Variant report

Variant	rs58577680
Chromosome Location	chr4:53734294-53734295
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	chr4:53586813..53589687-chr4:53732860..53735121,2	MCF-7	breast:
2	chr4:53587851..53589635-chr4:53733088..53734666,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000248375	Chromatin interaction

Extended variants
information (count: 28 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:25)

rs_ID	r²[population]
rs10517269	0.82[AMR][1000 genomes]
rs11938159	0.80[AMR][1000 genomes]
rs17082074	0.82[ASN][1000 genomes]
rs2200225	0.87[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs3811781	0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs41279517	0.85[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6554054	0.80[AMR][1000 genomes]
rs6554057	0.82[AFR][1000 genomes];0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6817433	0.83[AMR][1000 genomes];0.93[ASN][1000 genomes]
rs6818178	0.83[AMR][1000 genomes];0.93[ASN][1000 genomes]
rs6833350	0.80[EUR][1000 genomes]
rs6838718	0.80[AMR][1000 genomes]
rs6848200	0.81[AFR][1000 genomes];0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6855240	0.80[EUR][1000 genomes]
rs73814868	0.82[AMR][1000 genomes]
rs73814875	0.92[ASN][1000 genomes]
rs73814883	0.97[ASN][1000 genomes]
rs73814886	0.86[AFR][1000 genomes];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7655781	0.83[AMR][1000 genomes];0.93[ASN][1000 genomes]
rs7670068	0.86[AFR][1000 genomes];0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7677726	0.81[EUR][1000 genomes]
rs7685816	0.80[AMR][1000 genomes];0.90[ASN][1000 genomes]
rs7688141	0.80[AMR][1000 genomes]
rs7699960	0.86[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs881744	0.83[AMR][1000 genomes];0.93[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1004889	chr4:53436500-54106281	Weak transcription Enhancers Bivalent/Poised TSS ZNF genes & repeats Flanking Active TSS Strong transcription Bivalent Enhancer Active TSS Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	25 gene(s)	inside rSNPs	diseases
2	nsv537094	chr4:53436500-54106281	Bivalent/Poised TSS Weak transcription Enhancers Flanking Bivalent TSS/Enh Flanking Active TSS Active TSS ZNF genes & repeats Strong transcription Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	25 gene(s)	inside rSNPs	diseases
3	nsv1004086	chr4:53698581-53773183	Enhancers Weak transcription Strong transcription Active TSS Flanking Active TSS Flanking Bivalent TSS/Enh Genic enhancers Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:93 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:53728800-53738400	Weak transcription	Small Intestine	intestine
2	chr4:53729200-53734400	Weak transcription	HSMMtube	muscle
3	chr4:53729200-53735200	Weak transcription	Colonic Mucosa	Colon
4	chr4:53729200-53751200	Weak transcription	GM12878-XiMat	blood
5	chr4:53729200-53807800	Weak transcription	Esophagus	oesophagus
6	chr4:53729400-53738600	Weak transcription	HMEC	breast
7	chr4:53729400-53739200	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
8	chr4:53729400-53743200	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
9	chr4:53729400-53752400	Weak transcription	Primary B cells from cord blood	blood
10	chr4:53729400-53753800	Weak transcription	Duodenum Mucosa	Duodenum
11	chr4:53729600-53735200	Weak transcription	NHDF-Ad	bronchial
12	chr4:53729600-53739400	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
13	chr4:53729600-53739600	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
14	chr4:53729600-53742200	Weak transcription	Primary hematopoietic stem cells short term culture	blood
15	chr4:53729800-53734400	Weak transcription	Rectal Smooth Muscle	rectum
16	chr4:53729800-53737000	Weak transcription	Primary T cells from cord blood	blood
17	chr4:53729800-53739400	Weak transcription	Fetal Intestine Large	intestine
18	chr4:53730000-53743800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
19	chr4:53730200-53734600	Genic enhancers	ES-UCSF4 Cell Line	embryonic stem cell
20	chr4:53730200-53736600	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
21	chr4:53731000-53735400	Weak transcription	Sigmoid Colon	Sigmoid Colon
22	chr4:53731200-53736000	Enhancers	Right Atrium	heart
23	chr4:53731400-53734400	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
24	chr4:53731400-53734400	Weak transcription	Brain Substantia Nigra	brain
25	chr4:53731400-53751000	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
26	chr4:53731600-53734400	Transcr. at gene 5' and 3'	Fetal Brain Female	brain
27	chr4:53731600-53736200	Weak transcription	Stomach Mucosa	stomach
28	chr4:53731600-53739400	Weak transcription	Cortex derived primary cultured neurospheres	brain
29	chr4:53731800-53736600	Weak transcription	Colon Smooth Muscle	Colon
30	chr4:53731800-53738000	Weak transcription	Liver	Liver
31	chr4:53732000-53734400	Weak transcription	Brain Cingulate Gyrus	brain
32	chr4:53732000-53734400	Strong transcription	Fetal Stomach	stomach
33	chr4:53732000-53734400	Weak transcription	Skeletal Muscle Female	skeletal muscle
34	chr4:53732200-53734400	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
35	chr4:53732200-53734400	Weak transcription	Gastric	stomach
36	chr4:53732200-53734400	Weak transcription	Stomach Smooth Muscle	stomach
37	chr4:53732200-53735200	Weak transcription	Spleen	Spleen
38	chr4:53732200-53735200	Weak transcription	NHLF	lung
39	chr4:53732200-53735400	Weak transcription	Pancreas	Pancrea
40	chr4:53732400-53750200	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
41	chr4:53732400-53755000	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
42	chr4:53732800-53737400	Weak transcription	Fetal Intestine Small	intestine
43	chr4:53732800-53738400	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
44	chr4:53732800-53739400	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
45	chr4:53732800-53749400	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
46	chr4:53733000-53736000	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
47	chr4:53733000-53767800	Weak transcription	Monocytes-CD14+_RO01746	blood
48	chr4:53733200-53735000	Enhancers	Fetal Kidney	kidney
49	chr4:53733200-53737600	Enhancers	Breast Myoepithelial Primary Cells	Breast
50	chr4:53733200-53759000	Weak transcription	Osteobl	bone

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