Variant report

Variant	rs4405766
Chromosome Location	chr2:113389788-113389789
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr2:113383343..113387238-chr2:113388797..113391596,3	MCF-7	breast:
2	chr2:113389446..113391358-chr2:113401501..113403528,2	MCF-7	breast:
3	chr2:113389533..113392236-chr2:113492953..113495168,2	K562	blood:
4	chr2:113385104..113391547-chr2:113463938..113470179,6	K562	blood:
5	chr2:113388586..113390776-chr2:113395916..113398828,2	MCF-7	breast:
6	chr2:113388214..113390218-chr2:113391409..113393753,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000144136	Chromatin interaction
ENSG00000237753	Chromatin interaction

Extended variants
information (count: 24 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:20)

rs_ID	r²[population]
rs12987250	0.85[EUR][1000 genomes]
rs13025131	0.84[EUR][1000 genomes]
rs13030884	0.96[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs17586834	0.84[EUR][1000 genomes]
rs17587043	0.85[EUR][1000 genomes]
rs17587297	0.80[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs17647292	0.83[EUR][1000 genomes]
rs34015418	0.85[EUR][1000 genomes]
rs35670704	0.86[EUR][1000 genomes]
rs35995321	0.80[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs36079920	0.80[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs36082214	0.86[EUR][1000 genomes]
rs58770636	0.80[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs6716749	0.98[EUR][1000 genomes]
rs6716762	0.98[EUR][1000 genomes]
rs6737981	0.84[EUR][1000 genomes]
rs71414685	0.84[EUR][1000 genomes]
rs7566777	0.84[EUR][1000 genomes]
rs7607685	0.83[EUR][1000 genomes]
rs7607817	0.84[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv458997	chr2:113313794-113431092	Flanking Active TSS Strong transcription Weak transcription Genic enhancers Enhancers Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	73 gene(s)	inside rSNPs	diseases
2	nsv582708	chr2:113313794-113431092	Strong transcription Weak transcription Enhancers Flanking Active TSS Genic enhancers Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	73 gene(s)	inside rSNPs	diseases
3	nsv470480	chr2:113373950-113429752	Flanking Active TSS Strong transcription Enhancers Weak transcription Genic enhancers Bivalent Enhancer Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	51 gene(s)	inside rSNPs	diseases
4	nsv428724	chr2:113376894-113555421	Genic enhancers Strong transcription Weak transcription Enhancers Transcr. at gene 5' and 3' Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	56 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs4405766	AC079922.3	cis	Muscle Skeletal	GTEx
rs4405766	AC079922.3	cis	Artery Aorta	GTEx
rs4405766	AC079922.3	cis	Heart Left Ventricle	GTEx

Chromatin state (count:82 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:113384200-113392400	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
2	chr2:113384600-113389800	Enhancers	Primary monocytes fromperipheralblood	blood
3	chr2:113384600-113390000	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
4	chr2:113385000-113389800	Enhancers	NHDF-Ad	bronchial
5	chr2:113385000-113396000	Weak transcription	Colonic Mucosa	Colon
6	chr2:113385000-113402600	Weak transcription	Esophagus	oesophagus
7	chr2:113385200-113390600	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
8	chr2:113385800-113401800	Weak transcription	Brain Hippocampus Middle	brain
9	chr2:113386600-113390000	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
10	chr2:113387400-113389800	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
11	chr2:113387400-113389800	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
12	chr2:113387400-113389800	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
13	chr2:113387400-113389800	Enhancers	Breast Myoepithelial Primary Cells	Breast
14	chr2:113387400-113389800	Enhancers	HSMMtube	muscle
15	chr2:113387600-113389800	Enhancers	HUES48 Cell Line	embryonic stem cell
16	chr2:113387600-113389800	Enhancers	HUES6 Cell Line	embryonic stem cell
17	chr2:113387600-113389800	Enhancers	NHLF	lung
18	chr2:113387600-113390000	Enhancers	Primary mononuclear cells fromperipheralblood	Blood
19	chr2:113387800-113389800	Enhancers	H1 Cell Line	embryonic stem cell
20	chr2:113387800-113389800	Enhancers	Duodenum Smooth Muscle	Duodenum
21	chr2:113387800-113389800	Flanking Active TSS	Dnd41	blood
22	chr2:113388000-113389800	Enhancers	iPS DF 6.9 Cell Line	embryonic stem cell
23	chr2:113388000-113389800	Enhancers	Primary B cells from peripheral blood	blood
24	chr2:113388000-113389800	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
25	chr2:113388000-113389800	Enhancers	Cortex derived primary cultured neurospheres	brain
26	chr2:113388000-113389800	Enhancers	Duodenum Mucosa	Duodenum
27	chr2:113388000-113389800	Enhancers	Fetal Intestine Large	intestine
28	chr2:113388200-113389800	Flanking Active TSS	Muscle Satellite Cultured Cells	--
29	chr2:113388400-113389800	Flanking Active TSS	Primary hematopoietic stem cells short term culture	blood
30	chr2:113388400-113389800	Flanking Active TSS	GM12878-XiMat	blood
31	chr2:113388600-113389800	Enhancers	Fetal Intestine Small	intestine
32	chr2:113388600-113389800	Enhancers	Fetal Muscle Trunk	muscle
33	chr2:113388600-113389800	Enhancers	Fetal Stomach	stomach
34	chr2:113388600-113389800	Enhancers	Right Atrium	heart
35	chr2:113388800-113389800	Enhancers	Thymus	Thymus
36	chr2:113388800-113390000	Enhancers	Primary T cells effector/memory enriched fromperipheralblood	blood
37	chr2:113388800-113391400	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
38	chr2:113388800-113394800	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
39	chr2:113388800-113398200	Weak transcription	Lung	lung
40	chr2:113389000-113389800	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
41	chr2:113389000-113389800	Enhancers	Primary neutrophils fromperipheralblood	blood
42	chr2:113389000-113389800	Enhancers	Sigmoid Colon	Sigmoid Colon
43	chr2:113389000-113389800	Enhancers	A549	lung
44	chr2:113389000-113389800	Enhancers	HUVEC	blood vessel
45	chr2:113389000-113390000	Enhancers	HSMM	muscle
46	chr2:113389000-113390600	Enhancers	Primary T regulatory cells fromperipheralblood	blood
47	chr2:113389000-113390800	Enhancers	Primary hematopoietic stem cells	blood
48	chr2:113389000-113391200	Weak transcription	Placenta Amnion	Placenta Amnion
49	chr2:113389000-113391800	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
50	chr2:113389000-113395000	Enhancers	Primary T helper memory cells from peripheral blood 2	blood

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