Variant report

Variant	rs10473254
Chromosome Location	chr5:41920677-41920678
allele	C/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	POLR2A	chr5:41917385-41928379	K562	blood:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr5:41920030..41922138-chr5:41926101..41928998,2	MCF-7	breast:
2	chr5:41904013..41906078-chr5:41920302..41923061,3	MCF-7	breast:
3	chr5:41903408..41905883-chr5:41920189..41922331,2	MCF-7	breast:

Variant related genes	Relation type
FBXO4	TF binding region
ENSG00000205765	Chromatin interaction

Extended variants
information (count: 25 )
Associated
traits (count: 0)

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

rs_ID	r²[population]
rs10037152	0.83[AFR][1000 genomes]
rs10038717	0.91[AFR][1000 genomes]
rs10039091	0.95[AFR][1000 genomes]
rs10045224	0.91[AFR][1000 genomes]
rs10051536	1.00[YRI][hapmap];0.87[AFR][1000 genomes]
rs10061961	0.87[AFR][1000 genomes]
rs10064781	0.86[AFR][1000 genomes]
rs10071732	1.00[YRI][hapmap];0.84[AFR][1000 genomes]
rs10072903	0.95[AFR][1000 genomes]
rs10079775	1.00[YRI][hapmap];1.00[AFR][1000 genomes]
rs10080034	1.00[AFR][1000 genomes]
rs10214013	0.91[AFR][1000 genomes]
rs13354429	0.95[AFR][1000 genomes]
rs13357640	0.91[AFR][1000 genomes]
rs13358155	0.95[AFR][1000 genomes]
rs16872021	0.87[AFR][1000 genomes]
rs28429157	0.87[AFR][1000 genomes]
rs28588578	0.91[AFR][1000 genomes]
rs28661292	0.87[AFR][1000 genomes]
rs9292830	1.00[YRI][hapmap];0.87[AFR][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	esv2762518	chr5:41780210-41935113	Flanking Active TSS Weak transcription Enhancers Strong transcription Bivalent Enhancer Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS Genic enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	108 gene(s)	inside rSNPs	diseases
2	nsv830272	chr5:41833365-41986167	Strong transcription Enhancers Weak transcription Transcr. at gene 5' and 3' Active TSS Flanking Bivalent TSS/Enh Flanking Active TSS Genic enhancers Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	111 gene(s)	inside rSNPs	diseases
3	nsv830273	chr5:41867296-42066070	Flanking Active TSS Active TSS Genic enhancers Weak transcription Bivalent Enhancer Enhancers Strong transcription Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	111 gene(s)	inside rSNPs	diseases
4	nsv933208	chr5:41879946-42876624	Active TSS Enhancers Weak transcription Flanking Active TSS Strong transcription Flanking Bivalent TSS/Enh Genic enhancers Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	112 gene(s)	inside rSNPs	diseases
5	nsv492147	chr5:41902086-42896162	Enhancers Flanking Active TSS Active TSS Genic enhancers Weak transcription Strong transcription Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	113 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:124 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:41905000-41924800	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
2	chr5:41905200-41925000	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
3	chr5:41905600-41921000	Weak transcription	ES-I3 Cell Line	embryonic stem cell
4	chr5:41905600-41924600	Weak transcription	Small Intestine	intestine
5	chr5:41905800-41922200	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
6	chr5:41905800-41923800	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
7	chr5:41905800-41924400	Weak transcription	Stomach Mucosa	stomach
8	chr5:41905800-41925000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
9	chr5:41905800-41925000	Weak transcription	Gastric	stomach
10	chr5:41906200-41921200	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
11	chr5:41906400-41921000	Strong transcription	iPS-20b Cell Line	embryonic stem cell
12	chr5:41906400-41922200	Strong transcription	Fetal Muscle Trunk	muscle
13	chr5:41906800-41924600	Weak transcription	Pancreatic Islets	Pancreatic Islet
14	chr5:41907000-41922200	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
15	chr5:41907000-41923600	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
16	chr5:41907200-41922400	Strong transcription	Liver	Liver
17	chr5:41907400-41921600	Strong transcription	Duodenum Smooth Muscle	Duodenum
18	chr5:41907600-41921000	Strong transcription	Rectal Mucosa Donor 29	rectum
19	chr5:41907800-41920800	Strong transcription	Ganglion Eminence derived primary cultured neurospheres	brain
20	chr5:41907800-41921000	Strong transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
21	chr5:41907800-41921200	Strong transcription	Primary neutrophils fromperipheralblood	blood
22	chr5:41907800-41921200	Strong transcription	Brain Hippocampus Middle	brain
23	chr5:41907800-41922200	Strong transcription	Fetal Thymus	thymus
24	chr5:41907800-41922400	Strong transcription	Monocytes-CD14+_RO01746	blood
25	chr5:41908000-41920800	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
26	chr5:41908000-41920800	Strong transcription	Placenta	Placenta
27	chr5:41908000-41921200	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
28	chr5:41908000-41921400	Strong transcription	Primary T cells fromperipheralblood	blood
29	chr5:41908000-41922400	Strong transcription	Adipose Nuclei	Adipose
30	chr5:41908200-41921200	Strong transcription	Cortex derived primary cultured neurospheres	brain
31	chr5:41908200-41921400	Strong transcription	Left Ventricle	heart
32	chr5:41908200-41921600	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
33	chr5:41908200-41922000	Strong transcription	Primary hematopoietic stem cells	blood
34	chr5:41908200-41922400	Strong transcription	Dnd41	blood
35	chr5:41908400-41921200	Strong transcription	Fetal Lung	lung
36	chr5:41908800-41921400	Strong transcription	Primary hematopoietic stem cells short term culture	blood
37	chr5:41908800-41921400	Strong transcription	Primary T helper cells fromperipheralblood	blood
38	chr5:41909200-41920800	Strong transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
39	chr5:41909200-41921200	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
40	chr5:41909200-41921400	Strong transcription	Muscle Satellite Cultured Cells	--
41	chr5:41909200-41921600	Strong transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
42	chr5:41909200-41924600	Weak transcription	Fetal Heart	heart
43	chr5:41909400-41921000	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
44	chr5:41909400-41921400	Strong transcription	Skeletal Muscle Female	skeletal muscle
45	chr5:41910200-41920800	Strong transcription	Stomach Smooth Muscle	stomach
46	chr5:41911200-41922000	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
47	chr5:41911800-41921200	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
48	chr5:41913200-41921000	Weak transcription	iPS-15b Cell Line	embryonic stem cell
49	chr5:41913200-41921800	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
50	chr5:41913200-41925000	Weak transcription	Esophagus	oesophagus

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links