Variant report

Variant	rs4774222
Chromosome Location	chr15:56030756-56030757
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	chr15:56013890..56016353-chr15:56030511..56032311,2	MCF-7	breast:

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-NEDD4-2	chr15:56030403-56030857	NONHSAT044007

Extended variants
information (count: 58 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:49)

rs_ID	r²[population]
rs1011061	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.92[MEX][hapmap];1.00[TSI][hapmap];0.87[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10152116	0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10152830	0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10851590	0.89[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11071203	0.95[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11071204	0.93[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs11632579	0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs11632762	0.90[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs11639086	0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11852746	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs11853533	0.93[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11855737	0.81[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs11857254	1.00[CHB][hapmap];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11857271	0.95[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12324293	1.00[YRI][hapmap]
rs12438394	1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12439011	0.89[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12440103	0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12442165	0.89[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12899647	1.00[ASN][1000 genomes]
rs12899976	1.00[ASW][hapmap];0.96[CEU][hapmap];1.00[CHB][hapmap];0.92[GIH][hapmap];1.00[JPT][hapmap];0.87[MEX][hapmap];1.00[TSI][hapmap];0.86[AMR][1000 genomes];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12901963	1.00[ASN][1000 genomes]
rs12903239	1.00[ASN][1000 genomes]
rs12905693	0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12906885	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12907557	0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12907772	0.95[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12907892	1.00[ASN][1000 genomes]
rs12908232	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[AMR][1000 genomes];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12908813	0.89[AMR][1000 genomes];0.84[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12909497	1.00[CHB][hapmap]
rs12910180	0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12911682	0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12912118	0.90[ASN][1000 genomes]
rs12914863	0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12915092	0.95[AMR][1000 genomes];0.94[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs12915423	0.95[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1550326	1.00[CHB][hapmap]
rs34303822	1.00[ASN][1000 genomes]
rs3985768	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4412917	1.00[ASN][1000 genomes]
rs491014	1.00[CHB][hapmap];1.00[CHD][hapmap]
rs530798	1.00[CHB][hapmap];1.00[CHD][hapmap]
rs55874929	0.89[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs66519039	0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs8028880	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs8036481	0.84[ASW][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[TSI][hapmap]
rs934886	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs9920546	1.00[CHB][hapmap];1.00[JPT][hapmap]

Variant overlapped rSNPs/rCNVs (count:9 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv917323	chr15:55290499-56041334	Genic enhancers Active TSS ZNF genes & repeats Weak transcription Strong transcription Enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	57 gene(s)	inside rSNPs	diseases
2	nsv1043789	chr15:55400872-56092454	Weak transcription Enhancers Genic enhancers Strong transcription Flanking Bivalent TSS/Enh Active TSS Bivalent Enhancer Bivalent/Poised TSS Flanking Active TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	55 gene(s)	inside rSNPs	diseases
3	nsv948522	chr15:55639867-56032099	Weak transcription Strong transcription Flanking Active TSS Genic enhancers Enhancers Active TSS Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	31 gene(s)	inside rSNPs	diseases
4	nsv457157	chr15:55722213-56255774	Flanking Active TSS Enhancers Active TSS Strong transcription Weak transcription Genic enhancers Bivalent Enhancer 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	22 gene(s)	inside rSNPs	diseases
5	nsv569539	chr15:55722213-56255774	Enhancers Weak transcription Genic enhancers Flanking Active TSS Strong transcription Active TSS Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	22 gene(s)	inside rSNPs	diseases
6	nsv1049774	chr15:55759573-56044600	Weak transcription Strong transcription Active TSS Bivalent/Poised TSS Enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	14 gene(s)	inside rSNPs	diseases
7	nsv833017	chr15:55965957-56157912	Weak transcription Genic enhancers Strong transcription Bivalent Enhancer Enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Active TSS Flanking Active TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	8 gene(s)	inside rSNPs	diseases
8	esv3366380	chr15:56003224-56141650	Weak transcription Bivalent Enhancer Enhancers Flanking Bivalent TSS/Enh Active TSS Strong transcription Bivalent/Poised TSS Flanking Active TSS ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	7 gene(s)	inside rSNPs	diseases
9	nsv1052495	chr15:56013617-56102164	Weak transcription Enhancers Flanking Bivalent TSS/Enh Active TSS Flanking Active TSS Bivalent Enhancer Bivalent/Poised TSS Strong transcription Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs4774222	MYO5C	cis	parietal	SCAN

Chromatin state (count:33 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:56017800-56033400	Weak transcription	Ovary	ovary
2	chr15:56024400-56030800	Weak transcription	Psoas Muscle	Psoas
3	chr15:56025000-56033600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
4	chr15:56026400-56030800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
5	chr15:56027800-56033000	Weak transcription	Cortex derived primary cultured neurospheres	brain
6	chr15:56028400-56031600	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
7	chr15:56028600-56031000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
8	chr15:56028800-56031800	Enhancers	HUVEC	blood vessel
9	chr15:56028800-56033600	Weak transcription	HSMM	muscle
10	chr15:56029000-56031000	Enhancers	Hela-S3	cervix
11	chr15:56029200-56031000	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
12	chr15:56029600-56031000	Bivalent Enhancer	HUES64 Cell Line	embryonic stem cell
13	chr15:56029600-56031200	Enhancers	Fetal Stomach	stomach
14	chr15:56029800-56032200	Weak transcription	Primary hematopoietic stem cells	blood
15	chr15:56029800-56033200	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
16	chr15:56030000-56031200	Weak transcription	Placenta Amnion	Placenta Amnion
17	chr15:56030000-56031600	Weak transcription	HepG2	liver
18	chr15:56030000-56032600	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
19	chr15:56030000-56032600	Weak transcription	Stomach Smooth Muscle	stomach
20	chr15:56030000-56032600	Weak transcription	A549	lung
21	chr15:56030000-56033400	Weak transcription	Breast Myoepithelial Primary Cells	Breast
22	chr15:56030000-56033600	Weak transcription	Placenta	Placenta
23	chr15:56030200-56030800	Active TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
24	chr15:56030200-56032600	Weak transcription	Fetal Intestine Large	intestine
25	chr15:56030200-56032800	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
26	chr15:56030200-56032800	Weak transcription	Fetal Lung	lung
27	chr15:56030400-56034600	Transcr. at gene 5' and 3'	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
28	chr15:56030600-56030800	Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
29	chr15:56030600-56030800	Bivalent Enhancer	iPS-18 Cell Line	embryonic stem cell
30	chr15:56030600-56030800	Enhancers	Fetal Kidney	kidney
31	chr15:56030600-56031400	Flanking Active TSS	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
32	chr15:56030600-56033400	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
33	chr15:56030600-56034600	Transcr. at gene 5' and 3'	H9 Derived Neuron Cultured Cells	ES cell derived

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