Variant report

Variant	rs10068330
Chromosome Location	chr5:178299931-178299932
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr5:178299499..178302283-chr5:178303072..178304596,2	MCF-7	breast:

Extended variants
information (count: 28 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:25)

rs_ID	r²[population]
rs10035741	0.91[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs10037614	0.89[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs10039203	0.91[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs10039702	0.89[AMR][1000 genomes];0.92[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs10041805	0.91[AFR][1000 genomes];0.91[AMR][1000 genomes];0.92[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs10059618	0.83[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs10059708	0.96[AFR][1000 genomes];0.96[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10068408	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10074505	0.96[AFR][1000 genomes];0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs10223205	0.89[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs12657785	0.96[AFR][1000 genomes];0.98[AMR][1000 genomes];0.94[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs1963050	0.91[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs2411991	0.89[AMR][1000 genomes];0.86[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs61747996	0.91[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs6874421	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6877197	0.86[AFR][1000 genomes];0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6896077	0.95[ASN][1000 genomes]
rs72814700	0.96[AFR][1000 genomes];0.96[AMR][1000 genomes];0.94[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs72814702	0.96[AFR][1000 genomes];0.96[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72816603	0.96[AFR][1000 genomes];0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs72816608	0.91[AMR][1000 genomes];0.92[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs72816609	0.83[AMR][1000 genomes];0.82[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs72816613	0.91[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs72816625	0.83[AMR][1000 genomes]
rs72816629	0.91[AMR][1000 genomes];0.89[EUR][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	nsv883218	chr5:178219855-178349391	Strong transcription Weak transcription ZNF genes & repeats Enhancers Flanking Active TSS Active TSS Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases
2	nsv462574	chr5:178269682-178313078	Genic enhancers Strong transcription ZNF genes & repeats Weak transcription Flanking Active TSS Active TSS Transcr. at gene 5' and 3' Enhancers Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
3	nsv600463	chr5:178269682-178313078	Active TSS ZNF genes & repeats Genic enhancers Weak transcription Strong transcription Flanking Active TSS Transcr. at gene 5' and 3' Enhancers Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs10068330	ZNF454	cis	Skin Sun Exposed Lower leg	GTEx

Chromatin state (count:117 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:178287600-178302400	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
2	chr5:178288200-178317400	ZNF genes & repeats	Primary hematopoietic stem cells short term culture	blood
3	chr5:178288800-178300000	Strong transcription	Fetal Lung	lung
4	chr5:178288800-178302200	Strong transcription	Skeletal Muscle Male	skeletal muscle
5	chr5:178288800-178317400	ZNF genes & repeats	Primary hematopoietic stem cells G-CSF-mobilized Male	--
6	chr5:178289000-178301000	Strong transcription	Fetal Muscle Leg	muscle
7	chr5:178289000-178301600	Weak transcription	Stomach Mucosa	stomach
8	chr5:178289400-178302200	Strong transcription	Brain Anterior Caudate	brain
9	chr5:178289600-178317400	ZNF genes & repeats	Primary hematopoietic stem cells G-CSF-mobilized Female	--
10	chr5:178289800-178300200	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
11	chr5:178289800-178300200	Strong transcription	Muscle Satellite Cultured Cells	--
12	chr5:178290000-178302200	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
13	chr5:178290600-178301200	Strong transcription	Brain Cingulate Gyrus	brain
14	chr5:178290800-178300200	Strong transcription	Left Ventricle	heart
15	chr5:178291000-178300000	Strong transcription	Foreskin Fibroblast Primary Cells skin02	Skin
16	chr5:178291200-178317400	ZNF genes & repeats	Liver	Liver
17	chr5:178291400-178300200	Strong transcription	Dnd41	blood
18	chr5:178292000-178303000	Strong transcription	iPS-20b Cell Line	embryonic stem cell
19	chr5:178292200-178302200	Strong transcription	Primary T helper 17 cells PMA-I stimulated	--
20	chr5:178292600-178300200	Strong transcription	Primary B cells from peripheral blood	blood
21	chr5:178292600-178300200	Strong transcription	Brain Inferior Temporal Lobe	brain
22	chr5:178292600-178300600	Strong transcription	Rectal Mucosa Donor 31	rectum
23	chr5:178292600-178301200	Strong transcription	Osteobl	bone
24	chr5:178292600-178305000	ZNF genes & repeats	H9 Derived Neuron Cultured Cells	ES cell derived
25	chr5:178292600-178305200	Strong transcription	Stomach Smooth Muscle	stomach
26	chr5:178292800-178301400	Strong transcription	Rectal Smooth Muscle	rectum
27	chr5:178293000-178300000	Strong transcription	H1 Cell Line	embryonic stem cell
28	chr5:178293400-178301000	Weak transcription	iPS-15b Cell Line	embryonic stem cell
29	chr5:178294200-178301400	Weak transcription	Hela-S3	cervix
30	chr5:178294800-178300400	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
31	chr5:178295000-178300400	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
32	chr5:178295800-178300000	Strong transcription	NHDF-Ad	bronchial
33	chr5:178296000-178300000	ZNF genes & repeats	Foreskin Melanocyte Primary Cells skin03	Skin
34	chr5:178296000-178301200	Strong transcription	Brain Dorsolateral Prefrontal Cortex	brain
35	chr5:178296000-178305000	ZNF genes & repeats	A549	lung
36	chr5:178296000-178305200	ZNF genes & repeats	Primary B cells from cord blood	blood
37	chr5:178296000-178305400	ZNF genes & repeats	Primary neutrophils fromperipheralblood	blood
38	chr5:178296000-178319200	ZNF genes & repeats	Primary hematopoietic stem cells	blood
39	chr5:178296200-178315600	ZNF genes & repeats	Breast Myoepithelial Primary Cells	Breast
40	chr5:178296200-178319200	ZNF genes & repeats	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
41	chr5:178296400-178302400	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
42	chr5:178296400-178311200	ZNF genes & repeats	Pancreatic Islets	Pancreatic Islet
43	chr5:178296400-178317600	ZNF genes & repeats	Monocytes-CD14+_RO01746	blood
44	chr5:178297000-178300600	Weak transcription	Colon Smooth Muscle	Colon
45	chr5:178297000-178301200	Strong transcription	Ovary	ovary
46	chr5:178297200-178315800	ZNF genes & repeats	Primary T helper cells fromperipheralblood	blood
47	chr5:178297400-178300200	Strong transcription	K562	blood
48	chr5:178297400-178315600	ZNF genes & repeats	Primary T regulatory cells fromperipheralblood	blood
49	chr5:178297400-178317400	ZNF genes & repeats	IMR90 fetal lung fibroblasts Cell Line	lung
50	chr5:178297400-178317400	ZNF genes & repeats	Primary T helper naive cells fromperipheralblood	blood

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links