Variant report

Variant	rs12563479
Chromosome Location	chr1:170009546-170009547
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 26 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:24)

rs_ID	r²[population]
rs10127867	0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12023275	0.95[CEU][hapmap];0.91[CHB][hapmap];0.95[JPT][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12724797	0.83[CEU][hapmap];0.95[CHB][hapmap];0.91[JPT][hapmap];0.90[EUR][1000 genomes]
rs1330372	0.91[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1361088	0.95[CEU][hapmap];0.96[CHB][hapmap];1.00[JPT][hapmap];0.91[AMR][1000 genomes];0.96[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs16862933	0.87[CEU][hapmap];0.87[CHB][hapmap];0.95[JPT][hapmap];0.87[AMR][1000 genomes];0.83[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs1765696	0.83[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2050651	0.96[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2152831	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[AFR][1000 genomes];0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2273458	0.83[AFR][1000 genomes];0.80[AMR][1000 genomes];0.96[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2420514	0.80[CHB][hapmap]
rs2750014	0.83[CHB][hapmap];0.86[JPT][hapmap]
rs2806386	0.92[CHB][hapmap];0.91[JPT][hapmap]
rs33943686	0.80[AMR][1000 genomes];0.96[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs4141917	0.84[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.90[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs4656203	0.82[CEU][hapmap];0.95[CHB][hapmap];0.90[JPT][hapmap];0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs543894	0.83[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs574211	0.83[AFR][1000 genomes];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs6673712	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs6697581	0.97[AMR][1000 genomes];0.93[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs7418815	0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs7517490	0.95[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.97[AFR][1000 genomes];0.94[AMR][1000 genomes];0.95[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs824668	0.86[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs9426889	0.96[CEU][hapmap];0.96[CHB][hapmap];1.00[JPT][hapmap];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.91[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:2 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1014033	chr1:169968488-170453021	Flanking Active TSS Enhancers Active TSS Weak transcription Strong transcription ZNF genes & repeats Bivalent Enhancer Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	18 gene(s)	inside rSNPs	diseases
2	nsv535200	chr1:169968488-170453021	Weak transcription Flanking Active TSS Strong transcription Active TSS Enhancers ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	18 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs12563479	C1orf112	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:93 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:169904000-170010400	Weak transcription	Aorta	Aorta
2	chr1:169951600-170011800	Weak transcription	Primary T helper naive cells from peripheral blood	blood
3	chr1:169952000-170018000	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
4	chr1:169952400-170043000	Weak transcription	Skeletal Muscle Female	skeletal muscle
5	chr1:169967600-170013000	Weak transcription	Fetal Heart	heart
6	chr1:169968800-170010800	Weak transcription	Colon Smooth Muscle	Colon
7	chr1:169968800-170020200	Weak transcription	Brain Angular Gyrus	brain
8	chr1:169969000-170012600	Weak transcription	Brain Inferior Temporal Lobe	brain
9	chr1:169969600-170017800	Weak transcription	Esophagus	oesophagus
10	chr1:169979400-170018000	Weak transcription	Brain Cingulate Gyrus	brain
11	chr1:169979800-170015200	Weak transcription	HMEC	breast
12	chr1:169981600-170013400	Weak transcription	Lung	lung
13	chr1:169982400-170020600	Weak transcription	Rectal Smooth Muscle	rectum
14	chr1:169983000-170017200	Weak transcription	HSMMtube	muscle
15	chr1:169983800-170017600	Weak transcription	Spleen	Spleen
16	chr1:169984600-170020800	Weak transcription	Gastric	stomach
17	chr1:169984800-170027600	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
18	chr1:169985000-170010800	Weak transcription	Brain Hippocampus Middle	brain
19	chr1:169985000-170012800	Weak transcription	Brain Anterior Caudate	brain
20	chr1:169985200-170020400	Weak transcription	Primary T killer memory cells from peripheral blood	blood
21	chr1:169985800-170010800	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
22	chr1:169985800-170010800	Weak transcription	Rectal Mucosa Donor 29	rectum
23	chr1:169986200-170010600	Weak transcription	Stomach Smooth Muscle	stomach
24	chr1:169986400-170013600	Weak transcription	Left Ventricle	heart
25	chr1:169986400-170019800	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
26	chr1:169988000-170017600	Weak transcription	Fetal Lung	lung
27	chr1:169989600-170019800	Weak transcription	Right Ventricle	heart
28	chr1:169989800-170013400	Weak transcription	Psoas Muscle	Psoas
29	chr1:169990400-170017200	Weak transcription	Fetal Kidney	kidney
30	chr1:169993600-170010800	Weak transcription	Sigmoid Colon	Sigmoid Colon
31	chr1:169993600-170021400	Weak transcription	Fetal Brain Male	brain
32	chr1:169995400-170017800	Weak transcription	Pancreas	Pancrea
33	chr1:169996800-170010000	Weak transcription	Brain Germinal Matrix	brain
34	chr1:169997200-170010600	Weak transcription	Primary B cells from peripheral blood	blood
35	chr1:169997200-170010800	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
36	chr1:169997200-170012400	Weak transcription	Duodenum Mucosa	Duodenum
37	chr1:169997400-170012000	Weak transcription	Primary B cells from cord blood	blood
38	chr1:169997800-170010000	Weak transcription	Fetal Stomach	stomach
39	chr1:169997800-170010600	Weak transcription	Fetal Thymus	thymus
40	chr1:169997800-170017600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
41	chr1:169997800-170018600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
42	chr1:169998000-170010600	Weak transcription	Fetal Muscle Leg	muscle
43	chr1:169998000-170011400	Weak transcription	Primary hematopoietic stem cells	blood
44	chr1:169998200-170010400	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
45	chr1:169999800-170017600	Weak transcription	Colonic Mucosa	Colon
46	chr1:169999800-170036600	Weak transcription	Small Intestine	intestine
47	chr1:170000800-170014200	Weak transcription	Placenta	Placenta
48	chr1:170001200-170012400	Weak transcription	Fetal Intestine Large	intestine
49	chr1:170001800-170016200	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
50	chr1:170001800-170017400	Weak transcription	NH-A	brain

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