Variant report

Variant	rs72823519
Chromosome Location	chr17:46061885-46061886
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr17:46053682..46056585-chr17:46059998..46062709,2	K562	blood:
2	chr17:46059948..46063060-chr17:46063175..46066138,4	MCF-7	breast:
3	chr17:46058631..46063478-chr17:46064617..46070061,8	K562	blood:
4	chr17:46046877..46049388-chr17:46060915..46063110,2	K562	blood:
5	chr17:46058567..46062223-chr17:46094441..46097254,3	K562	blood:

Variant related genes	Relation type
ENSG00000108465	Chromatin interaction

Extended variants
information (count: 25 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:22)

rs_ID	r²[population]
rs12601350	0.85[EUR][1000 genomes]
rs12602131	0.85[EUR][1000 genomes]
rs12602670	0.85[EUR][1000 genomes]
rs1473117	0.83[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs17616799	0.91[EUR][1000 genomes]
rs1986694	0.82[EUR][1000 genomes]
rs2023885	0.81[EUR][1000 genomes]
rs2229369	0.81[EUR][1000 genomes]
rs2240119	0.85[EUR][1000 genomes]
rs2240120	0.81[EUR][1000 genomes]
rs2285860	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2325783	0.81[EUR][1000 genomes]
rs2525105	0.88[EUR][1000 genomes]
rs55982711	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs56402159	0.91[EUR][1000 genomes]
rs57782323	0.94[EUR][1000 genomes]
rs58554000	0.83[EUR][1000 genomes]
rs61396871	0.91[EUR][1000 genomes]
rs72823528	0.85[EUR][1000 genomes]
rs72823532	0.85[EUR][1000 genomes]
rs72823533	0.85[EUR][1000 genomes]
rs757353	0.85[EUR][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	nsv498122	chr17:45763853-46064327	Enhancers Flanking Active TSS Bivalent Enhancer Weak transcription Strong transcription Flanking Bivalent TSS/Enh Active TSS Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	67 gene(s)	inside rSNPs	diseases
2	nsv469808	chr17:46049868-46228673	Enhancers Weak transcription Bivalent/Poised TSS Strong transcription Bivalent Enhancer Flanking Active TSS Active TSS Transcr. at gene 5' and 3' Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	85 gene(s)	inside rSNPs	diseases
3	nsv482897	chr17:46049868-46228673	Enhancers Active TSS Weak transcription Strong transcription Bivalent Enhancer Flanking Active TSS Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	85 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs72823519	CDK5RAP3	cis	Nerve Tibial	GTEx

Chromatin state (count:115 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr17:46049800-46066600	Weak transcription	Small Intestine	intestine
2	chr17:46050200-46062000	Strong transcription	NHEK	skin
3	chr17:46050200-46062200	Strong transcription	Primary neutrophils fromperipheralblood	blood
4	chr17:46050200-46062800	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
5	chr17:46050200-46063000	Strong transcription	Fetal Muscle Trunk	muscle
6	chr17:46050200-46063400	Strong transcription	Fetal Stomach	stomach
7	chr17:46050400-46062000	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
8	chr17:46050400-46062200	Strong transcription	Foreskin Fibroblast Primary Cells skin01	Skin
9	chr17:46050400-46063000	Strong transcription	HUES6 Cell Line	embryonic stem cell
10	chr17:46050600-46062200	Strong transcription	Breast Myoepithelial Primary Cells	Breast
11	chr17:46050600-46062200	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
12	chr17:46050800-46062000	Strong transcription	iPS-18 Cell Line	embryonic stem cell
13	chr17:46050800-46062000	Strong transcription	Primary B cells from peripheral blood	blood
14	chr17:46050800-46062200	Strong transcription	iPS-20b Cell Line	embryonic stem cell
15	chr17:46050800-46062400	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
16	chr17:46050800-46062600	Strong transcription	Fetal Intestine Small	intestine
17	chr17:46050800-46062800	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
18	chr17:46050800-46063000	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
19	chr17:46050800-46063000	Strong transcription	Fetal Muscle Leg	muscle
20	chr17:46051000-46062000	Strong transcription	Primary B cells from cord blood	blood
21	chr17:46051000-46062200	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
22	chr17:46051000-46062200	Strong transcription	Placenta Amnion	Placenta Amnion
23	chr17:46051000-46063000	Strong transcription	Primary T cells from cord blood	blood
24	chr17:46051000-46063000	Strong transcription	Sigmoid Colon	Sigmoid Colon
25	chr17:46051200-46062000	Strong transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
26	chr17:46051800-46062400	Strong transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
27	chr17:46054200-46063000	Strong transcription	Thymus	Thymus
28	chr17:46056200-46064000	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
29	chr17:46056400-46062200	Strong transcription	Foreskin Fibroblast Primary Cells skin02	Skin
30	chr17:46056400-46063200	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
31	chr17:46057000-46064000	Weak transcription	Fetal Brain Male	brain
32	chr17:46057800-46062000	Genic enhancers	Monocytes-CD14+_RO01746	blood
33	chr17:46058200-46064400	Weak transcription	Fetal Kidney	kidney
34	chr17:46058400-46062000	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
35	chr17:46059000-46064600	Weak transcription	NHDF-Ad	bronchial
36	chr17:46059400-46062000	Strong transcription	Primary T helper cells fromperipheralblood	blood
37	chr17:46059400-46064000	Weak transcription	ES-I3 Cell Line	embryonic stem cell
38	chr17:46059400-46064600	Weak transcription	HUVEC	blood vessel
39	chr17:46059400-46064800	Weak transcription	Colon Smooth Muscle	Colon
40	chr17:46059600-46062000	Strong transcription	Placenta	Placenta
41	chr17:46059600-46064600	Weak transcription	Psoas Muscle	Psoas
42	chr17:46059800-46062600	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
43	chr17:46059800-46062800	Strong transcription	Fetal Thymus	thymus
44	chr17:46060000-46062200	Strong transcription	Fetal Intestine Large	intestine
45	chr17:46060400-46063600	Weak transcription	Colonic Mucosa	Colon
46	chr17:46060400-46064600	Weak transcription	Fetal Lung	lung
47	chr17:46060400-46065200	Weak transcription	Osteobl	bone
48	chr17:46060600-46062000	Strong transcription	Primary T cells fromperipheralblood	blood
49	chr17:46060600-46062400	Weak transcription	Aorta	Aorta
50	chr17:46060600-46063400	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links