Variant report

Variant	rs10057258
Chromosome Location	chr5:70771693-70771694
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	chr5:70771514..70772083-chr5:71053551..71054371,2	MCF-7	breast:

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-GTF2H2-8	chr5:70771588-70772143	NONHSAT102027

Extended variants
information (count: 65 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:62)

rs_ID	r²[population]
rs10038709	0.84[ASN][1000 genomes]
rs10079014	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1017225	0.95[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs10942288	0.81[EUR][1000 genomes]
rs10942548	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12187886	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs12652916	0.92[AFR][1000 genomes];0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs13169095	0.90[AMR][1000 genomes];0.94[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs13182226	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs13183892	0.90[AMR][1000 genomes];0.95[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs156756	0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs157192	0.87[AMR][1000 genomes]
rs157193	0.81[AMR][1000 genomes]
rs166758	0.96[CEU][hapmap];0.91[CHB][hapmap];0.91[JPT][hapmap];0.83[YRI][hapmap]
rs16871757	0.91[AMR][1000 genomes];0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1990996	0.91[AMR][1000 genomes];0.95[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2059196	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs276589	0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs277927	0.85[AMR][1000 genomes]
rs277941	0.93[AMR][1000 genomes];0.91[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs277946	0.92[AFR][1000 genomes];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs277947	0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs277952	0.96[CEU][hapmap];0.91[CHB][hapmap];0.87[JPT][hapmap];0.91[TSI][hapmap]
rs277955	0.96[CEU][hapmap];0.91[CHB][hapmap];0.95[JPT][hapmap];0.87[AMR][1000 genomes]
rs277975	0.86[CHB][hapmap];0.91[JPT][hapmap];0.81[YRI][hapmap]
rs277982	0.84[AMR][1000 genomes]
rs277983	0.87[ASW][hapmap];0.96[CEU][hapmap];0.91[CHB][hapmap];0.91[GIH][hapmap];0.91[JPT][hapmap];0.91[MEX][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.84[AMR][1000 genomes]
rs277987	0.96[CEU][hapmap];0.91[CHB][hapmap];0.83[CHD][hapmap];0.97[GIH][hapmap];0.95[JPT][hapmap];0.96[MEX][hapmap];1.00[TSI][hapmap];0.81[AMR][1000 genomes]
rs277988	0.96[CEU][hapmap];0.91[CHB][hapmap];0.95[JPT][hapmap];0.85[AMR][1000 genomes]
rs277990	0.89[ASW][hapmap];0.96[CEU][hapmap];0.91[CHB][hapmap];0.83[CHD][hapmap];0.97[GIH][hapmap];0.95[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.86[AMR][1000 genomes]
rs277991	0.95[CEU][hapmap];0.90[CHB][hapmap];0.95[JPT][hapmap];0.87[AMR][1000 genomes]
rs277992	0.85[AMR][1000 genomes]
rs277993	0.96[CEU][hapmap];0.91[CHB][hapmap];0.97[GIH][hapmap];0.95[JPT][hapmap];0.91[MEX][hapmap];1.00[TSI][hapmap];0.81[AMR][1000 genomes]
rs277994	0.96[CEU][hapmap];0.80[AMR][1000 genomes]
rs279289	0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs282357	0.87[ASW][hapmap];0.96[CEU][hapmap];0.91[CHB][hapmap];0.91[JPT][hapmap];0.89[TSI][hapmap];0.83[YRI][hapmap]
rs368462	0.85[AMR][1000 genomes]
rs3761966	1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs388918	0.93[AMR][1000 genomes];0.91[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs411050	0.85[AFR][1000 genomes];0.91[AMR][1000 genomes];0.91[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs412766	0.95[CEU][hapmap];0.95[CHB][hapmap];0.95[JPT][hapmap];1.00[YRI][hapmap];0.86[AMR][1000 genomes]
rs421128	0.92[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs457889	0.88[AFR][1000 genomes];0.93[AMR][1000 genomes];0.91[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs458829	0.93[AMR][1000 genomes];0.90[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs4602607	0.89[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs461942	0.81[AFR][1000 genomes];0.93[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs462534	0.93[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs464639	0.93[AMR][1000 genomes];0.91[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs467880	0.88[AFR][1000 genomes];0.93[AMR][1000 genomes];0.90[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs467883	0.93[AMR][1000 genomes];0.91[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs468010	0.88[AFR][1000 genomes];0.93[AMR][1000 genomes];0.90[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs468796	0.88[AFR][1000 genomes];0.93[AMR][1000 genomes];0.90[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs4703987	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4704050	0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs55884527	0.80[ASN][1000 genomes]
rs561139	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs617876	0.93[AMR][1000 genomes];0.91[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs67735897	0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6872978	0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7443752	0.81[ASN][1000 genomes]
rs875136	0.91[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs9885334	0.91[AMR][1000 genomes];0.95[EUR][1000 genomes];0.99[ASN][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	nsv1034703	chr5:70391173-70995695	Weak transcription Strong transcription Flanking Active TSS Enhancers Active TSS Genic enhancers ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	28 gene(s)	inside rSNPs	diseases
2	nsv882176	chr5:70738250-70860665	Genic enhancers Weak transcription Strong transcription Enhancers Active TSS ZNF genes & repeats Flanking Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	10 gene(s)	inside rSNPs	diseases
3	esv2754424	chr5:70749744-70885544	Weak transcription Flanking Active TSS Active TSS Strong transcription Enhancers Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	12 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs10057258	MRPS27	cis	cerebellum	SCAN

Chromatin state (count:125 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:70752600-70777200	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
2	chr5:70752600-70789200	Weak transcription	Small Intestine	intestine
3	chr5:70752600-70794800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
4	chr5:70753000-70781400	Weak transcription	Fetal Heart	heart
5	chr5:70753400-70771800	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
6	chr5:70753600-70777800	Weak transcription	Stomach Mucosa	stomach
7	chr5:70754200-70815800	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
8	chr5:70754400-70772200	Strong transcription	Dnd41	blood
9	chr5:70754400-70773200	Strong transcription	Adipose Nuclei	Adipose
10	chr5:70754400-70773600	Strong transcription	Skeletal Muscle Female	skeletal muscle
11	chr5:70754400-70773800	Strong transcription	Rectal Mucosa Donor 29	rectum
12	chr5:70754400-70774800	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
13	chr5:70754400-70774800	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
14	chr5:70754400-70774800	Strong transcription	Placenta	Placenta
15	chr5:70754400-70777800	Strong transcription	Breast Myoepithelial Primary Cells	Breast
16	chr5:70754400-70778200	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
17	chr5:70754400-70795800	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
18	chr5:70754400-70807200	Strong transcription	Primary hematopoietic stem cells short term culture	blood
19	chr5:70754400-70809800	Strong transcription	Fetal Intestine Large	intestine
20	chr5:70754400-70824200	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
21	chr5:70754600-70773600	Strong transcription	Fetal Thymus	thymus
22	chr5:70754600-70774400	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
23	chr5:70754600-70774800	Strong transcription	Duodenum Mucosa	Duodenum
24	chr5:70754600-70820400	Strong transcription	Primary T helper cells fromperipheralblood	blood
25	chr5:70754600-70820400	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
26	chr5:70755800-70777800	Weak transcription	Psoas Muscle	Psoas
27	chr5:70759400-70779000	Weak transcription	Primary T killer memory cells from peripheral blood	blood
28	chr5:70759400-70780000	Weak transcription	Fetal Brain Male	brain
29	chr5:70759600-70778200	Weak transcription	NHLF	lung
30	chr5:70759800-70833400	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
31	chr5:70760200-70798400	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
32	chr5:70761400-70777800	Weak transcription	Rectal Smooth Muscle	rectum
33	chr5:70761600-70776400	Weak transcription	Esophagus	oesophagus
34	chr5:70761800-70777800	Weak transcription	Pancreatic Islets	Pancreatic Islet
35	chr5:70761800-70786800	Weak transcription	Aorta	Aorta
36	chr5:70763000-70779800	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
37	chr5:70763400-70773800	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
38	chr5:70763400-70777400	Strong transcription	Fetal Intestine Small	intestine
39	chr5:70763400-70777600	Strong transcription	Fetal Stomach	stomach
40	chr5:70763800-70777800	Weak transcription	Primary hematopoietic stem cells	blood
41	chr5:70764800-70774200	Strong transcription	Placenta Amnion	Placenta Amnion
42	chr5:70765200-70774200	Strong transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
43	chr5:70765400-70820400	Strong transcription	Primary monocytes fromperipheralblood	blood
44	chr5:70765400-70820400	Strong transcription	Primary B cells from peripheral blood	blood
45	chr5:70765800-70775400	Strong transcription	Primary T cells fromperipheralblood	blood
46	chr5:70766000-70820400	Strong transcription	Monocytes-CD14+_RO01746	blood
47	chr5:70766200-70778000	Strong transcription	Primary T helper 17 cells PMA-I stimulated	--
48	chr5:70766200-70807000	Strong transcription	Fetal Muscle Trunk	muscle
49	chr5:70766400-70772600	Strong transcription	Lung	lung
50	chr5:70766400-70773800	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung

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