Variant report

Variant	rs10473253
Chromosome Location	chr5:41908556-41908557
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr5:41867500..41871930-chr5:41901815..41908844,17	K562	blood:
2	chr5:41903420..41907025-chr5:41907482..41911451,8	MCF-7	breast:
3	chr5:41903099..41906960-chr5:41907853..41912550,6	MCF-7	breast:
4	chr5:41905678..41908829-chr5:41924042..41927034,3	MCF-7	breast:

Variant related genes	Relation type
ENSG00000151876	Chromatin interaction
ENSG00000205765	Chromatin interaction
ENSG00000083720	Chromatin interaction
ENSG00000248668	Chromatin interaction

Extended variants
information (count: 13 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:7)

rs_ID	r²[population]
rs10035745	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs10069904	0.83[AMR][1000 genomes]
rs10079575	0.81[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs10472358	0.90[YRI][hapmap]
rs10473251	0.90[YRI][hapmap]
rs16872112	0.83[AMR][1000 genomes]
rs6896762	0.83[AMR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:6 , 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	nsv327668	chr5:41901383-41909830	Flanking Active TSS Weak transcription Enhancers Strong transcription Active TSS Transcr. at gene 5' and 3' Genic enhancers Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	44 gene(s)	inside rSNPs	diseases
6	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:125 , 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	chr5:41905200-41908600	Weak transcription	Ovary	ovary
3	chr5:41905200-41912600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
4	chr5:41905200-41912600	Weak transcription	Fetal Stomach	stomach
5	chr5:41905200-41915400	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
6	chr5:41905200-41918200	Weak transcription	Aorta	Aorta
7	chr5:41905200-41925000	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
8	chr5:41905400-41910200	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
9	chr5:41905600-41908600	Weak transcription	Fetal Brain Female	brain
10	chr5:41905600-41908600	Weak transcription	Fetal Kidney	kidney
11	chr5:41905600-41910000	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
12	chr5:41905600-41910200	Weak transcription	Colon Smooth Muscle	Colon
13	chr5:41905600-41911200	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
14	chr5:41905600-41912600	Weak transcription	H9 Cell Line	embryonic stem cell
15	chr5:41905600-41912600	Weak transcription	Lung	lung
16	chr5:41905600-41912600	Weak transcription	Thymus	Thymus
17	chr5:41905600-41912800	Weak transcription	iPS-15b Cell Line	embryonic stem cell
18	chr5:41905600-41921000	Weak transcription	ES-I3 Cell Line	embryonic stem cell
19	chr5:41905600-41924600	Weak transcription	Small Intestine	intestine
20	chr5:41905800-41908600	Weak transcription	Fetal Muscle Leg	muscle
21	chr5:41905800-41908600	Weak transcription	NHLF	lung
22	chr5:41905800-41910200	Weak transcription	Esophagus	oesophagus
23	chr5:41905800-41910200	Weak transcription	Stomach Smooth Muscle	stomach
24	chr5:41905800-41911400	Weak transcription	Brain Germinal Matrix	brain
25	chr5:41905800-41911400	Weak transcription	Fetal Brain Male	brain
26	chr5:41905800-41912200	Weak transcription	NHEK	skin
27	chr5:41905800-41912600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
28	chr5:41905800-41912600	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
29	chr5:41905800-41912600	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
30	chr5:41905800-41912600	Weak transcription	Pancreas	Pancrea
31	chr5:41905800-41912800	Weak transcription	Placenta Amnion	Placenta Amnion
32	chr5:41905800-41918200	Weak transcription	Psoas Muscle	Psoas
33	chr5:41905800-41918200	Weak transcription	Spleen	Spleen
34	chr5:41905800-41922200	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
35	chr5:41905800-41923800	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
36	chr5:41905800-41924400	Weak transcription	Stomach Mucosa	stomach
37	chr5:41905800-41925000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
38	chr5:41905800-41925000	Weak transcription	Gastric	stomach
39	chr5:41906000-41910200	Weak transcription	A549	lung
40	chr5:41906200-41921200	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
41	chr5:41906400-41916400	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
42	chr5:41906400-41920600	Strong transcription	HUES48 Cell Line	embryonic stem cell
43	chr5:41906400-41921000	Strong transcription	iPS-20b Cell Line	embryonic stem cell
44	chr5:41906400-41922200	Strong transcription	Fetal Muscle Trunk	muscle
45	chr5:41906600-41909200	Genic enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
46	chr5:41906600-41918200	Strong transcription	Primary B cells from peripheral blood	blood
47	chr5:41906800-41924600	Weak transcription	Pancreatic Islets	Pancreatic Islet
48	chr5:41907000-41908600	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
49	chr5:41907000-41908600	Weak transcription	Brain Cingulate Gyrus	brain
50	chr5:41907000-41910200	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links