Variant report

Variant	rs56279820
Chromosome Location	chr5:37672418-37672419
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 61 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:51)

rs_ID	r²[population]
rs10071815	0.86[EUR][1000 genomes]
rs13188890	0.86[EUR][1000 genomes]
rs1549251	0.86[EUR][1000 genomes]
rs1549252	0.86[EUR][1000 genomes]
rs28377651	0.86[EUR][1000 genomes]
rs28874633	0.86[EUR][1000 genomes]
rs2910798	0.86[EUR][1000 genomes]
rs2972941	0.86[EUR][1000 genomes]
rs2973074	0.84[EUR][1000 genomes]
rs41270339	1.00[AFR][1000 genomes];0.91[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs55633811	1.00[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs55654436	1.00[AFR][1000 genomes];0.82[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs56003317	0.87[EUR][1000 genomes]
rs59898254	0.86[EUR][1000 genomes]
rs6451341	0.86[EUR][1000 genomes]
rs67885658	1.00[EUR][1000 genomes]
rs72740972	1.00[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs72740973	1.00[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs72740974	0.84[AMR][1000 genomes]
rs72740975	1.00[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs72740978	0.84[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs72740981	1.00[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs72740983	1.00[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs72740989	0.84[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs72740990	0.84[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs72740991	0.84[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs72743159	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs72743164	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs72743166	0.88[EUR][1000 genomes]
rs72743167	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs72743169	1.00[EUR][1000 genomes]
rs72743170	1.00[AFR][1000 genomes];0.91[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs72743176	1.00[AFR][1000 genomes];0.91[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs72743180	1.00[AFR][1000 genomes];0.91[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs72743185	1.00[AFR][1000 genomes];0.91[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs72743187	1.00[AFR][1000 genomes];0.82[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs72743190	1.00[AFR][1000 genomes];0.82[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs72743192	0.82[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs72743193	0.82[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs72743196	0.82[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs72743200	0.82[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs72743201	0.82[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs72743202	0.82[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs72745106	0.82[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs72745108	0.82[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs7448783	0.86[EUR][1000 genomes]
rs7705963	0.86[EUR][1000 genomes]
rs7709969	0.84[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs7722257	0.86[EUR][1000 genomes]
rs7737640	0.86[EUR][1000 genomes]
rs9283746	0.84[AMR][1000 genomes];0.94[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:10 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1026554	chr5:37112133-37734859	Strong transcription Weak transcription Active TSS Flanking Active TSS Enhancers Bivalent/Poised TSS ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	45 gene(s)	inside rSNPs	diseases
2	nsv537726	chr5:37112133-37734859	Weak transcription Strong transcription Enhancers Active TSS Genic enhancers Flanking Active TSS Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	45 gene(s)	inside rSNPs	diseases
3	nsv949716	chr5:37179341-37967352	Weak transcription Strong transcription Flanking Active TSS Enhancers Bivalent Enhancer Active TSS ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	58 gene(s)	inside rSNPs	diseases
4	nsv1023871	chr5:37330018-37804744	Enhancers Strong transcription Weak transcription Active TSS ZNF genes & repeats Genic enhancers Flanking Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	23 gene(s)	inside rSNPs	diseases
5	nsv537729	chr5:37330018-37804744	Weak transcription Flanking Active TSS Strong transcription Genic enhancers Enhancers Active TSS ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	23 gene(s)	inside rSNPs	diseases
6	nsv432744	chr5:37374124-37743077	ZNF genes & repeats Strong transcription Weak transcription Enhancers Active TSS Flanking Active TSS Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases
7	nsv597846	chr5:37430215-37813591	Weak transcription Strong transcription Enhancers ZNF genes & repeats Genic enhancers Flanking Active TSS Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
8	nsv880890	chr5:37443079-37681646	Weak transcription Enhancers Flanking Active TSS ZNF genes & repeats Strong transcription Genic enhancers Bivalent Enhancer Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
9	nsv1030250	chr5:37478163-37734859	ZNF genes & repeats Enhancers Weak transcription Strong transcription Active TSS Genic enhancers Flanking Active TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
10	nsv881383	chr5:37485316-37773877	Strong transcription Enhancers Weak transcription ZNF genes & repeats Flanking Active TSS Bivalent Enhancer Active TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:39 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:37669200-37672800	Weak transcription	Rectal Smooth Muscle	rectum
2	chr5:37669600-37680000	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
3	chr5:37669800-37672800	Weak transcription	NHDF-Ad	bronchial
4	chr5:37671400-37672800	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
5	chr5:37671400-37673000	Enhancers	Primary T helper cells fromperipheralblood	blood
6	chr5:37671400-37673600	Enhancers	Primary hematopoietic stem cells short term culture	blood
7	chr5:37671800-37672600	Enhancers	Primary T helper 17 cells PMA-I stimulated	--
8	chr5:37671800-37672800	Enhancers	Ovary	ovary
9	chr5:37671800-37673000	Enhancers	Primary neutrophils fromperipheralblood	blood
10	chr5:37671800-37673000	Enhancers	Primary B cells from peripheral blood	blood
11	chr5:37671800-37673000	Enhancers	Fetal Adrenal Gland	Adrenal Gland
12	chr5:37671800-37673000	Enhancers	Fetal Heart	heart
13	chr5:37671800-37673000	Enhancers	K562	blood
14	chr5:37671800-37673000	Enhancers	Monocytes-CD14+_RO01746	blood
15	chr5:37671800-37673400	Enhancers	Dnd41	blood
16	chr5:37671800-37673600	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
17	chr5:37672000-37673000	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
18	chr5:37672000-37673200	Enhancers	Psoas Muscle	Psoas
19	chr5:37672200-37672600	Weak transcription	NH-A	brain
20	chr5:37672200-37673000	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
21	chr5:37672200-37673000	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
22	chr5:37672200-37673000	Enhancers	Primary monocytes fromperipheralblood	blood
23	chr5:37672200-37673000	Enhancers	Primary T killer memory cells from peripheral blood	blood
24	chr5:37672200-37673000	Enhancers	Lung	lung
25	chr5:37672200-37673000	Enhancers	Right Ventricle	heart
26	chr5:37672200-37673000	Enhancers	Skeletal Muscle Male	skeletal muscle
27	chr5:37672200-37673000	Enhancers	Spleen	Spleen
28	chr5:37672200-37673400	Enhancers	Skeletal Muscle Female	skeletal muscle
29	chr5:37672200-37674000	Enhancers	Primary T cells fromperipheralblood	blood
30	chr5:37672400-37673000	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
31	chr5:37672400-37673000	Enhancers	Primary B cells from cord blood	blood
32	chr5:37672400-37673000	Enhancers	Primary T cells from cord blood	blood
33	chr5:37672400-37673000	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
34	chr5:37672400-37673000	Enhancers	Adipose Nuclei	Adipose
35	chr5:37672400-37673000	Enhancers	Placenta	Placenta
36	chr5:37672400-37673000	Enhancers	Left Ventricle	heart
37	chr5:37672400-37673000	Enhancers	GM12878-XiMat	blood
38	chr5:37672400-37674000	Enhancers	Primary hematopoietic stem cells	blood
39	chr5:37672400-37674000	Enhancers	Primary Natural Killer cells fromperipheralblood	blood

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links