Variant report

Variant	rs1139093
Chromosome Location	chr3:27520757-27520758
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr3:27493036..27497434-chr3:27518755..27521162,3	MCF-7	breast:
2	chr3:27520223..27522526-chr3:27523841..27526838,2	K562	blood:
3	chr3:27519424..27523145-chr3:27523341..27526018,5	MCF-7	breast:

Variant related genes	Relation type
ENSG00000033867	Chromatin interaction

Extended variants
information (count: 10 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:8)

rs_ID	r²[population]
rs17149152	0.95[AFR][1000 genomes]
rs17149156	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs17149166	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs17149176	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs17149182	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs17149190	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs58497241	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs60142486	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:2 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv876645	chr3:27431898-27674567	Enhancers Strong transcription Weak transcription Genic enhancers ZNF genes & repeats Active TSS Flanking Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	17 gene(s)	inside rSNPs	diseases
2	nsv876646	chr3:27432206-27583317	Flanking Active TSS Weak transcription Strong transcription Active TSS ZNF genes & repeats Enhancers Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	14 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:89 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:27482000-27522000	Weak transcription	Stomach Smooth Muscle	stomach
2	chr3:27482600-27523400	Weak transcription	H1 Cell Line	embryonic stem cell
3	chr3:27483000-27524200	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
4	chr3:27484400-27524600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
5	chr3:27490600-27524200	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
6	chr3:27499400-27523800	Weak transcription	iPS-18 Cell Line	embryonic stem cell
7	chr3:27500800-27524400	Weak transcription	Ovary	ovary
8	chr3:27505600-27521400	Weak transcription	NHEK	skin
9	chr3:27505600-27524200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
10	chr3:27506200-27523400	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
11	chr3:27506600-27520800	Weak transcription	Thymus	Thymus
12	chr3:27506800-27523200	Weak transcription	Fetal Stomach	stomach
13	chr3:27508400-27523800	Weak transcription	Fetal Muscle Trunk	muscle
14	chr3:27508800-27520800	Weak transcription	Fetal Brain Female	brain
15	chr3:27509000-27521400	Weak transcription	Colon Smooth Muscle	Colon
16	chr3:27509200-27520800	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
17	chr3:27509200-27521200	Weak transcription	HepG2	liver
18	chr3:27509400-27521000	Weak transcription	Duodenum Mucosa	Duodenum
19	chr3:27509400-27523200	Weak transcription	iPS-20b Cell Line	embryonic stem cell
20	chr3:27510600-27520800	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
21	chr3:27511000-27523600	Weak transcription	HSMMtube	muscle
22	chr3:27512400-27523600	Weak transcription	HUES48 Cell Line	embryonic stem cell
23	chr3:27512800-27521600	ZNF genes & repeats	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
24	chr3:27513400-27523200	Weak transcription	Small Intestine	intestine
25	chr3:27514000-27522600	Weak transcription	Duodenum Smooth Muscle	Duodenum
26	chr3:27514000-27524600	Weak transcription	Left Ventricle	heart
27	chr3:27514200-27521000	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
28	chr3:27514400-27522600	Weak transcription	HUES64 Cell Line	embryonic stem cell
29	chr3:27514600-27524000	Weak transcription	Fetal Muscle Leg	muscle
30	chr3:27514800-27520800	Weak transcription	Sigmoid Colon	Sigmoid Colon
31	chr3:27514800-27521600	Weak transcription	Breast Myoepithelial Primary Cells	Breast
32	chr3:27515200-27523800	Weak transcription	Fetal Intestine Small	intestine
33	chr3:27515600-27521200	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
34	chr3:27516600-27523400	Weak transcription	Esophagus	oesophagus
35	chr3:27516800-27524200	Weak transcription	Fetal Lung	lung
36	chr3:27517600-27520800	Weak transcription	Muscle Satellite Cultured Cells	--
37	chr3:27517600-27521800	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
38	chr3:27517600-27523600	Weak transcription	Pancreatic Islets	Pancreatic Islet
39	chr3:27518000-27520800	Genic enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
40	chr3:27518000-27521000	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
41	chr3:27518000-27521000	Weak transcription	HUVEC	blood vessel
42	chr3:27518200-27520800	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
43	chr3:27518200-27521200	Weak transcription	NHDF-Ad	bronchial
44	chr3:27518400-27520800	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
45	chr3:27518800-27521000	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
46	chr3:27518800-27521000	Weak transcription	Monocytes-CD14+_RO01746	blood
47	chr3:27518800-27522200	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
48	chr3:27519000-27520800	Strong transcription	HUES6 Cell Line	embryonic stem cell
49	chr3:27519000-27520800	Weak transcription	Primary hematopoietic stem cells	blood
50	chr3:27519000-27522000	Weak transcription	ES-I3 Cell Line	embryonic stem cell

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links