Variant report

Variant	rs543894
Chromosome Location	chr1:170020435-170020436
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 23 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:21)

rs_ID	r²[population]
rs10127867	0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs12023275	0.86[AFR][1000 genomes];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs12563479	0.83[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs12724797	0.91[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs1330372	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs1361088	0.91[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs16862933	0.87[AMR][1000 genomes];0.84[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs1765696	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2050651	0.85[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2152831	0.89[AFR][1000 genomes];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2273458	0.80[AMR][1000 genomes];0.97[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs33943686	0.80[AMR][1000 genomes];0.97[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs4141917	0.91[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs4656203	0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs574211	0.85[AFR][1000 genomes];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6673712	0.86[AFR][1000 genomes];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs6697581	0.89[AFR][1000 genomes];0.97[AMR][1000 genomes];0.94[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs7418815	0.89[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7517490	0.86[AFR][1000 genomes];0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs824668	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9426889	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[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
rs543894	C1orf112	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:72 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:169952400-170043000	Weak transcription	Skeletal Muscle Female	skeletal muscle
2	chr1:169982400-170020600	Weak transcription	Rectal Smooth Muscle	rectum
3	chr1:169984600-170020800	Weak transcription	Gastric	stomach
4	chr1:169984800-170027600	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
5	chr1:169993600-170021400	Weak transcription	Fetal Brain Male	brain
6	chr1:169999800-170036600	Weak transcription	Small Intestine	intestine
7	chr1:170002800-170036400	Weak transcription	NHDF-Ad	bronchial
8	chr1:170003600-170027600	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
9	chr1:170005200-170025200	Weak transcription	Brain Substantia Nigra	brain
10	chr1:170007000-170026200	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
11	chr1:170007600-170031800	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
12	chr1:170008200-170032200	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
13	chr1:170008800-170031800	Weak transcription	Placenta Amnion	Placenta Amnion
14	chr1:170012200-170027000	Weak transcription	Pancreatic Islets	Pancreatic Islet
15	chr1:170014000-170025600	Weak transcription	Sigmoid Colon	Sigmoid Colon
16	chr1:170014000-170032200	Weak transcription	Left Ventricle	heart
17	chr1:170014600-170025200	Weak transcription	Rectal Mucosa Donor 29	rectum
18	chr1:170014600-170031400	Weak transcription	GM12878-XiMat	blood
19	chr1:170016000-170031000	Weak transcription	Rectal Mucosa Donor 31	rectum
20	chr1:170016000-170031400	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
21	chr1:170016400-170025800	Weak transcription	Primary B cells from cord blood	blood
22	chr1:170017200-170025600	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
23	chr1:170018200-170025400	Weak transcription	Brain Hippocampus Middle	brain
24	chr1:170018200-170026200	Weak transcription	Esophagus	oesophagus
25	chr1:170018200-170042400	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
26	chr1:170018600-170035800	Weak transcription	Liver	Liver
27	chr1:170018800-170020600	Weak transcription	Fetal Stomach	stomach
28	chr1:170018800-170020800	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
29	chr1:170018800-170022000	Weak transcription	Duodenum Mucosa	Duodenum
30	chr1:170018800-170022400	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
31	chr1:170018800-170023000	Weak transcription	Duodenum Smooth Muscle	Duodenum
32	chr1:170018800-170023800	Weak transcription	Brain Cingulate Gyrus	brain
33	chr1:170018800-170026000	Weak transcription	Primary B cells from peripheral blood	blood
34	chr1:170018800-170026400	Weak transcription	Adipose Nuclei	Adipose
35	chr1:170018800-170026800	Weak transcription	Dnd41	blood
36	chr1:170018800-170027400	Weak transcription	Fetal Brain Female	brain
37	chr1:170018800-170032200	Weak transcription	Ovary	ovary
38	chr1:170018800-170034600	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
39	chr1:170018800-170037000	Weak transcription	Primary T helper naive cells from peripheral blood	blood
40	chr1:170018800-170040600	Weak transcription	Aorta	Aorta
41	chr1:170019000-170020600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
42	chr1:170019000-170020600	Weak transcription	Lung	lung
43	chr1:170019000-170020800	Weak transcription	Fetal Intestine Small	intestine
44	chr1:170019000-170020800	Weak transcription	Fetal Muscle Leg	muscle
45	chr1:170019000-170022200	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
46	chr1:170019000-170022600	Weak transcription	Breast Myoepithelial Primary Cells	Breast
47	chr1:170019000-170023200	Weak transcription	Primary T helper cells fromperipheralblood	blood
48	chr1:170019000-170023400	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
49	chr1:170019000-170023400	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
50	chr1:170019000-170023600	Weak transcription	Fetal Thymus	thymus

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