Variant report

Variant	rs256417
Chromosome Location	chr5:14371180-14371181
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr5:14370789..14372438-chr5:14374024..14376617,2	MCF-7	breast:

Extended variants
information (count: 36 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:29)

rs_ID	r²[population]
rs154152	0.90[AMR][1000 genomes];0.96[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs154159	0.96[ASN][1000 genomes]
rs154161	0.93[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1664507	0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs247134	0.88[EUR][1000 genomes]
rs247139	0.90[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs247140	0.90[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs247142	0.95[CEU][hapmap];0.85[JPT][hapmap];0.95[TSI][hapmap];0.88[EUR][1000 genomes]
rs247143	0.90[EUR][1000 genomes]
rs247144	0.88[EUR][1000 genomes]
rs256416	0.88[ASN][1000 genomes]
rs256423	0.91[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs30623	0.85[JPT][hapmap]
rs30624	0.85[JPT][hapmap]
rs30769	0.87[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs30770	0.87[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs30771	0.87[AFR][1000 genomes];0.87[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs30782	0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs30783	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs30784	1.00[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.93[MEX][hapmap];0.95[MKK][hapmap];1.00[TSI][hapmap];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs30792	1.00[ASW][hapmap];0.90[CEU][hapmap];1.00[CHB][hapmap];0.83[JPT][hapmap];0.87[LWK][hapmap];0.86[MEX][hapmap];0.86[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.87[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs39857	0.95[CEU][hapmap];0.81[EUR][1000 genomes]
rs39866	0.98[ASN][1000 genomes]
rs409214	0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs415341	0.87[AMR][1000 genomes];0.95[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs42259	0.95[CEU][hapmap];1.00[CHB][hapmap];0.83[JPT][hapmap];0.86[MEX][hapmap];1.00[TSI][hapmap];0.87[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs42407	0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs42551	0.95[CEU][hapmap];0.89[TSI][hapmap];0.81[EUR][1000 genomes]
rs43171	0.81[CHD][hapmap]

Variant overlapped rSNPs/rCNVs (count:7 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv948355	chr5:14160447-14395478	Weak transcription Enhancers Genic enhancers Strong transcription Flanking Active TSS ZNF genes & repeats Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region	4 gene(s)	inside rSNPs	diseases
2	nsv1026914	chr5:14237782-14751588	Weak transcription Transcr. at gene 5' and 3' Strong transcription Flanking Active TSS Enhancers Bivalent/Poised TSS Genic enhancers ZNF genes & repeats Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	37 gene(s)	inside rSNPs	diseases
3	nsv830210	chr5:14255039-14431552	Weak transcription Strong transcription Enhancers Genic enhancers Flanking Active TSS ZNF genes & repeats Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
4	esv3470347	chr5:14370407-14372176	Strong transcription Weak transcription Enhancers Genic enhancers	Chromatin interactive region	n/a	inside rSNPs	diseases
5	nsv823010	chr5:14370475-14371595	Strong transcription Weak transcription Genic enhancers Enhancers	Chromatin interactive region	n/a	inside rSNPs	diseases
6	esv3470346	chr5:14370511-14371987	Strong transcription Weak transcription Genic enhancers Enhancers	Chromatin interactive region	n/a	inside rSNPs	diseases
7	esv3470348	chr5:14370511-14371987	Strong transcription Weak transcription Enhancers Genic enhancers	Chromatin interactive region	n/a	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs256417	LOC285696	cis	parietal	SCAN
rs256417	MYO10	cis	cerebellum	SCAN
rs256417	FAM105B	cis	cerebellum	SCAN

Chromatin state (count:112 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:14350400-14373800	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
2	chr5:14351600-14399400	Weak transcription	Primary neutrophils fromperipheralblood	blood
3	chr5:14353600-14385200	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
4	chr5:14353600-14398800	Strong transcription	Rectal Mucosa Donor 29	rectum
5	chr5:14354400-14374800	Strong transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
6	chr5:14354600-14402400	Strong transcription	Liver	Liver
7	chr5:14355000-14392400	Strong transcription	HSMMtube	muscle
8	chr5:14355000-14398800	Strong transcription	Rectal Mucosa Donor 31	rectum
9	chr5:14355600-14375000	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
10	chr5:14356400-14373800	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
11	chr5:14356800-14376000	Strong transcription	HepG2	liver
12	chr5:14357000-14371200	Strong transcription	Sigmoid Colon	Sigmoid Colon
13	chr5:14357000-14374000	Strong transcription	Breast Myoepithelial Primary Cells	Breast
14	chr5:14357000-14376400	Strong transcription	NHLF	lung
15	chr5:14357000-14376600	Strong transcription	Duodenum Mucosa	Duodenum
16	chr5:14357600-14422000	Weak transcription	Stomach Mucosa	stomach
17	chr5:14357800-14385000	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
18	chr5:14357800-14389800	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
19	chr5:14358000-14373800	Strong transcription	Placenta Amnion	Placenta Amnion
20	chr5:14358000-14377000	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
21	chr5:14358000-14385800	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
22	chr5:14358000-14389800	Strong transcription	Adipose Nuclei	Adipose
23	chr5:14358200-14375800	Strong transcription	Stomach Smooth Muscle	stomach
24	chr5:14358200-14391600	Strong transcription	Primary B cells from cord blood	blood
25	chr5:14358400-14371200	Strong transcription	Fetal Brain Female	brain
26	chr5:14358400-14374200	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
27	chr5:14358400-14374600	Strong transcription	Fetal Stomach	stomach
28	chr5:14358400-14385600	Strong transcription	Fetal Intestine Large	intestine
29	chr5:14358400-14392000	Strong transcription	Fetal Muscle Leg	muscle
30	chr5:14358600-14373600	Strong transcription	HUES48 Cell Line	embryonic stem cell
31	chr5:14358600-14374000	Strong transcription	Cortex derived primary cultured neurospheres	brain
32	chr5:14358600-14392600	Strong transcription	Duodenum Smooth Muscle	Duodenum
33	chr5:14358800-14373200	Strong transcription	NHDF-Ad	bronchial
34	chr5:14358800-14375600	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
35	chr5:14360000-14373800	Strong transcription	Foreskin Fibroblast Primary Cells skin02	Skin
36	chr5:14360000-14398400	Strong transcription	Fetal Muscle Trunk	muscle
37	chr5:14363400-14373800	Strong transcription	H1 Cell Line	embryonic stem cell
38	chr5:14363600-14374800	Strong transcription	Ganglion Eminence derived primary cultured neurospheres	brain
39	chr5:14363600-14386000	Strong transcription	Skeletal Muscle Female	skeletal muscle
40	chr5:14363600-14396000	Strong transcription	Foreskin Fibroblast Primary Cells skin01	Skin
41	chr5:14363800-14371400	Strong transcription	Brain Hippocampus Middle	brain
42	chr5:14363800-14373800	Strong transcription	HUES6 Cell Line	embryonic stem cell
43	chr5:14363800-14373800	Strong transcription	Ovary	ovary
44	chr5:14363800-14374600	Strong transcription	Rectal Smooth Muscle	rectum
45	chr5:14363800-14380000	Strong transcription	Placenta	Placenta
46	chr5:14363800-14380400	Strong transcription	Hela-S3	cervix
47	chr5:14363800-14383200	Strong transcription	Colonic Mucosa	Colon
48	chr5:14363800-14383800	Strong transcription	HUVEC	blood vessel
49	chr5:14363800-14385600	Strong transcription	A549	lung
50	chr5:14363800-14430600	Strong transcription	Primary monocytes fromperipheralblood	blood

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links