Variant report

Variant	rs11485123
Chromosome Location	chr1:222878175-222878176
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr1:222874210..222877170-chr1:222877743..222880359,4	K562	blood:
2	chr1:222875651..222878245-chr1:222884079..222886750,3	MCF-7	breast:

Variant related genes	Relation type
ENSG00000186063	Chromatin interaction
ENSG00000162819	Chromatin interaction

Extended variants
information (count: 37 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:33)

rs_ID	r²[population]
rs12063226	0.92[EUR][1000 genomes]
rs1391557	0.86[EUR][1000 genomes]
rs1391558	1.00[ASW][hapmap];0.91[CEU][hapmap];0.95[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.95[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.96[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.91[AFR][1000 genomes];0.88[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs1498382	0.86[EUR][1000 genomes]
rs17011666	0.95[MEX][hapmap]
rs17011686	0.90[CHB][hapmap];1.00[JPT][hapmap];0.85[YRI][hapmap];0.92[ASN][1000 genomes]
rs17163337	0.85[JPT][hapmap]
rs17163450	0.90[CHB][hapmap];0.97[CHD][hapmap];0.95[JPT][hapmap];0.85[YRI][hapmap];0.95[ASN][1000 genomes]
rs17163468	0.90[CHB][hapmap];0.97[CHD][hapmap];0.95[JPT][hapmap];0.85[YRI][hapmap];0.95[ASN][1000 genomes]
rs2030076	1.00[ASW][hapmap];0.83[CEU][hapmap];0.90[CHB][hapmap];0.97[CHD][hapmap];0.87[GIH][hapmap];0.90[JPT][hapmap];0.90[LWK][hapmap];0.90[MEX][hapmap];0.89[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.93[AFR][1000 genomes];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2088514	1.00[CHB][hapmap];0.93[CHD][hapmap];0.83[GIH][hapmap];0.86[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.88[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2133188	0.90[CHB][hapmap];0.93[CHD][hapmap];0.95[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.86[EUR][1000 genomes]
rs2270707	1.00[MEX][hapmap]
rs2378604	0.93[AFR][1000 genomes];0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2936020	0.86[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2936023	0.86[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2936049	1.00[ASW][hapmap];0.91[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.96[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.90[AFR][1000 genomes];0.84[AMR][1000 genomes];0.90[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2936051	0.81[EUR][1000 genomes]
rs2936052	0.81[EUR][1000 genomes]
rs3002129	0.92[ASN][1000 genomes]
rs3002146	0.86[EUR][1000 genomes]
rs3002148	0.86[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs3008618	0.82[EUR][1000 genomes]
rs3008622	0.84[AFR][1000 genomes];0.81[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs3008625	0.86[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs3008629	0.88[AFR][1000 genomes];0.84[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs3008637	0.88[AFR][1000 genomes];0.84[AMR][1000 genomes];0.90[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs34433664	0.93[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs35507977	1.00[ASW][hapmap];0.91[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];0.95[MEX][hapmap];0.94[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.90[AFR][1000 genomes];0.90[AMR][1000 genomes];0.91[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs3811465	1.00[ASW][hapmap];0.91[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.93[LWK][hapmap];1.00[MEX][hapmap];0.96[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.93[AFR][1000 genomes];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs61824336	0.84[AFR][1000 genomes]
rs61827168	0.81[EUR][1000 genomes]
rs6683071	0.80[ASW][hapmap]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv999185	chr1:222500725-223278032	Strong transcription Enhancers Weak transcription Flanking Active TSS Transcr. at gene 5' and 3' Active TSS Genic enhancers Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	45 gene(s)	inside rSNPs	diseases
2	nsv535304	chr1:222500725-223278032	Enhancers Flanking Active TSS Weak transcription Active TSS Genic enhancers Strong transcription Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	45 gene(s)	inside rSNPs	diseases
3	nsv873205	chr1:222718718-222923351	Weak transcription Strong transcription Active TSS Transcr. at gene 5' and 3' Flanking Active TSS Enhancers Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	34 gene(s)	inside rSNPs	diseases
4	nsv1012537	chr1:222755091-223512243	Weak transcription Strong transcription Enhancers Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Active TSS Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats	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
rs11485123	C1orf58	cis	parietal	SCAN

Chromatin state (count:116 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:222835200-222884600	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
2	chr1:222839000-222884600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
3	chr1:222839600-222884600	Weak transcription	Esophagus	oesophagus
4	chr1:222840000-222884600	Weak transcription	Colonic Mucosa	Colon
5	chr1:222841200-222883400	Weak transcription	ES-I3 Cell Line	embryonic stem cell
6	chr1:222841400-222883200	Weak transcription	Fetal Heart	heart
7	chr1:222845000-222884600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
8	chr1:222849400-222883200	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
9	chr1:222852400-222883800	Weak transcription	iPS-15b Cell Line	embryonic stem cell
10	chr1:222855200-222884600	Weak transcription	Pancreas	Pancrea
11	chr1:222855600-222883800	Weak transcription	Placenta Amnion	Placenta Amnion
12	chr1:222860000-222884600	Weak transcription	Left Ventricle	heart
13	chr1:222860200-222883000	Weak transcription	Duodenum Smooth Muscle	Duodenum
14	chr1:222860200-222883000	Weak transcription	Hela-S3	cervix
15	chr1:222860200-222883200	Weak transcription	Brain Anterior Caudate	brain
16	chr1:222860200-222883600	Weak transcription	Rectal Smooth Muscle	rectum
17	chr1:222860200-222883800	Weak transcription	Fetal Kidney	kidney
18	chr1:222860200-222884000	Weak transcription	Brain Angular Gyrus	brain
19	chr1:222860200-222884200	Weak transcription	Brain Substantia Nigra	brain
20	chr1:222860200-222884400	Weak transcription	Placenta	Placenta
21	chr1:222860200-222884600	Weak transcription	Aorta	Aorta
22	chr1:222860200-222884600	Weak transcription	Brain Inferior Temporal Lobe	brain
23	chr1:222860200-222884600	Weak transcription	Gastric	stomach
24	chr1:222860200-222884600	Weak transcription	Lung	lung
25	chr1:222860600-222880600	Weak transcription	Ovary	ovary
26	chr1:222860600-222882400	Weak transcription	Small Intestine	intestine
27	chr1:222860600-222884200	Weak transcription	H9 Cell Line	embryonic stem cell
28	chr1:222861000-222885000	Weak transcription	Spleen	Spleen
29	chr1:222866600-222883000	Weak transcription	Fetal Brain Male	brain
30	chr1:222866800-222883800	Weak transcription	Brain Hippocampus Middle	brain
31	chr1:222867200-222882600	Weak transcription	HepG2	liver
32	chr1:222869400-222883200	Weak transcription	GM12878-XiMat	blood
33	chr1:222871400-222878600	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
34	chr1:222873600-222883200	Weak transcription	Brain Germinal Matrix	brain
35	chr1:222873800-222883000	Weak transcription	Breast Myoepithelial Primary Cells	Breast
36	chr1:222873800-222883200	Weak transcription	Duodenum Mucosa	Duodenum
37	chr1:222873800-222884600	Weak transcription	Sigmoid Colon	Sigmoid Colon
38	chr1:222874000-222883400	Weak transcription	Skeletal Muscle Male	skeletal muscle
39	chr1:222874000-222884600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
40	chr1:222874200-222878400	Strong transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
41	chr1:222874600-222883600	Weak transcription	Fetal Stomach	stomach
42	chr1:222874800-222883600	Weak transcription	Thymus	Thymus
43	chr1:222875200-222883200	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
44	chr1:222876200-222878800	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
45	chr1:222876200-222881800	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
46	chr1:222876200-222883000	Weak transcription	Muscle Satellite Cultured Cells	--
47	chr1:222876200-222883000	Weak transcription	Adipose Nuclei	Adipose
48	chr1:222876200-222883000	Weak transcription	Brain Cingulate Gyrus	brain
49	chr1:222876200-222883200	Weak transcription	Stomach Mucosa	stomach
50	chr1:222876200-222883400	Weak transcription	Liver	Liver

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