Variant report

Variant	rs11119310
Chromosome Location	chr1:209742852-209742853
allele	A/G
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	ZNF143	chr1:209742823-209743101	Hela-S3	cervix:	n/a	n/a
2	RAD21	chr1:209742714-209743109	MCF-7	breast:	n/a	chr1:209742967-209742981 chr1:209742966-209742985
3	CTCF	chr1:209742850-209743119	GM13977	blood:	n/a	chr1:209742965-209742983 chr1:209742967-209742988 chr1:209742966-209742982
4	RAD21	chr1:209742738-209743197	MCF-7	breast:	n/a	chr1:209742967-209742981 chr1:209742966-209742985
5	CTCF	chr1:209742835-209743148	K562	blood:	n/a	chr1:209742965-209742983 chr1:209742967-209742988 chr1:209742966-209742982
6	CTCF	chr1:209742821-209743126	K562	blood:	n/a	chr1:209742965-209742983 chr1:209742967-209742988 chr1:209742966-209742982
7	CTCF	chr1:209742840-209742990	WI-38	lung:	n/a	chr1:209742965-209742983 chr1:209742967-209742988 chr1:209742966-209742982
8	CTCF	chr1:209742843-209743092	GM10248	blood:	n/a	chr1:209742965-209742983 chr1:209742967-209742988 chr1:209742966-209742982
9	RAD21	chr1:209742811-209743154	GM12878	blood:	n/a	chr1:209742967-209742981 chr1:209742966-209742985
10	SMC3	chr1:209742804-209743155	HepG2	liver:	n/a	chr1:209742967-209742981
11	CTCF	chr1:209742749-209743171	HepG2	liver:	n/a	chr1:209742965-209742983 chr1:209742967-209742988 chr1:209742966-209742982
12	CTCF	chr1:209742767-209743211	HCT-116	colon:	n/a	chr1:209742965-209742983 chr1:209742967-209742988 chr1:209742966-209742982
13	CTCF	chr1:209742765-209743197	GM12878	blood:	n/a	chr1:209742965-209742983 chr1:209742967-209742988 chr1:209742966-209742982
14	CTCF	chr1:209742851-209743112	Kidney_OC	kidney:	n/a	chr1:209742965-209742983 chr1:209742967-209742988 chr1:209742966-209742982
15	RAD21	chr1:209742566-209743562	SK-N-SH	brain:	n/a	chr1:209742967-209742981 chr1:209742966-209742985
16	CTCF	chr1:209742697-209743234	K562	blood:	n/a	chr1:209742965-209742983 chr1:209742967-209742988 chr1:209742966-209742982
17	SMC3	chr1:209742535-209743391	SK-N-SH	brain:	n/a	chr1:209742967-209742981
18	RAD21	chr1:209742798-209743164	HepG2	liver:	n/a	chr1:209742967-209742981 chr1:209742966-209742985
19	RAD21	chr1:209742789-209743171	H1-hESC	embryonic stem cell:	n/a	chr1:209742967-209742981 chr1:209742966-209742985
20	RAD21	chr1:209742775-209743191	Hela-S3	cervix:	n/a	chr1:209742967-209742981 chr1:209742966-209742985
21	RAD21	chr1:209742823-209743203	SK-N-SH_RA	brain:	n/a	chr1:209742967-209742981 chr1:209742966-209742985
22	CTCF	chr1:209742747-209743115	H1-hESC	embryonic stem cell:	n/a	chr1:209742965-209742983 chr1:209742967-209742988 chr1:209742966-209742982
23	CTCF	chr1:209742803-209743079	A549	lung:	n/a	chr1:209742965-209742983 chr1:209742967-209742988 chr1:209742966-209742982
24	CTCF	chr1:209742820-209742970	HCM	heart:	n/a	n/a
25	SMC3	chr1:209742785-209743408	K562	blood:	n/a	chr1:209742967-209742981
26	CTCF	chr1:209742777-209743156	ECC-1	luminal epithelium:	n/a	chr1:209742965-209742983 chr1:209742967-209742988 chr1:209742966-209742982
27	CTCF	chr1:209742738-209743127	K562	blood:	n/a	chr1:209742965-209742983 chr1:209742967-209742988 chr1:209742966-209742982
28	CTCF	chr1:209742755-209743128	A549	lung:	n/a	chr1:209742965-209742983 chr1:209742967-209742988 chr1:209742966-209742982
29	RAD21	chr1:209742712-209743240	A549	lung:	n/a	chr1:209742967-209742981 chr1:209742966-209742985
30	CTCF	chr1:209742836-209743097	LNCaP	prostate:	n/a	chr1:209742965-209742983 chr1:209742967-209742988 chr1:209742966-209742982
31	RAD21	chr1:209742806-209743083	GM12878	blood:	n/a	chr1:209742967-209742981 chr1:209742966-209742985
32	RAD21	chr1:209742726-209743380	HCT-116	colon:	n/a	chr1:209742967-209742981 chr1:209742966-209742985
33	CTCF	chr1:209742479-209743485	A549	lung:	n/a	chr1:209742965-209742983 chr1:209742967-209742988 chr1:209742966-209742982
34	ZNF143	chr1:209742796-209743161	K562	blood:	n/a	n/a
35	CTCF	chr1:209742800-209743143	Spleen_OC	spleen:	n/a	chr1:209742965-209742983 chr1:209742967-209742988 chr1:209742966-209742982
36	CTCF	chr1:209742840-209743087	Lung_OC	lung:	n/a	chr1:209742965-209742983 chr1:209742967-209742988 chr1:209742966-209742982
37	CTCF	chr1:209742574-209743752	SK-N-SH	brain:	n/a	chr1:209742965-209742983 chr1:209742967-209742988 chr1:209742966-209742982
38	TEAD4	chr1:209742840-209743263	H1-hESC	embryonic stem cell:	n/a	n/a
39	CTCF	chr1:209742804-209743111	HUVEC	blood vessel:	n/a	chr1:209742965-209742983 chr1:209742967-209742988 chr1:209742966-209742982
40	CTCF	chr1:209742848-209743101	A549	lung:	n/a	chr1:209742965-209742983 chr1:209742967-209742988 chr1:209742966-209742982
41	SMC3	chr1:209742776-209743388	GM12878	blood:	n/a	chr1:209742967-209742981
42	RAD21	chr1:209742837-209743160	SK-N-SH_RA	brain:	n/a	chr1:209742967-209742981 chr1:209742966-209742985
43	RFX5	chr1:209742811-209743160	Hela-S3	cervix:	n/a	n/a
44	RAD21	chr1:209742702-209743267	ECC-1	luminal epithelium:	n/a	chr1:209742967-209742981 chr1:209742966-209742985
45	ZNF143	chr1:209742790-209743160	GM12878	blood:	n/a	n/a
46	CTCF	chr1:209742837-209743114	NHEK	skin:	n/a	chr1:209742965-209742983 chr1:209742967-209742988 chr1:209742966-209742982
47	CTCF	chr1:209742744-209743157	A549	lung:	n/a	chr1:209742965-209742983 chr1:209742967-209742988 chr1:209742966-209742982
48	CBX3	chr1:209742712-209743308	HCT-116	colon:	n/a	n/a
49	CTCF	chr1:209742797-209743143	ECC-1	luminal epithelium:	n/a	chr1:209742965-209742983 chr1:209742967-209742988 chr1:209742966-209742982
50	MAZ	chr1:209742819-209743076	GM12878	blood:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr1:209742599..209743311-chr1:209800709..209801256,2	MCF-7	breast:
2	chr1:209742327..209743226-chr1:209920951..209921587,3	MCF-7	breast:
3	chr1:209742263..209743556-chr1:209920676..209921449,8	K562	blood:
4	chr1:209742622..209744127-chr1:209864930..209867210,2	MCF-7	breast:
5	chr1:209742477..209743064-chr1:209800705..209801620,3	K562	blood:
6	chr1:209742414..209743881-chr1:209865939..209867133,12	K562	blood:

Variant related genes	Relation type
ENSG00000224260	TF binding region

Extended variants
information (count: 21 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:20)

rs_ID	r²[population]
rs11119311	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2003682	0.90[AFR][1000 genomes];0.99[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2076223	0.92[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2076224	0.90[ASN][1000 genomes]
rs2356933	0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4433397	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4556360	0.96[AMR][1000 genomes];0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6540544	0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6683256	0.85[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs713073	0.86[AMR][1000 genomes];0.94[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs713074	0.86[AMR][1000 genomes];0.94[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs736137	0.90[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7518521	0.86[AMR][1000 genomes];0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7522730	0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7528476	0.96[AMR][1000 genomes];0.94[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7538805	0.89[EUR][1000 genomes]
rs7541558	0.84[ASN][1000 genomes]
rs926386	0.86[AMR][1000 genomes];0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs9429819	0.92[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs977441	0.92[EUR][1000 genomes];0.90[ASN][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	nsv999901	chr1:209600631-210205379	Flanking Active TSS Enhancers Weak transcription Active TSS Bivalent Enhancer Strong transcription Flanking Bivalent TSS/Enh ZNF genes & repeats Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	76 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:20 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:209738400-209743000	Weak transcription	Fetal Kidney	kidney
2	chr1:209739600-209743000	Weak transcription	Primary T helper naive cells from peripheral blood	blood
3	chr1:209739800-209743000	Weak transcription	Brain Substantia Nigra	brain
4	chr1:209741200-209743000	Weak transcription	Osteobl	bone
5	chr1:209741200-209743200	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
6	chr1:209741200-209743600	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
7	chr1:209741400-209743400	Enhancers	NHEK	skin
8	chr1:209741600-209743000	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
9	chr1:209741600-209743000	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
10	chr1:209741600-209743000	Weak transcription	HSMM	muscle
11	chr1:209741800-209743000	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
12	chr1:209741800-209743000	Weak transcription	Muscle Satellite Cultured Cells	--
13	chr1:209742000-209743000	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
14	chr1:209742000-209743000	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
15	chr1:209742400-209743000	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
16	chr1:209742600-209743400	Enhancers	Primary T killer memory cells from peripheral blood	blood
17	chr1:209742800-209743200	Bivalent Enhancer	Primary T cells from cord blood	blood
18	chr1:209742800-209743200	Active TSS	Monocytes-CD14+_RO01746	blood
19	chr1:209742800-209743400	Enhancers	Primary T regulatory cells fromperipheralblood	blood
20	chr1:209742800-209743600	Enhancers	HMEC	breast

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