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
6	chr11:58973800-58979600	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
7	chr11:58973800-58984000	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
8	chr11:58974600-58978600	Weak transcription	Pancreas	Pancrea
9	chr11:58974600-58978800	Weak transcription	Brain Inferior Temporal Lobe	brain
10	chr11:58974800-58977800	Weak transcription	Colonic Mucosa	Colon
11	chr11:58974800-58980200	Weak transcription	Brain Germinal Matrix	brain
12	chr11:58975000-58980400	Weak transcription	Fetal Brain Female	brain
13	chr11:58975200-58977800	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
14	chr11:58975200-58980000	Weak transcription	Lung	lung
15	chr11:58975400-58980000	Active TSS	Duodenum Mucosa	Duodenum
16	chr11:58975400-58986600	Weak transcription	Gastric	stomach
17	chr11:58975600-58978200	Enhancers	Fetal Brain Male	brain
18	chr11:58975600-58978200	Weak transcription	Small Intestine	intestine
19	chr11:58975600-58978800	Weak transcription	Brain Substantia Nigra	brain
20	chr11:58975600-58980200	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
21	chr11:58975800-58977800	Weak transcription	Fetal Intestine Small	intestine
22	chr11:58975800-58978000	Weak transcription	Brain Hippocampus Middle	brain
23	chr11:58975800-58978400	Weak transcription	Primary T helper cells fromperipheralblood	blood
24	chr11:58975800-58978400	Weak transcription	Brain Anterior Caudate	brain
25	chr11:58975800-58980000	Weak transcription	Primary hematopoietic stem cells short term culture	blood
26	chr11:58975800-58980400	Active TSS	Primary Natural Killer cells fromperipheralblood	blood
27	chr11:58975800-58980400	Active TSS	Fetal Intestine Large	intestine
28	chr11:58975800-58980800	Active TSS	Adipose Nuclei	Adipose
29	chr11:58975800-58981800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
30	chr11:58976000-58977800	Active TSS	Primary mononuclear cells fromperipheralblood	Blood
31	chr11:58976000-58978200	Weak transcription	Colon Smooth Muscle	Colon
32	chr11:58976000-58980400	Active TSS	Placenta	Placenta
33	chr11:58976000-58989400	Weak transcription	Stomach Mucosa	stomach
34	chr11:58976200-58977800	Weak transcription	Spleen	Spleen
35	chr11:58976200-58980400	Active TSS	Duodenum Smooth Muscle	Duodenum
36	chr11:58976200-58980400	Active TSS	Fetal Muscle Leg	muscle
37	chr11:58976400-58978200	Active TSS	Primary B cells from peripheral blood	blood
38	chr11:58976400-58979200	Flanking Active TSS	Primary neutrophils fromperipheralblood	blood
39	chr11:58976400-58979200	Weak transcription	Primary T helper cells PMA-I stimulated	--
40	chr11:58976400-58979200	Active TSS	Right Atrium	heart
41	chr11:58976400-58981000	Active TSS	Rectal Mucosa Donor 29	rectum
42	chr11:58976600-58980400	Active TSS	Liver	Liver
43	chr11:58976800-58978200	Active TSS	Primary hematopoietic stem cells	blood
44	chr11:58976800-58978200	Weak transcription	Fetal Stomach	stomach
45	chr11:58977000-58978600	Active TSS	Fetal Thymus	thymus
46	chr11:58977000-58978800	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
47	chr11:58977000-58980400	Active TSS	Rectal Mucosa Donor 31	rectum
48	chr11:58977000-58981000	Flanking Active TSS	Primary B cells from cord blood	blood
49	chr11:58977200-58977800	Active TSS	Stomach Smooth Muscle	stomach
50	chr11:58977200-58978400	Weak transcription	Sigmoid Colon	Sigmoid Colon

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