Variant report

Variant	rs56227025
Chromosome Location	chr5:14385434-14385435
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	ELF1	chr5:14385172-14385459	K562	blood:	n/a	chr5:14385310-14385323
2	USF2	chr5:14385308-14385475	H1-hESC	embryonic stem cell:	n/a	n/a
3	POLR2A	chr5:14385249-14385775	PANC-1	pancreas:	n/a	n/a
4	POLR2A	chr5:14385327-14385522	ProgFib	skin:	n/a	n/a
5	POLR2A	chr5:14385082-14385594	GM12892	blood:	n/a	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr5:14380580..14382137-chr5:14384251..14386172,2	MCF-7	breast:

Variant related genes	Relation type
TRIO	TF binding region

Extended variants
information (count: 57 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:53)

rs_ID	r²[population]
rs10062034	1.00[AMR][1000 genomes]
rs10076925	1.00[AMR][1000 genomes]
rs16903350	0.83[AMR][1000 genomes]
rs16903399	1.00[AMR][1000 genomes]
rs16903467	0.84[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs55750919	1.00[AMR][1000 genomes]
rs55754427	1.00[AMR][1000 genomes]
rs55773296	1.00[AMR][1000 genomes]
rs56114434	1.00[AMR][1000 genomes]
rs56141029	1.00[AMR][1000 genomes]
rs56664186	1.00[AMR][1000 genomes]
rs56712870	1.00[AMR][1000 genomes]
rs57560019	1.00[AMR][1000 genomes]
rs57974400	1.00[AMR][1000 genomes]
rs58324829	1.00[AMR][1000 genomes]
rs58443103	1.00[AMR][1000 genomes]
rs58716074	0.83[AMR][1000 genomes]
rs58897996	1.00[AMR][1000 genomes]
rs59499572	0.83[AMR][1000 genomes]
rs59853866	0.89[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs60077210	1.00[AMR][1000 genomes]
rs60568524	0.83[AMR][1000 genomes]
rs61180647	0.83[AMR][1000 genomes]
rs61396062	1.00[AMR][1000 genomes]
rs61509800	0.83[AMR][1000 genomes]
rs6868596	0.83[AMR][1000 genomes]
rs73748806	1.00[AMR][1000 genomes]
rs73748810	0.83[AMR][1000 genomes]
rs73748811	1.00[AMR][1000 genomes]
rs73749082	1.00[AMR][1000 genomes]
rs73749083	1.00[AMR][1000 genomes]
rs73749085	0.83[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs73749234	0.84[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs73749235	0.84[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs73751307	0.83[AMR][1000 genomes]
rs73751311	0.83[AMR][1000 genomes]
rs73751318	0.83[AMR][1000 genomes]
rs73751322	1.00[AMR][1000 genomes]
rs73751323	1.00[AMR][1000 genomes]
rs73751327	0.83[AMR][1000 genomes]
rs73751329	1.00[AMR][1000 genomes]
rs73751335	0.83[AMR][1000 genomes]
rs73751336	0.83[AMR][1000 genomes]
rs73751337	1.00[AMR][1000 genomes]
rs73751338	0.83[AMR][1000 genomes]
rs73751339	0.83[AMR][1000 genomes]
rs73751340	0.83[AMR][1000 genomes]
rs7703674	0.83[AMR][1000 genomes]
rs7705426	0.83[AMR][1000 genomes]
rs7713114	0.83[AMR][1000 genomes]
rs7716460	1.00[AMR][1000 genomes]
rs7723309	1.00[AMR][1000 genomes]
rs7724084	1.00[AMR][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	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
2	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
3	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
4	nsv1018187	chr5:14385164-15127103	Strong transcription Flanking Bivalent TSS/Enh Weak transcription Enhancers Genic enhancers Active TSS Flanking Active TSS ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	61 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:113 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:14351600-14399400	Weak transcription	Primary neutrophils fromperipheralblood	blood
2	chr5:14353600-14398800	Strong transcription	Rectal Mucosa Donor 29	rectum
3	chr5:14354600-14402400	Strong transcription	Liver	Liver
4	chr5:14355000-14392400	Strong transcription	HSMMtube	muscle
5	chr5:14355000-14398800	Strong transcription	Rectal Mucosa Donor 31	rectum
6	chr5:14357600-14422000	Weak transcription	Stomach Mucosa	stomach
7	chr5:14357800-14389800	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
8	chr5:14358000-14385800	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
9	chr5:14358000-14389800	Strong transcription	Adipose Nuclei	Adipose
10	chr5:14358200-14391600	Strong transcription	Primary B cells from cord blood	blood
11	chr5:14358400-14385600	Strong transcription	Fetal Intestine Large	intestine
12	chr5:14358400-14392000	Strong transcription	Fetal Muscle Leg	muscle
13	chr5:14358600-14392600	Strong transcription	Duodenum Smooth Muscle	Duodenum
14	chr5:14360000-14398400	Strong transcription	Fetal Muscle Trunk	muscle
15	chr5:14363600-14386000	Strong transcription	Skeletal Muscle Female	skeletal muscle
16	chr5:14363600-14396000	Strong transcription	Foreskin Fibroblast Primary Cells skin01	Skin
17	chr5:14363800-14385600	Strong transcription	A549	lung
18	chr5:14363800-14430600	Strong transcription	Primary monocytes fromperipheralblood	blood
19	chr5:14363800-14430600	Strong transcription	Monocytes-CD14+_RO01746	blood
20	chr5:14366000-14392400	Strong transcription	HSMM	muscle
21	chr5:14366600-14385600	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
22	chr5:14366600-14391600	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
23	chr5:14366800-14403200	Strong transcription	Primary hematopoietic stem cells short term culture	blood
24	chr5:14367400-14399800	Strong transcription	Left Ventricle	heart
25	chr5:14371200-14388000	Weak transcription	Small Intestine	intestine
26	chr5:14372400-14398600	Strong transcription	Sigmoid Colon	Sigmoid Colon
27	chr5:14372600-14389800	Weak transcription	Fetal Brain Male	brain
28	chr5:14373800-14388600	Weak transcription	Fetal Heart	heart
29	chr5:14374400-14385600	Strong transcription	HUES64 Cell Line	embryonic stem cell
30	chr5:14374400-14391800	Strong transcription	Breast Myoepithelial Primary Cells	Breast
31	chr5:14374400-14392000	Strong transcription	NHEK	skin
32	chr5:14374400-14397000	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
33	chr5:14374400-14399600	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
34	chr5:14374600-14392200	Strong transcription	HMEC	breast
35	chr5:14375400-14386200	Strong transcription	Ganglion Eminence derived primary cultured neurospheres	brain
36	chr5:14375400-14387000	Strong transcription	NH-A	brain
37	chr5:14375600-14387000	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
38	chr5:14375800-14386800	Strong transcription	Osteobl	bone
39	chr5:14375800-14396200	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
40	chr5:14376200-14392600	Strong transcription	NHDF-Ad	bronchial
41	chr5:14376800-14392200	Strong transcription	NHLF	lung
42	chr5:14377000-14386200	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
43	chr5:14377000-14396200	Strong transcription	Muscle Satellite Cultured Cells	--
44	chr5:14377200-14388800	Strong transcription	Fetal Stomach	stomach
45	chr5:14377200-14390000	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
46	chr5:14377400-14385600	Strong transcription	Ovary	ovary
47	chr5:14377400-14388400	Strong transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
48	chr5:14377400-14391000	Strong transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
49	chr5:14377600-14388800	Strong transcription	Lung	lung
50	chr5:14377800-14388800	Strong transcription	Foreskin Fibroblast Primary Cells skin02	Skin

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links