Variant report

Variant	rs29454
Chromosome Location	chr5:16913578-16913579
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr5:16875713..16877407-chr5:16911491..16914086,2	MCF-7	breast:
2	chr5:16805947..16808433-chr5:16911651..16914280,2	MCF-7	breast:
3	chr5:16903174..16906084-chr5:16912041..16914007,3	MCF-7	breast:
4	chr5:16913129..16917002-chr5:16934060..16938960,5	MCF-7	breast:
5	chr5:16911519..16914596-chr5:16934738..16936991,3	MCF-7	breast:

Variant related genes	Relation type
ENSG00000145555	Chromatin interaction

Extended variants
information (count: 13 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:7)

rs_ID	r²[population]
rs194135	0.90[AMR][1000 genomes];0.91[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs29448	0.95[CEU][hapmap];0.83[GIH][hapmap];1.00[MEX][hapmap];0.88[TSI][hapmap];0.93[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs29449	0.81[AMR][1000 genomes]
rs29450	0.81[AMR][1000 genomes]
rs31454	0.80[CHD][hapmap];0.89[JPT][hapmap];0.94[MEX][hapmap]
rs39896	0.86[LWK][hapmap];0.83[AFR][1000 genomes]
rs40983	0.97[AMR][1000 genomes];0.89[EUR][1000 genomes];0.95[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:6 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1025225	chr5:16714512-17234866	Enhancers Flanking Bivalent TSS/Enh Weak transcription Genic enhancers Strong transcription Active TSS Flanking Active TSS ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	27 gene(s)	inside rSNPs	diseases
2	nsv1015247	chr5:16748966-17133274	Flanking Active TSS Weak transcription Enhancers Bivalent/Poised TSS Bivalent Enhancer Strong transcription Active TSS Genic enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	14 gene(s)	inside rSNPs	diseases
3	esv2762500	chr5:16815489-16952565	Enhancers Bivalent/Poised TSS Weak transcription Flanking Bivalent TSS/Enh Flanking Active TSS Strong transcription Active TSS ZNF genes & repeats Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region	10 gene(s)	inside rSNPs	diseases
4	nsv880277	chr5:16829442-17316288	Weak transcription Enhancers Bivalent/Poised TSS Flanking Active TSS Genic enhancers Strong transcription Flanking Bivalent TSS/Enh Active TSS ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	28 gene(s)	inside rSNPs	diseases
5	esv3485757	chr5:16856475-16966851	Weak transcription Bivalent/Poised TSS Enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Genic enhancers Active TSS Strong transcription Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region	9 gene(s)	inside rSNPs	diseases
6	esv3485758	chr5:16856475-16966851	Weak transcription Enhancers Flanking Active TSS Genic enhancers Strong transcription Bivalent/Poised TSS Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region	9 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs29454	MYO10	cis	multi-tissue	Pritchard

Chromatin state (count:61 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:16902200-16913800	Weak transcription	iPS-15b Cell Line	embryonic stem cell
2	chr5:16902200-16919000	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
3	chr5:16902200-16930000	Weak transcription	HUES48 Cell Line	embryonic stem cell
4	chr5:16904400-16933200	Weak transcription	Fetal Stomach	stomach
5	chr5:16904800-16913600	Weak transcription	Fetal Muscle Trunk	muscle
6	chr5:16906400-16913600	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
7	chr5:16906800-16913600	Weak transcription	Psoas Muscle	Psoas
8	chr5:16907000-16913600	Weak transcription	Spleen	Spleen
9	chr5:16908200-16913800	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
10	chr5:16908800-16913600	Enhancers	Foreskin Melanocyte Primary Cells skin01	Skin
11	chr5:16909400-16914600	Enhancers	Pancreas	Pancrea
12	chr5:16909400-16916400	Enhancers	Ovary	ovary
13	chr5:16909800-16915600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
14	chr5:16910800-16924000	Weak transcription	Small Intestine	intestine
15	chr5:16911600-16914600	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
16	chr5:16911600-16916400	Genic enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
17	chr5:16912200-16913800	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
18	chr5:16912200-16914000	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
19	chr5:16912200-16914200	Enhancers	Fetal Lung	lung
20	chr5:16912200-16914800	Enhancers	Breast Myoepithelial Primary Cells	Breast
21	chr5:16912200-16919800	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
22	chr5:16912400-16913600	Enhancers	Rectal Mucosa Donor 29	rectum
23	chr5:16912400-16913600	Enhancers	HSMM	muscle
24	chr5:16912400-16913600	Enhancers	NHEK	skin
25	chr5:16912400-16913800	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
26	chr5:16912400-16913800	Enhancers	Stomach Smooth Muscle	stomach
27	chr5:16912400-16914000	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
28	chr5:16912400-16914000	Enhancers	NHLF	lung
29	chr5:16912400-16914200	Enhancers	Osteobl	bone
30	chr5:16912400-16914400	Enhancers	Lung	lung
31	chr5:16912400-16914400	Enhancers	Hela-S3	cervix
32	chr5:16912400-16914400	Enhancers	NHDF-Ad	bronchial
33	chr5:16912400-16914600	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
34	chr5:16912400-16914600	Enhancers	Foreskin Fibroblast Primary Cells skin02	Skin
35	chr5:16912400-16914600	Enhancers	Esophagus	oesophagus
36	chr5:16912400-16915400	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
37	chr5:16912600-16913600	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
38	chr5:16912600-16913600	Enhancers	Fetal Intestine Small	intestine
39	chr5:16912600-16914400	Enhancers	Cortex derived primary cultured neurospheres	brain
40	chr5:16912600-16914600	Enhancers	NH-A	brain
41	chr5:16912600-16915600	Enhancers	Stomach Mucosa	stomach
42	chr5:16912800-16913800	Enhancers	Duodenum Mucosa	Duodenum
43	chr5:16912800-16913800	Enhancers	Fetal Brain Male	brain
44	chr5:16912800-16914400	Enhancers	Left Ventricle	heart
45	chr5:16912800-16914600	Flanking Active TSS	HMEC	breast
46	chr5:16912800-16914800	Enhancers	Fetal Intestine Large	intestine
47	chr5:16912800-16915200	Enhancers	HUVEC	blood vessel
48	chr5:16912800-16915600	Enhancers	Fetal Adrenal Gland	Adrenal Gland
49	chr5:16913000-16913600	Enhancers	Fetal Brain Female	brain
50	chr5:16913000-16915400	Enhancers	Fetal Muscle Leg	muscle

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links