Variant report

Variant	rs4509570
Chromosome Location	chr1:154436384-154436385
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr1:154425985..154428453-chr1:154436104..154438755,2	MCF-7	breast:
2	chr1:154423682..154425869-chr1:154434875..154437152,2	MCF-7	breast:
3	chr1:154435097..154437712-chr1:154439386..154441987,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000160712	Chromatin interaction

Extended variants
information (count: 22 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:19)

rs_ID	r²[population]
rs10752641	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10908839	0.84[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2229238	0.86[CHB][hapmap];1.00[JPT][hapmap];0.95[ASN][1000 genomes]
rs35699331	0.96[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4072391	1.00[JPT][hapmap];0.91[ASN][1000 genomes]
rs4240872	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4291493	0.81[AFR][1000 genomes];0.82[AMR][1000 genomes]
rs4341355	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.99[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4379670	0.86[ASN][1000 genomes]
rs55668699	0.84[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs6427672	0.97[AFR][1000 genomes];0.90[AMR][1000 genomes];0.94[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs6687597	0.93[AFR][1000 genomes];0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6698040	0.96[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7514452	0.86[CHB][hapmap];1.00[JPT][hapmap];0.95[ASN][1000 genomes]
rs7537291	0.95[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7537316	0.96[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7546068	0.95[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7546552	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7546555	0.95[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][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	nsv948413	chr1:153974621-154797272	Enhancers Weak transcription Strong transcription Flanking Active TSS Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3' Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	132 gene(s)	inside rSNPs	diseases
2	nsv1000402	chr1:153991106-154527053	Strong transcription Flanking Active TSS Enhancers Genic enhancers Flanking Bivalent TSS/Enh Weak transcription Transcr. at gene 5' and 3' Active TSS Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	106 gene(s)	inside rSNPs	diseases
3	nsv521887	chr1:154236570-154684106	Strong transcription Flanking Active TSS Active TSS Weak transcription Enhancers Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	65 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs4509570	TDRD10	cis	lung	GTEx

Chromatin state (count:105 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:154418000-154440000	Weak transcription	Small Intestine	intestine
2	chr1:154422600-154437600	Weak transcription	Pancreas	Pancrea
3	chr1:154425000-154437200	Weak transcription	Fetal Stomach	stomach
4	chr1:154426400-154438000	Weak transcription	Psoas Muscle	Psoas
5	chr1:154426600-154440600	Weak transcription	Brain Angular Gyrus	brain
6	chr1:154426800-154441200	Weak transcription	Brain Substantia Nigra	brain
7	chr1:154426800-154442200	Weak transcription	HepG2	liver
8	chr1:154426800-154450000	Weak transcription	Fetal Intestine Small	intestine
9	chr1:154427800-154464800	Weak transcription	Ovary	ovary
10	chr1:154428600-154437600	Weak transcription	Gastric	stomach
11	chr1:154429800-154446200	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
12	chr1:154430400-154438800	Weak transcription	Primary B cells from cord blood	blood
13	chr1:154431000-154437400	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
14	chr1:154431200-154437600	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
15	chr1:154431600-154441400	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
16	chr1:154432000-154437400	Weak transcription	Left Ventricle	heart
17	chr1:154432000-154437800	Enhancers	Primary T helper naive cells fromperipheralblood	blood
18	chr1:154432000-154442000	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
19	chr1:154432800-154437400	Enhancers	Primary T cells fromperipheralblood	blood
20	chr1:154434200-154436600	Genic enhancers	Primary monocytes fromperipheralblood	blood
21	chr1:154434400-154438600	Enhancers	Primary T killer naive cells fromperipheralblood	blood
22	chr1:154434800-154436600	Genic enhancers	Monocytes-CD14+_RO01746	blood
23	chr1:154434800-154439600	Weak transcription	Pancreatic Islets	Pancreatic Islet
24	chr1:154435000-154437600	Enhancers	Placenta	Placenta
25	chr1:154435200-154436600	Genic enhancers	Primary neutrophils fromperipheralblood	blood
26	chr1:154435200-154441000	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
27	chr1:154435400-154436400	Enhancers	HMEC	breast
28	chr1:154435400-154436600	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
29	chr1:154435400-154436600	Enhancers	Muscle Satellite Cultured Cells	--
30	chr1:154435400-154436600	Enhancers	Adipose Nuclei	Adipose
31	chr1:154435600-154436400	Enhancers	A549	lung
32	chr1:154435600-154436400	Enhancers	NHEK	skin
33	chr1:154435600-154436600	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
34	chr1:154435600-154436600	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
35	chr1:154435600-154436600	Enhancers	Dnd41	blood
36	chr1:154435600-154436600	Enhancers	GM12878-XiMat	blood
37	chr1:154435600-154436600	Enhancers	HUVEC	blood vessel
38	chr1:154435600-154436600	Enhancers	K562	blood
39	chr1:154435600-154436600	Enhancers	NHDF-Ad	bronchial
40	chr1:154435600-154436800	Enhancers	Cortex derived primary cultured neurospheres	brain
41	chr1:154435600-154437800	Enhancers	Stomach Mucosa	stomach
42	chr1:154435600-154440000	Enhancers	Primary hematopoietic stem cells	blood
43	chr1:154435600-154441400	Enhancers	Fetal Thymus	thymus
44	chr1:154435800-154436400	Enhancers	iPS-18 Cell Line	embryonic stem cell
45	chr1:154435800-154436400	Enhancers	iPS-20b Cell Line	embryonic stem cell
46	chr1:154435800-154436400	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
47	chr1:154435800-154436400	Genic enhancers	Liver	Liver
48	chr1:154435800-154436400	Enhancers	Brain Hippocampus Middle	brain
49	chr1:154435800-154436400	Enhancers	Colon Smooth Muscle	Colon
50	chr1:154435800-154436400	Genic enhancers	Rectal Smooth Muscle	rectum

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