Variant report

Variant	rs11607673
Chromosome Location	chr11:58953420-58953421
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr11:58938579..58939084-chr11:58953392..58953945,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000110042	Chromatin interaction

Extended variants
information (count: 26 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:21)

rs_ID	r²[population]
rs11600401	0.83[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs11606140	0.84[AMR][1000 genomes];0.88[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs11607278	0.81[AFR][1000 genomes];0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs12419479	0.85[EUR][1000 genomes]
rs2000478	0.84[AMR][1000 genomes];0.89[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2211912	0.90[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs34697089	0.85[AMR][1000 genomes];0.87[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs3944255	0.83[EUR][1000 genomes]
rs4369428	0.85[AMR][1000 genomes];0.87[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs5029315	0.90[AMR][1000 genomes];0.93[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs610123	0.81[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs61903328	0.85[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs6591509	0.91[AMR][1000 genomes];0.93[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7113633	0.85[AMR][1000 genomes];0.87[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs7113936	0.85[AMR][1000 genomes];0.88[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs7131079	0.84[EUR][1000 genomes]
rs7928981	0.84[AMR][1000 genomes];0.87[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs7942710	0.84[AMR][1000 genomes];0.87[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs7944135	0.87[EUR][1000 genomes]
rs7944319	0.91[AMR][1000 genomes];0.93[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7952377	0.85[AMR][1000 genomes];0.86[EUR][1000 genomes];0.85[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
rs11607673	DTX4	cis	Esophagus Muscularis	GTEx

Chromatin state (count:86 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr11:58941600-58964000	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
2	chr11:58943400-58954800	Weak transcription	Hela-S3	cervix
3	chr11:58943600-58975400	Weak transcription	NHEK	skin
4	chr11:58947600-58955000	Weak transcription	Primary monocytes fromperipheralblood	blood
5	chr11:58948600-58953600	Strong transcription	Primary B cells from peripheral blood	blood
6	chr11:58949400-58973400	Weak transcription	Right Ventricle	heart
7	chr11:58950000-58978400	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
8	chr11:58950200-58958600	Weak transcription	Aorta	Aorta
9	chr11:58950400-58953800	Enhancers	Brain Hippocampus Middle	brain
10	chr11:58950400-58957400	Weak transcription	iPS-15b Cell Line	embryonic stem cell
11	chr11:58950400-58972200	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
12	chr11:58950600-58953600	Weak transcription	ES-I3 Cell Line	embryonic stem cell
13	chr11:58950800-58955800	Enhancers	Brain Cingulate Gyrus	brain
14	chr11:58950800-58957400	Weak transcription	H9 Cell Line	embryonic stem cell
15	chr11:58950800-58957800	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
16	chr11:58951000-58955400	Enhancers	Brain Angular Gyrus	brain
17	chr11:58951000-58955800	Genic enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
18	chr11:58951000-58956000	Enhancers	Brain Dorsolateral Prefrontal Cortex	brain
19	chr11:58951000-58956200	Weak transcription	Primary neutrophils fromperipheralblood	blood
20	chr11:58951000-58956600	Enhancers	Stomach Smooth Muscle	stomach
21	chr11:58951200-58953600	Enhancers	Ovary	ovary
22	chr11:58951400-58954000	Enhancers	Brain Inferior Temporal Lobe	brain
23	chr11:58951400-58954400	Enhancers	Brain Anterior Caudate	brain
24	chr11:58951400-58957200	Enhancers	Placenta	Placenta
25	chr11:58951600-58953600	Enhancers	Cortex derived primary cultured neurospheres	brain
26	chr11:58951600-58954800	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
27	chr11:58951600-58954800	Enhancers	Colon Smooth Muscle	Colon
28	chr11:58951600-58957800	Enhancers	Fetal Adrenal Gland	Adrenal Gland
29	chr11:58951800-58953800	Enhancers	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
30	chr11:58951800-58953800	Weak transcription	Gastric	stomach
31	chr11:58951800-58955000	Enhancers	Sigmoid Colon	Sigmoid Colon
32	chr11:58951800-58955000	Weak transcription	Monocytes-CD14+_RO01746	blood
33	chr11:58951800-58955200	Enhancers	Placenta Amnion	Placenta Amnion
34	chr11:58951800-58955400	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
35	chr11:58951800-58957200	Enhancers	Adipose Nuclei	Adipose
36	chr11:58952000-58954000	Weak transcription	Small Intestine	intestine
37	chr11:58952000-58954000	Weak transcription	NHLF	lung
38	chr11:58952000-58954800	Genic enhancers	Fetal Lung	lung
39	chr11:58952200-58953800	Enhancers	iPS-18 Cell Line	embryonic stem cell
40	chr11:58952200-58953800	Enhancers	iPS-20b Cell Line	embryonic stem cell
41	chr11:58952200-58954400	Flanking Active TSS	Duodenum Mucosa	Duodenum
42	chr11:58952200-58954800	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
43	chr11:58952200-58954800	Flanking Active TSS	Rectal Mucosa Donor 29	rectum
44	chr11:58952200-58955600	Enhancers	Fetal Muscle Leg	muscle
45	chr11:58952400-58953600	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
46	chr11:58952400-58953800	Enhancers	Fetal Brain Male	brain
47	chr11:58952400-58953800	Flanking Active TSS	Rectal Mucosa Donor 31	rectum
48	chr11:58952400-58955000	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
49	chr11:58952400-58960200	Genic enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
50	chr11:58952600-58953600	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived

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