Variant report

Variant	rs351933
Chromosome Location	chr5:52004844-52004845
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	chr5:52004585..52006251-chr5:52102692..52104640,2	K562	blood:
2	chr5:52002898..52006870-chr5:52009396..52011891,3	MCF-7	breast:

Extended variants
information (count: 27 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:23)

rs_ID	r²[population]
rs12332623	0.83[AMR][1000 genomes];0.98[ASN][1000 genomes]
rs1626287	0.92[AMR][1000 genomes];0.96[ASN][1000 genomes]
rs1645393	0.92[AMR][1000 genomes];0.96[ASN][1000 genomes]
rs1645394	0.92[AMR][1000 genomes];0.96[ASN][1000 genomes]
rs164611	0.88[AMR][1000 genomes];0.98[ASN][1000 genomes]
rs164612	0.93[AMR][1000 genomes];0.98[ASN][1000 genomes]
rs1668506	0.96[ASN][1000 genomes]
rs244481	0.91[ASN][1000 genomes]
rs244491	0.85[ASN][1000 genomes]
rs244493	0.87[ASN][1000 genomes]
rs244495	0.87[ASN][1000 genomes]
rs29976	0.89[ASN][1000 genomes]
rs29977	0.91[ASN][1000 genomes]
rs29980	0.88[ASN][1000 genomes]
rs29982	0.91[ASN][1000 genomes]
rs351937	0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs351940	0.92[AMR][1000 genomes];0.83[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs39811	0.81[AMR][1000 genomes];0.95[ASN][1000 genomes]
rs599698	0.92[AMR][1000 genomes];0.81[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs651393	0.88[AMR][1000 genomes];0.98[ASN][1000 genomes]
rs657796	1.00[AFR][1000 genomes];0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs658771	0.90[AMR][1000 genomes];0.98[ASN][1000 genomes]
rs664248	0.88[AMR][1000 genomes];0.97[ASN][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	esv2754787	chr5:51688543-52193243	Enhancers Active TSS Genic enhancers Weak transcription Flanking Active TSS Strong transcription Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	28 gene(s)	inside rSNPs	diseases
2	nsv462187	chr5:51758804-52333420	Enhancers Weak transcription Strong transcription Flanking Active TSS Bivalent/Poised TSS Active TSS Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	43 gene(s)	inside rSNPs	diseases
3	nsv598163	chr5:51758804-52333420	Strong transcription Weak transcription Enhancers Active TSS Genic enhancers Flanking Active TSS Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	43 gene(s)	inside rSNPs	diseases
4	nsv471013	chr5:51779197-52339114	Weak transcription Enhancers Flanking Active TSS Active TSS Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer Strong transcription Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	43 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:46 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:51992800-52005200	Weak transcription	Fetal Kidney	kidney
2	chr5:51998600-52008800	Enhancers	Primary T cells from cord blood	blood
3	chr5:51999600-52007000	Weak transcription	Psoas Muscle	Psoas
4	chr5:52000800-52009000	Enhancers	Dnd41	blood
5	chr5:52001200-52006600	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
6	chr5:52001600-52005400	Enhancers	HepG2	liver
7	chr5:52001800-52005400	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
8	chr5:52002000-52005000	Weak transcription	NHEK	skin
9	chr5:52002200-52005000	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
10	chr5:52002200-52007600	Enhancers	Fetal Adrenal Gland	Adrenal Gland
11	chr5:52002400-52005000	Weak transcription	HSMM	muscle
12	chr5:52002400-52008200	Enhancers	Small Intestine	intestine
13	chr5:52002600-52005000	Weak transcription	Primary T killer memory cells from peripheral blood	blood
14	chr5:52002600-52005000	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
15	chr5:52002600-52005000	Weak transcription	HSMMtube	muscle
16	chr5:52002600-52005600	Weak transcription	Left Ventricle	heart
17	chr5:52002800-52005000	Weak transcription	Primary T helper cells fromperipheralblood	blood
18	chr5:52002800-52005200	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
19	chr5:52003000-52005400	Weak transcription	Primary T cells fromperipheralblood	blood
20	chr5:52003000-52005400	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
21	chr5:52003000-52005400	Weak transcription	Fetal Thymus	thymus
22	chr5:52003000-52005600	Weak transcription	Fetal Muscle Leg	muscle
23	chr5:52003000-52007800	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
24	chr5:52003800-52005400	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
25	chr5:52003800-52005800	Enhancers	Duodenum Mucosa	Duodenum
26	chr5:52003800-52006200	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
27	chr5:52003800-52007200	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
28	chr5:52004000-52005600	Enhancers	NH-A	brain
29	chr5:52004000-52005800	Weak transcription	Rectal Mucosa Donor 31	rectum
30	chr5:52004000-52006400	Weak transcription	Spleen	Spleen
31	chr5:52004000-52007600	Enhancers	Muscle Satellite Cultured Cells	--
32	chr5:52004000-52007600	Enhancers	Osteobl	bone
33	chr5:52004200-52005200	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
34	chr5:52004200-52005800	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
35	chr5:52004200-52005800	Enhancers	HUVEC	blood vessel
36	chr5:52004200-52006400	Enhancers	Primary T helper naive cells from peripheral blood	blood
37	chr5:52004200-52007400	Enhancers	NHLF	lung
38	chr5:52004400-52006000	Enhancers	Primary hematopoietic stem cells	blood
39	chr5:52004400-52006000	Enhancers	Primary T helper cells PMA-I stimulated	--
40	chr5:52004400-52006200	Enhancers	Primary T helper 17 cells PMA-I stimulated	--
41	chr5:52004400-52007000	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
42	chr5:52004400-52007200	Enhancers	Primary hematopoietic stem cells short term culture	blood
43	chr5:52004400-52007400	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
44	chr5:52004600-52005000	Weak transcription	Pancreatic Islets	Pancreatic Islet
45	chr5:52004600-52007400	Enhancers	NHDF-Ad	bronchial
46	chr5:52004800-52005800	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links