Variant report

Variant	rs30605
Chromosome Location	chr5:14259489-14259490
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr5:14152848..14154362-chr5:14257510..14259958,2	MCF-7	breast:
2	chr5:14143210..14148732-chr5:14254944..14261067,10	MCF-7	breast:

Variant related genes	Relation type
ENSG00000038382	Chromatin interaction

Extended variants
information (count: 32 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:27)

rs_ID	r²[population]
rs12659261	0.81[AMR][1000 genomes];0.91[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs154150	0.83[AMR][1000 genomes];0.96[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs154153	0.82[EUR][1000 genomes]
rs154154	0.82[EUR][1000 genomes]
rs154155	0.82[EUR][1000 genomes]
rs164862	0.82[ASN][1000 genomes]
rs165083	0.82[EUR][1000 genomes]
rs165094	0.81[ASN][1000 genomes]
rs165096	0.85[ASN][1000 genomes]
rs16903326	0.81[AMR][1000 genomes];0.95[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs16903338	0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs30603	0.86[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs30604	0.84[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs30618	0.81[AMR][1000 genomes];0.96[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs354303	0.84[ASN][1000 genomes]
rs42204	0.86[EUR][1000 genomes]
rs42405	0.82[EUR][1000 genomes]
rs56226439	0.81[AMR][1000 genomes];0.95[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs56334634	0.87[ASN][1000 genomes]
rs58221971	0.84[ASN][1000 genomes]
rs6554849	0.84[ASN][1000 genomes]
rs6554850	0.87[ASN][1000 genomes]
rs6554851	0.87[ASN][1000 genomes]
rs67084079	0.94[AMR][1000 genomes];0.93[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs72744279	0.83[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7380307	0.81[AMR][1000 genomes];0.94[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs7700787	0.83[AMR][1000 genomes];0.96[EUR][1000 genomes];0.93[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	esv1825924	chr5:14147376-14270450	Flanking Active TSS Weak transcription Enhancers Genic enhancers Flanking Bivalent TSS/Enh Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer Strong transcription ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
2	nsv830209	chr5:14154989-14301758	Flanking Active TSS Enhancers Weak transcription Genic enhancers Strong transcription Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
3	nsv948355	chr5:14160447-14395478	Weak transcription Enhancers Genic enhancers Strong transcription Flanking Active TSS ZNF genes & repeats Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region	4 gene(s)	inside rSNPs	diseases
4	nsv1026914	chr5:14237782-14751588	Weak transcription Transcr. at gene 5' and 3' Strong transcription Flanking Active TSS Enhancers Bivalent/Poised TSS Genic enhancers ZNF genes & repeats Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	37 gene(s)	inside rSNPs	diseases
5	nsv830210	chr5:14255039-14431552	Weak transcription Strong transcription Enhancers Genic enhancers Flanking Active TSS ZNF genes & repeats Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:102 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:14253800-14264400	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
2	chr5:14254000-14261400	Weak transcription	Thymus	Thymus
3	chr5:14255400-14260400	Enhancers	Skeletal Muscle Female	skeletal muscle
4	chr5:14255400-14262400	Enhancers	HUVEC	blood vessel
5	chr5:14255600-14259800	Enhancers	Left Ventricle	heart
6	chr5:14256200-14260400	Enhancers	Fetal Thymus	thymus
7	chr5:14256200-14264200	Enhancers	H1 Cell Line	embryonic stem cell
8	chr5:14256400-14265400	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
9	chr5:14256600-14259800	Enhancers	Adipose Nuclei	Adipose
10	chr5:14256600-14264400	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
11	chr5:14256800-14260200	Enhancers	Duodenum Smooth Muscle	Duodenum
12	chr5:14256800-14261800	Enhancers	Colon Smooth Muscle	Colon
13	chr5:14257000-14260200	Enhancers	Breast Myoepithelial Primary Cells	Breast
14	chr5:14257000-14260200	Enhancers	Primary B cells from peripheral blood	blood
15	chr5:14257000-14260400	Enhancers	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
16	chr5:14257000-14260400	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
17	chr5:14257000-14260600	Enhancers	Fetal Heart	heart
18	chr5:14257000-14264600	Enhancers	NH-A	brain
19	chr5:14257200-14260200	Weak transcription	HSMMtube	muscle
20	chr5:14257200-14264800	Weak transcription	Stomach Mucosa	stomach
21	chr5:14257200-14265000	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
22	chr5:14257400-14261000	Weak transcription	Aorta	Aorta
23	chr5:14257600-14261800	Weak transcription	Brain Angular Gyrus	brain
24	chr5:14257800-14259600	Flanking Active TSS	GM12878-XiMat	blood
25	chr5:14258000-14260200	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
26	chr5:14258000-14260400	Enhancers	Fetal Brain Female	brain
27	chr5:14258200-14259600	Genic enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
28	chr5:14258200-14259800	Enhancers	Brain Hippocampus Middle	brain
29	chr5:14258200-14259800	Enhancers	Fetal Lung	lung
30	chr5:14258200-14261800	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
31	chr5:14258400-14259800	Flanking Active TSS	iPS-15b Cell Line	embryonic stem cell
32	chr5:14258400-14261400	Weak transcription	Placenta Amnion	Placenta Amnion
33	chr5:14258400-14261400	Enhancers	Osteobl	bone
34	chr5:14258400-14264600	Weak transcription	Rectal Mucosa Donor 29	rectum
35	chr5:14258600-14259600	Flanking Active TSS	Ganglion Eminence derived primary cultured neurospheres	brain
36	chr5:14258600-14261200	Weak transcription	NHEK	skin
37	chr5:14258600-14261800	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
38	chr5:14258800-14259600	Flanking Active TSS	iPS-18 Cell Line	embryonic stem cell
39	chr5:14258800-14259600	Weak transcription	A549	lung
40	chr5:14258800-14259800	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
41	chr5:14258800-14260000	Flanking Active TSS	HUES64 Cell Line	embryonic stem cell
42	chr5:14258800-14260000	Enhancers	Fetal Stomach	stomach
43	chr5:14258800-14260400	Flanking Active TSS	HUES48 Cell Line	embryonic stem cell
44	chr5:14258800-14260400	Flanking Active TSS	iPS-20b Cell Line	embryonic stem cell
45	chr5:14258800-14260800	Enhancers	NHDF-Ad	bronchial
46	chr5:14258800-14264400	Weak transcription	Fetal Intestine Small	intestine
47	chr5:14258800-14265000	Enhancers	Muscle Satellite Cultured Cells	--
48	chr5:14259000-14259800	Enhancers	HMEC	breast
49	chr5:14259000-14261000	Weak transcription	H9 Cell Line	embryonic stem cell
50	chr5:14259000-14261000	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links