Variant report

Variant	rs1281411
Chromosome Location	chr1:179814457-179814458
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr1:179813084..179815774-chr1:179817497..179820242,2	K562	blood:

Extended variants
information (count: 66 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:60)

rs_ID	r²[population]
rs1014394	0.81[TSI][hapmap];0.83[EUR][1000 genomes]
rs1144575	0.86[CHB][hapmap];0.91[CHD][hapmap];0.94[JPT][hapmap];0.91[ASN][1000 genomes]
rs1148812	0.86[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs1148815	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.94[GIH][hapmap];1.00[JPT][hapmap];0.89[MEX][hapmap];0.97[TSI][hapmap];0.89[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1148817	0.82[EUR][1000 genomes]
rs12062341	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.94[JPT][hapmap];0.84[MEX][hapmap];0.88[TSI][hapmap];0.85[AMR][1000 genomes];0.88[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs12062383	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.91[GIH][hapmap];0.94[JPT][hapmap];0.90[MEX][hapmap];0.97[TSI][hapmap];0.92[AMR][1000 genomes];0.90[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1281378	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.94[GIH][hapmap];0.94[JPT][hapmap];0.90[MEX][hapmap];0.97[TSI][hapmap];0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1281408	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1281410	0.83[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs1281412	0.91[AMR][1000 genomes];0.89[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs1281413	0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1281428	0.95[ASN][1000 genomes]
rs1281429	0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1281430	0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1281432	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.95[MEX][hapmap];0.97[TSI][hapmap];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1298477	0.83[EUR][1000 genomes]
rs1298479	0.88[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.94[JPT][hapmap];0.80[MEX][hapmap];0.85[TSI][hapmap];0.85[AMR][1000 genomes];0.86[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs1300068	0.85[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.91[GIH][hapmap];0.94[JPT][hapmap];0.90[MEX][hapmap];0.95[TSI][hapmap];0.92[AMR][1000 genomes];0.91[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2007148	0.88[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.94[JPT][hapmap];0.95[MEX][hapmap];0.97[TSI][hapmap];0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2245425	0.81[CEU][hapmap];1.00[CHB][hapmap];0.94[JPT][hapmap];0.85[AMR][1000 genomes];0.87[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2249346	0.88[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.94[JPT][hapmap];0.95[MEX][hapmap];0.97[TSI][hapmap];0.94[AMR][1000 genomes];0.94[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2762858	0.85[AMR][1000 genomes];0.86[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2777908	0.96[AMR][1000 genomes];0.90[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2777909	0.90[AMR][1000 genomes];0.86[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2777917	0.89[AFR][1000 genomes];0.98[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs2794582	0.96[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs2794583	0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs474258	0.88[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.94[JPT][hapmap];0.90[MEX][hapmap];0.83[TSI][hapmap];0.87[AMR][1000 genomes];0.85[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs475233	0.88[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.94[JPT][hapmap];0.90[MEX][hapmap];0.83[TSI][hapmap];0.87[AMR][1000 genomes];0.85[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs475434	0.85[AMR][1000 genomes];0.85[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs479094	0.89[CEU][hapmap];1.00[CHB][hapmap];0.94[JPT][hapmap];0.94[AMR][1000 genomes];0.91[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs480377	0.92[CEU][hapmap];1.00[CHB][hapmap];0.94[JPT][hapmap];0.85[AMR][1000 genomes];0.88[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs480498	0.92[AMR][1000 genomes];0.91[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs486906	0.85[EUR][1000 genomes]
rs501300	0.85[AMR][1000 genomes];0.87[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs502036	0.84[CHD][hapmap];0.82[MEX][hapmap];0.81[AMR][1000 genomes]
rs505789	0.85[AMR][1000 genomes];0.88[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs505837	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.94[JPT][hapmap];0.80[MEX][hapmap];0.88[TSI][hapmap];0.85[AMR][1000 genomes];0.89[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs507603	0.86[CHB][hapmap];0.94[CHD][hapmap];0.94[JPT][hapmap];0.86[ASN][1000 genomes]
rs514421	0.81[CEU][hapmap];1.00[CHB][hapmap];0.94[JPT][hapmap];0.85[AMR][1000 genomes];0.85[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs518774	0.85[CEU][hapmap];1.00[CHB][hapmap];0.94[JPT][hapmap];0.86[YRI][hapmap];0.95[AMR][1000 genomes];0.93[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs522534	0.92[AMR][1000 genomes];0.89[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs530369	0.92[CEU][hapmap];0.88[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs530854	0.96[AMR][1000 genomes];0.92[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs531814	0.82[CEU][hapmap];0.84[CHD][hapmap]
rs538512	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.94[JPT][hapmap];0.80[MEX][hapmap];0.88[TSI][hapmap];0.85[AMR][1000 genomes];0.93[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs547776	0.92[AMR][1000 genomes];0.91[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs549650	0.85[AMR][1000 genomes];0.88[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs553830	0.93[CHB][hapmap];0.94[JPT][hapmap];0.87[AMR][1000 genomes];0.91[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs555270	0.96[CEU][hapmap];1.00[CHB][hapmap];0.94[JPT][hapmap];0.86[YRI][hapmap];0.96[AMR][1000 genomes];0.92[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs555526	0.84[CHB][hapmap];0.94[JPT][hapmap];0.87[ASN][1000 genomes]
rs589780	1.00[CEU][hapmap];1.00[CHB][hapmap];0.94[JPT][hapmap];0.86[YRI][hapmap];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs599185	0.96[CEU][hapmap];1.00[CHB][hapmap];0.93[JPT][hapmap];0.90[AMR][1000 genomes];0.90[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs600046	0.91[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.85[AMR][1000 genomes];0.88[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs600553	0.85[AMR][1000 genomes];0.88[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs605807	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.94[GIH][hapmap];0.94[JPT][hapmap];0.90[MEX][hapmap];0.97[TSI][hapmap];0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs609521	0.96[CEU][hapmap];1.00[CHB][hapmap];0.94[JPT][hapmap];0.93[AMR][1000 genomes];0.90[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs612215	0.90[AMR][1000 genomes];0.89[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs644412	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.91[GIH][hapmap];0.94[JPT][hapmap];0.90[MEX][hapmap];0.95[TSI][hapmap];0.92[AMR][1000 genomes];0.89[EUR][1000 genomes];0.90[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	nsv1005808	chr1:179783922-179864710	Enhancers Strong transcription Weak transcription Genic enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Active TSS Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	40 gene(s)	inside rSNPs	diseases
2	nsv1005051	chr1:179785643-179861950	Flanking Active TSS Strong transcription Genic enhancers Weak transcription Enhancers Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	40 gene(s)	inside rSNPs	diseases
3	nsv429936	chr1:179790343-180214343	Active TSS Strong transcription Flanking Active TSS Weak transcription Enhancers Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	72 gene(s)	inside rSNPs	diseases
4	nsv429947	chr1:179790518-179925104	Strong transcription Enhancers Genic enhancers Weak transcription Flanking Active TSS Transcr. at gene 5' and 3' Active TSS ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	49 gene(s)	inside rSNPs	diseases
5	esv1815608	chr1:179813499-180067988	Strong transcription Enhancers Flanking Active TSS Active TSS Weak transcription Genic enhancers ZNF genes & repeats 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	48 gene(s)	inside rSNPs	diseases
6	nsv429958	chr1:179814306-179994628	Genic enhancers Enhancers Strong transcription Weak transcription Flanking Active TSS Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	48 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs1281411	MRPS14	cis	cerebellum	SCAN

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:179795200-179815200	Weak transcription	Ovary	ovary
2	chr1:179795400-179815200	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
3	chr1:179795600-179834200	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
4	chr1:179799600-179815200	Weak transcription	Brain Angular Gyrus	brain
5	chr1:179800400-179815200	Weak transcription	Psoas Muscle	Psoas
6	chr1:179800600-179815200	Weak transcription	Esophagus	oesophagus
7	chr1:179800800-179815200	Weak transcription	Hela-S3	cervix
8	chr1:179801000-179815000	Weak transcription	K562	blood
9	chr1:179801200-179815200	Weak transcription	Lung	lung
10	chr1:179801200-179815200	Weak transcription	Sigmoid Colon	Sigmoid Colon
11	chr1:179801200-179815200	Weak transcription	Spleen	Spleen
12	chr1:179801800-179815200	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
13	chr1:179801800-179815200	Weak transcription	NHDF-Ad	bronchial
14	chr1:179802200-179815200	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
15	chr1:179802400-179815000	Weak transcription	H1 Cell Line	embryonic stem cell
16	chr1:179802400-179815200	Weak transcription	Thymus	Thymus
17	chr1:179802400-179836200	Weak transcription	Primary T killer memory cells from peripheral blood	blood
18	chr1:179802600-179815200	Weak transcription	Primary T helper naive cells from peripheral blood	blood
19	chr1:179802600-179819800	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
20	chr1:179803200-179815200	Weak transcription	Brain Anterior Caudate	brain
21	chr1:179803400-179815200	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
22	chr1:179803400-179815200	Weak transcription	Small Intestine	intestine
23	chr1:179803600-179815000	Weak transcription	iPS-20b Cell Line	embryonic stem cell
24	chr1:179803600-179815200	Weak transcription	Brain Germinal Matrix	brain
25	chr1:179803600-179833600	Weak transcription	Fetal Brain Male	brain
26	chr1:179803800-179815000	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
27	chr1:179804000-179815000	Weak transcription	iPS-18 Cell Line	embryonic stem cell
28	chr1:179804000-179815000	Weak transcription	Fetal Lung	lung
29	chr1:179804200-179815400	Weak transcription	Pancreatic Islets	Pancreatic Islet
30	chr1:179805400-179815200	Weak transcription	Aorta	Aorta
31	chr1:179805400-179815200	Weak transcription	Right Ventricle	heart
32	chr1:179805800-179815200	Weak transcription	Fetal Muscle Leg	muscle
33	chr1:179805800-179818200	Weak transcription	ES-I3 Cell Line	embryonic stem cell
34	chr1:179806200-179815000	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
35	chr1:179806200-179817600	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
36	chr1:179807600-179815000	Weak transcription	Brain Inferior Temporal Lobe	brain
37	chr1:179807600-179815600	Weak transcription	Colon Smooth Muscle	Colon
38	chr1:179807600-179827400	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
39	chr1:179807800-179815000	Weak transcription	NHLF	lung
40	chr1:179807800-179833800	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
41	chr1:179808200-179815000	Weak transcription	Placenta Amnion	Placenta Amnion
42	chr1:179808200-179815200	Weak transcription	H9 Cell Line	embryonic stem cell
43	chr1:179808200-179815200	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
44	chr1:179808600-179822600	Strong transcription	Fetal Intestine Large	intestine
45	chr1:179808600-179837000	Strong transcription	Liver	Liver
46	chr1:179808600-179839800	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
47	chr1:179808800-179836000	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
48	chr1:179809000-179815200	Weak transcription	Gastric	stomach
49	chr1:179809200-179815200	Weak transcription	Rectal Smooth Muscle	rectum
50	chr1:179809200-179821600	Strong transcription	Primary monocytes fromperipheralblood	blood

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