Variant report

Variant	rs59841593
Chromosome Location	chr10:5499163-5499164
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr10:5497532..5500030-chr10:5644484..5646584,2	MCF-7	breast:
2	chr10:5497697..5500055-chr10:5587894..5589744,2	K562	blood:
3	chr10:5496908..5513504-chr10:5583876..5597686,82	MCF-7	breast:
4	chr10:4855102..4856671-chr10:5498046..5499803,2	K562	blood:

Extended variants
information (count: 19 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:14)

rs_ID	r²[population]
rs10450530	1.00[AMR][1000 genomes]
rs10450531	1.00[AMR][1000 genomes]
rs4242793	0.84[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs4415657	0.85[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs4880730	1.00[AMR][1000 genomes]
rs56724201	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs56959063	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs58833507	1.00[AMR][1000 genomes]
rs59584726	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs60653996	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs60863214	0.87[AFR][1000 genomes]
rs7904871	1.00[AMR][1000 genomes]
rs7922103	0.81[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs9423432	0.84[AFR][1000 genomes];1.00[AMR][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	nsv534685	chr10:4914018-5853324	Weak transcription Enhancers Flanking Active TSS Strong transcription Bivalent Enhancer Active TSS Genic enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	68 gene(s)	inside rSNPs	diseases
2	nsv932104	chr10:5203626-5641023	Enhancers Weak transcription Flanking Active TSS ZNF genes & repeats Bivalent Enhancer Genic enhancers Active TSS Strong transcription Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	45 gene(s)	inside rSNPs	diseases
3	nsv549886	chr10:5205437-5632060	Strong transcription Weak transcription Flanking Active TSS Active TSS Enhancers Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3' Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	45 gene(s)	inside rSNPs	diseases
4	nsv1054865	chr10:5225305-5638119	Weak transcription Enhancers Genic enhancers Active TSS Strong transcription Flanking Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	45 gene(s)	inside rSNPs	diseases
5	nsv831774	chr10:5463556-5657421	Enhancers Weak transcription Bivalent Enhancer Flanking Active TSS Active TSS Genic enhancers ZNF genes & repeats Strong transcription Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	30 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:123 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr10:5489800-5508400	Weak transcription	Cortex derived primary cultured neurospheres	brain
2	chr10:5490200-5503800	Weak transcription	Primary B cells from cord blood	blood
3	chr10:5490400-5499800	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
4	chr10:5490400-5500200	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
5	chr10:5490600-5507400	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
6	chr10:5492600-5502400	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
7	chr10:5493200-5502200	Strong transcription	Placenta	Placenta
8	chr10:5493400-5501000	Strong transcription	NHDF-Ad	bronchial
9	chr10:5493400-5503400	Strong transcription	NHEK	skin
10	chr10:5493400-5503800	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
11	chr10:5493400-5503800	Weak transcription	Stomach Mucosa	stomach
12	chr10:5493600-5503000	Strong transcription	Osteobl	bone
13	chr10:5493600-5503200	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
14	chr10:5493600-5503800	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
15	chr10:5493800-5501000	Strong transcription	HUVEC	blood vessel
16	chr10:5493800-5501200	Strong transcription	HepG2	liver
17	chr10:5493800-5502800	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
18	chr10:5493800-5502800	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
19	chr10:5493800-5503000	Strong transcription	iPS-18 Cell Line	embryonic stem cell
20	chr10:5493800-5503000	Strong transcription	NH-A	brain
21	chr10:5493800-5503200	Strong transcription	Stomach Smooth Muscle	stomach
22	chr10:5493800-5503400	Strong transcription	HUES48 Cell Line	embryonic stem cell
23	chr10:5493800-5503600	Strong transcription	HUES6 Cell Line	embryonic stem cell
24	chr10:5493800-5503600	Strong transcription	HUES64 Cell Line	embryonic stem cell
25	chr10:5493800-5503800	Strong transcription	iPS-20b Cell Line	embryonic stem cell
26	chr10:5493800-5504600	Strong transcription	A549	lung
27	chr10:5494000-5499200	Strong transcription	HMEC	breast
28	chr10:5494000-5502600	Strong transcription	Duodenum Smooth Muscle	Duodenum
29	chr10:5494000-5502800	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
30	chr10:5494000-5503200	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
31	chr10:5494000-5503200	Strong transcription	Duodenum Mucosa	Duodenum
32	chr10:5494000-5503400	Strong transcription	HSMM	muscle
33	chr10:5494200-5499200	Strong transcription	Primary B cells from peripheral blood	blood
34	chr10:5494200-5499200	Strong transcription	Fetal Stomach	stomach
35	chr10:5494200-5499200	Strong transcription	Ovary	ovary
36	chr10:5494200-5499200	Strong transcription	Skeletal Muscle Female	skeletal muscle
37	chr10:5494200-5500600	Strong transcription	GM12878-XiMat	blood
38	chr10:5494200-5502000	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
39	chr10:5494200-5502600	Strong transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
40	chr10:5494200-5502800	Strong transcription	Primary hematopoietic stem cells short term culture	blood
41	chr10:5494200-5502800	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
42	chr10:5494200-5503000	Strong transcription	H1 Cell Line	embryonic stem cell
43	chr10:5494200-5503000	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
44	chr10:5494200-5503000	Strong transcription	Liver	Liver
45	chr10:5494400-5499200	Strong transcription	Primary neutrophils fromperipheralblood	blood
46	chr10:5494400-5499400	Strong transcription	HSMMtube	muscle
47	chr10:5494400-5499600	Strong transcription	Hela-S3	cervix
48	chr10:5494400-5499800	Strong transcription	Colonic Mucosa	Colon
49	chr10:5494400-5500600	Strong transcription	Primary monocytes fromperipheralblood	blood
50	chr10:5494400-5502800	Strong 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