Variant report

Variant	rs60458375
Chromosome Location	chr1:93684998-93684999
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	YY1	chr1:93684937-93685327	GM12891	blood:	n/a	n/a
2	RUNX3	chr1:93684988-93685521	GM12878	blood:	n/a	n/a
3	YY1	chr1:93684938-93685231	GM12892	blood:	n/a	n/a
4	YY1	chr1:93684911-93685280	GM12878	blood:	n/a	n/a
5	RUNX3	chr1:93684996-93685527	GM12878	blood:	n/a	n/a
6	YY1	chr1:93684943-93685293	GM12878	blood:	n/a	n/a
7	POLR2A	chr1:93684985-93685072	GM12878	blood:	n/a	n/a

Variant related genes	Relation type
CCDC18	TF binding region

Extended variants
information (count: 69 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:68)

rs_ID	r²[population]
rs1064797	0.86[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs11164922	0.81[EUR][1000 genomes]
rs12404947	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs12405666	0.97[EUR][1000 genomes]
rs12409621	0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs12411095	0.81[EUR][1000 genomes]
rs17131703	0.86[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs17131705	0.86[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs17131709	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs17131710	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs17131718	0.81[EUR][1000 genomes]
rs17131741	0.81[EUR][1000 genomes]
rs17386609	0.92[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs2749734	0.92[EUR][1000 genomes]
rs2785602	0.92[EUR][1000 genomes]
rs2785605	0.92[EUR][1000 genomes]
rs2815419	0.92[EUR][1000 genomes]
rs2815423	0.92[EUR][1000 genomes]
rs2815424	0.94[EUR][1000 genomes]
rs41286823	1.00[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs41292137	1.00[EUR][1000 genomes]
rs4240965	0.85[EUR][1000 genomes]
rs4347219	0.97[EUR][1000 genomes]
rs475120	0.86[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs488345	0.94[EUR][1000 genomes]
rs495580	0.94[EUR][1000 genomes]
rs500349	0.94[EUR][1000 genomes]
rs502651	0.83[EUR][1000 genomes]
rs519319	0.94[EUR][1000 genomes]
rs539544	0.92[EUR][1000 genomes]
rs548751	0.94[EUR][1000 genomes]
rs571439	0.86[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs574687	0.86[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs57992499	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs580828	0.92[EUR][1000 genomes]
rs60013975	0.81[EUR][1000 genomes]
rs61101021	0.81[EUR][1000 genomes]
rs61433067	0.92[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs6604042	0.95[EUR][1000 genomes]
rs66501175	0.86[AFR][1000 genomes];0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs66804824	0.81[EUR][1000 genomes]
rs6689007	0.94[EUR][1000 genomes]
rs67002303	0.89[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs6703169	0.91[EUR][1000 genomes]
rs67262037	1.00[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs67337461	1.00[EUR][1000 genomes]
rs67395827	0.86[AFR][1000 genomes];0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs67711178	0.86[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs67723709	0.89[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs67768103	0.86[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs67992203	1.00[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs67998457	0.81[EUR][1000 genomes]
rs72715364	0.92[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs72715394	0.85[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs72717318	0.85[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs72717334	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72717337	0.85[AMR][1000 genomes];0.97[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs72717346	0.86[AFR][1000 genomes];0.92[AMR][1000 genomes];0.98[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs72717352	0.86[AFR][1000 genomes];0.92[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs72717354	0.97[EUR][1000 genomes]
rs72717374	0.85[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs72719120	1.00[EUR][1000 genomes]
rs72955366	1.00[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs72955388	1.00[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs72959223	0.86[AFR][1000 genomes];0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs72959288	1.00[EUR][1000 genomes]
rs72959296	0.97[EUR][1000 genomes]
rs797594	0.84[EUR][1000 genomes]

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

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv830625	chr1:93566378-93735246	Weak transcription Strong transcription Flanking Active TSS Enhancers ZNF genes & repeats Active TSS Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	22 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:104 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:93647000-93688000	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
2	chr1:93647000-93688600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
3	chr1:93647000-93756400	Weak transcription	Gastric	stomach
4	chr1:93647200-93685000	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
5	chr1:93647200-93707400	Weak transcription	Duodenum Smooth Muscle	Duodenum
6	chr1:93647200-93757600	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
7	chr1:93647600-93706600	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
8	chr1:93654200-93708400	Weak transcription	Esophagus	oesophagus
9	chr1:93654600-93708000	Weak transcription	Ovary	ovary
10	chr1:93656400-93686200	Weak transcription	Aorta	Aorta
11	chr1:93657600-93708400	Weak transcription	Left Ventricle	heart
12	chr1:93660600-93705200	Weak transcription	Lung	lung
13	chr1:93660800-93685000	Weak transcription	Primary T cells fromperipheralblood	blood
14	chr1:93661400-93708200	Weak transcription	Fetal Muscle Trunk	muscle
15	chr1:93661800-93702800	Weak transcription	Fetal Heart	heart
16	chr1:93661800-93708200	Weak transcription	Fetal Brain Female	brain
17	chr1:93663600-93705600	Weak transcription	Skeletal Muscle Female	skeletal muscle
18	chr1:93665400-93685000	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
19	chr1:93665400-93688800	Weak transcription	NHLF	lung
20	chr1:93665400-93708400	Weak transcription	Breast Myoepithelial Primary Cells	Breast
21	chr1:93665400-93708400	Weak transcription	Spleen	Spleen
22	chr1:93665600-93697600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
23	chr1:93665600-93702600	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
24	chr1:93665600-93707800	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
25	chr1:93665800-93693200	Weak transcription	Fetal Intestine Small	intestine
26	chr1:93665800-93706600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
27	chr1:93665800-93707800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
28	chr1:93666600-93727000	Weak transcription	Rectal Mucosa Donor 31	rectum
29	chr1:93667400-93687600	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
30	chr1:93667400-93695400	Strong transcription	HUES48 Cell Line	embryonic stem cell
31	chr1:93668800-93685200	Weak transcription	Muscle Satellite Cultured Cells	--
32	chr1:93668800-93686000	Weak transcription	Fetal Lung	lung
33	chr1:93668800-93695200	Weak transcription	Rectal Mucosa Donor 29	rectum
34	chr1:93668800-93697600	Weak transcription	Fetal Intestine Large	intestine
35	chr1:93668800-93708400	Weak transcription	Duodenum Mucosa	Duodenum
36	chr1:93669600-93685200	Weak transcription	Right Ventricle	heart
37	chr1:93670400-93686200	Strong transcription	HUES64 Cell Line	embryonic stem cell
38	chr1:93670800-93686200	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
39	chr1:93672200-93693200	Strong transcription	iPS-20b Cell Line	embryonic stem cell
40	chr1:93672600-93686800	Weak transcription	HepG2	liver
41	chr1:93672600-93708400	Weak transcription	Placenta	Placenta
42	chr1:93672800-93685000	Weak transcription	Liver	Liver
43	chr1:93673800-93685000	Weak transcription	Primary B cells from peripheral blood	blood
44	chr1:93673800-93707400	Weak transcription	A549	lung
45	chr1:93674400-93685000	Weak transcription	Thymus	Thymus
46	chr1:93674600-93692200	Weak transcription	Fetal Stomach	stomach
47	chr1:93675000-93693000	Strong transcription	Monocytes-CD14+_RO01746	blood
48	chr1:93675800-93687000	Weak transcription	HSMM	muscle
49	chr1:93676000-93685000	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
50	chr1:93677200-93688800	Weak transcription	Fetal Kidney	kidney

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