Variant report

Variant	rs10065444
Chromosome Location	chr5:60569280-60569281
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	chr5:60457988..60459859-chr5:60568864..60572383,3	MCF-7	breast:
2	chr5:60568345..60570305-chr5:60576207..60578303,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000188725	Chromatin interaction

Extended variants
information (count: 35 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:33)

rs_ID	r²[population]
rs10037643	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs10052765	0.94[YRI][hapmap];0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs10062338	0.88[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs10071763	0.96[ASN][1000 genomes]
rs10434526	1.00[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10461467	0.94[CEU][hapmap];0.92[CHB][hapmap];1.00[JPT][hapmap];0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10471510	0.83[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs10939888	0.86[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs10939890	0.84[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs10939892	0.92[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs10939893	0.92[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs12189426	0.86[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12518152	1.00[CEU][hapmap];0.92[CHB][hapmap];1.00[JPT][hapmap];0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12523278	0.86[JPT][hapmap];0.92[ASN][1000 genomes]
rs12696979	0.86[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs12696980	0.86[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs13175564	0.92[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs34439016	1.00[ASN][1000 genomes]
rs35310874	0.91[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4129437	0.81[AMR][1000 genomes];0.82[ASN][1000 genomes]
rs4400074	0.88[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4441832	0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4540126	0.86[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4699974	0.88[AFR][1000 genomes];0.98[AMR][1000 genomes];0.86[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs4699975	0.98[AMR][1000 genomes];0.86[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs6864367	0.98[AMR][1000 genomes];0.86[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs6867268	0.88[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6867417	0.88[AMR][1000 genomes];0.99[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs6885499	0.98[AMR][1000 genomes];0.85[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs6892128	0.88[CEU][hapmap];0.92[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.93[AFR][1000 genomes];0.87[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7448844	0.88[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7737448	1.00[CEU][hapmap];0.92[CHB][hapmap];0.92[JPT][hapmap];0.80[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs9291718	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:2 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1034038	chr5:60375328-60607654	Weak transcription Flanking Active TSS Enhancers ZNF genes & repeats Active TSS Strong transcription Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	31 gene(s)	inside rSNPs	diseases
2	nsv1028884	chr5:60414723-60732779	Bivalent Enhancer Enhancers Weak transcription Strong transcription Flanking Active TSS Flanking Bivalent TSS/Enh Active TSS Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	46 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs10065444	DEPDC1B	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:40 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:60550400-60573400	Weak transcription	Gastric	stomach
2	chr5:60556000-60570200	Weak transcription	HSMM	muscle
3	chr5:60560400-60569400	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
4	chr5:60560800-60571200	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
5	chr5:60561000-60573200	Weak transcription	Brain Hippocampus Middle	brain
6	chr5:60564600-60570800	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
7	chr5:60564600-60575400	Weak transcription	Fetal Intestine Small	intestine
8	chr5:60564600-60576000	Weak transcription	Psoas Muscle	Psoas
9	chr5:60565600-60570600	Weak transcription	HUVEC	blood vessel
10	chr5:60565800-60571000	Weak transcription	Primary B cells from peripheral blood	blood
11	chr5:60565800-60571200	Weak transcription	Primary T helper cells PMA-I stimulated	--
12	chr5:60566000-60571200	Weak transcription	Primary T helper cells fromperipheralblood	blood
13	chr5:60566000-60573200	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
14	chr5:60566400-60573000	Weak transcription	Stomach Mucosa	stomach
15	chr5:60566600-60573800	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
16	chr5:60567000-60571000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
17	chr5:60567000-60571000	Weak transcription	Lung	lung
18	chr5:60567600-60571200	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
19	chr5:60567800-60571000	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
20	chr5:60567800-60577200	Enhancers	Primary monocytes fromperipheralblood	blood
21	chr5:60568200-60573000	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
22	chr5:60568400-60569400	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
23	chr5:60568400-60569600	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
24	chr5:60568400-60569600	Enhancers	HUES6 Cell Line	embryonic stem cell
25	chr5:60568400-60570600	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
26	chr5:60568400-60571000	Weak transcription	NHEK	skin
27	chr5:60568600-60569400	Enhancers	ES-I3 Cell Line	embryonic stem cell
28	chr5:60568600-60569400	Enhancers	ES-WA7 Cell Line	embryonic stem cell
29	chr5:60568600-60569600	Enhancers	iPS-20b Cell Line	embryonic stem cell
30	chr5:60568600-60571200	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
31	chr5:60568800-60569600	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
32	chr5:60568800-60573200	Weak transcription	HSMMtube	muscle
33	chr5:60569000-60569400	Enhancers	Brain Substantia Nigra	brain
34	chr5:60569000-60571000	Enhancers	Primary neutrophils fromperipheralblood	blood
35	chr5:60569000-60571800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
36	chr5:60569000-60572800	Weak transcription	HUES48 Cell Line	embryonic stem cell
37	chr5:60569000-60572800	Weak transcription	iPS-18 Cell Line	embryonic stem cell
38	chr5:60569000-60574000	Enhancers	Primary hematopoietic stem cells short term culture	blood
39	chr5:60569200-60570400	Enhancers	Primary hematopoietic stem cells	blood
40	chr5:60569200-60574600	Flanking Active TSS	Monocytes-CD14+_RO01746	blood

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