Variant report

Variant	rs30770
Chromosome Location	chr5:14378068-14378069
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	chr5:14360819..14363309-chr5:14376690..14379574,2	MCF-7	breast:

Extended variants
information (count: 28 )
Associated
traits (count: 3 )

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

rs_ID	r²[population]
rs154152	0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs154161	0.89[EUR][1000 genomes]
rs1664507	0.91[AMR][1000 genomes];0.96[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs247134	0.84[EUR][1000 genomes]
rs247139	0.86[EUR][1000 genomes]
rs247140	0.86[EUR][1000 genomes]
rs247142	0.90[CEU][hapmap];0.95[TSI][hapmap];1.00[YRI][hapmap];0.84[EUR][1000 genomes]
rs247143	0.86[EUR][1000 genomes]
rs247144	0.84[EUR][1000 genomes]
rs256417	0.87[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs256423	0.87[EUR][1000 genomes]
rs30618	1.00[YRI][hapmap]
rs30769	0.81[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs30771	0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs30782	0.88[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs30783	0.95[CEU][hapmap];1.00[CHB][hapmap];0.83[JPT][hapmap];1.00[YRI][hapmap];0.90[AMR][1000 genomes];0.96[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs30784	0.95[CEU][hapmap];1.00[CHB][hapmap];0.81[CHD][hapmap];0.83[JPT][hapmap];0.93[MEX][hapmap];1.00[TSI][hapmap];0.88[AMR][1000 genomes];0.96[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs30792	0.95[CEU][hapmap];1.00[CHB][hapmap];0.86[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs39857	0.90[CEU][hapmap];1.00[YRI][hapmap]
rs409214	0.88[AMR][1000 genomes];0.96[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs415341	0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs42259	1.00[CEU][hapmap];1.00[CHB][hapmap];0.86[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs42407	0.87[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs42551	0.90[CEU][hapmap];0.89[TSI][hapmap]
rs7380307	1.00[YRI][hapmap]

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	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

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs30770	LOC285696	cis	parietal	SCAN
rs30770	MYO10	cis	cerebellum	SCAN
rs30770	FAM105B	cis	cerebellum	SCAN

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:14351600-14399400	Weak transcription	Primary neutrophils fromperipheralblood	blood
2	chr5:14353600-14385200	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
3	chr5:14353600-14398800	Strong transcription	Rectal Mucosa Donor 29	rectum
4	chr5:14354600-14402400	Strong transcription	Liver	Liver
5	chr5:14355000-14392400	Strong transcription	HSMMtube	muscle
6	chr5:14355000-14398800	Strong transcription	Rectal Mucosa Donor 31	rectum
7	chr5:14357600-14422000	Weak transcription	Stomach Mucosa	stomach
8	chr5:14357800-14385000	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
9	chr5:14357800-14389800	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
10	chr5:14358000-14385800	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
11	chr5:14358000-14389800	Strong transcription	Adipose Nuclei	Adipose
12	chr5:14358200-14391600	Strong transcription	Primary B cells from cord blood	blood
13	chr5:14358400-14385600	Strong transcription	Fetal Intestine Large	intestine
14	chr5:14358400-14392000	Strong transcription	Fetal Muscle Leg	muscle
15	chr5:14358600-14392600	Strong transcription	Duodenum Smooth Muscle	Duodenum
16	chr5:14360000-14398400	Strong transcription	Fetal Muscle Trunk	muscle
17	chr5:14363600-14386000	Strong transcription	Skeletal Muscle Female	skeletal muscle
18	chr5:14363600-14396000	Strong transcription	Foreskin Fibroblast Primary Cells skin01	Skin
19	chr5:14363800-14380000	Strong transcription	Placenta	Placenta
20	chr5:14363800-14380400	Strong transcription	Hela-S3	cervix
21	chr5:14363800-14383200	Strong transcription	Colonic Mucosa	Colon
22	chr5:14363800-14383800	Strong transcription	HUVEC	blood vessel
23	chr5:14363800-14385600	Strong transcription	A549	lung
24	chr5:14363800-14430600	Strong transcription	Primary monocytes fromperipheralblood	blood
25	chr5:14363800-14430600	Strong transcription	Monocytes-CD14+_RO01746	blood
26	chr5:14365600-14379200	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
27	chr5:14366000-14392400	Strong transcription	HSMM	muscle
28	chr5:14366600-14379200	Strong transcription	Primary B cells from peripheral blood	blood
29	chr5:14366600-14380000	Strong transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
30	chr5:14366600-14385600	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
31	chr5:14366600-14391600	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
32	chr5:14366800-14403200	Strong transcription	Primary hematopoietic stem cells short term culture	blood
33	chr5:14367400-14399800	Strong transcription	Left Ventricle	heart
34	chr5:14369000-14381200	Weak transcription	Fetal Kidney	kidney
35	chr5:14369800-14379200	Weak transcription	Brain Angular Gyrus	brain
36	chr5:14370200-14378800	Weak transcription	Brain Substantia Nigra	brain
37	chr5:14371000-14379600	Weak transcription	iPS-15b Cell Line	embryonic stem cell
38	chr5:14371200-14388000	Weak transcription	Small Intestine	intestine
39	chr5:14372400-14398600	Strong transcription	Sigmoid Colon	Sigmoid Colon
40	chr5:14372600-14389800	Weak transcription	Fetal Brain Male	brain
41	chr5:14373200-14383400	Strong transcription	Fetal Lung	lung
42	chr5:14373800-14385400	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
43	chr5:14373800-14388600	Weak transcription	Fetal Heart	heart
44	chr5:14374200-14379800	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
45	chr5:14374200-14379800	Weak transcription	Pancreas	Pancrea
46	chr5:14374200-14383600	Strong transcription	Primary hematopoietic stem cells	blood
47	chr5:14374400-14379200	Weak transcription	Spleen	Spleen
48	chr5:14374400-14379400	Strong transcription	HUES6 Cell Line	embryonic stem cell
49	chr5:14374400-14379800	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
50	chr5:14374400-14385600	Strong transcription	HUES64 Cell Line	embryonic stem cell

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