Variant report

Variant	rs58868226
Chromosome Location	chr3:113416674-113416675
allele	C/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	E2F4	chr3:113416637-113416964	MCF10A-Er-Src	breast:	n/a	n/a
2	KAP1	chr3:113415699-113416767	U2OS	brain:	n/a	n/a
3	SIN3AK20	chr3:113415273-113416698	MCF-7	breast:	n/a	n/a
4	GTF2F1	chr3:113415624-113416755	Hela-S3	cervix:	n/a	n/a
5	MYC	chr3:113416446-113416728	MCF10A-Er-Src	breast:	n/a	n/a
6	TBP	chr3:113415665-113416927	Hela-S3	cervix:	n/a	n/a
7	MAZ	chr3:113414194-113417282	IMR90	lung:	n/a	chr3:113415400-113415410
8	MYC	chr3:113416436-113416837	MCF10A-Er-Src	breast:	n/a	n/a
9	POLR2A	chr3:113414767-113416688	GM15510	blood:	n/a	n/a
10	POLR2A	chr3:113414727-113416742	GM12878	blood:	n/a	n/a
11	MYBL2	chr3:113415395-113416776	HepG2	liver:	n/a	n/a
12	WRNIP1	chr3:113415594-113416758	GM12878	blood:	n/a	n/a
13	TFAP2A	chr3:113415666-113416698	Hela-S3	cervix:	n/a	chr3:113416202-113416214 chr3:113415725-113415737 chr3:113416202-113416214 chr3:113416202-113416214 chr3:113415725-113415736 chr3:113416202-113416214 chr3:113416201-113416216
14	RUNX3	chr3:113414834-113416733	GM12878	blood:	n/a	chr3:113416448-113416457
15	TFAP2C	chr3:113415538-113416712	Hela-S3	cervix:	n/a	chr3:113416201-113416216
16	MAX	chr3:113415474-113416778	Hela-S3	cervix:	n/a	n/a
17	CEBPB	chr3:113415494-113416843	Hela-S3	cervix:	n/a	chr3:113416483-113416496
18	HCFC1	chr3:113414170-113416977	Hela-S3	cervix:	n/a	n/a
19	POLR2A	chr3:113414410-113416722	Raji	blood:	n/a	n/a
20	TBL1XR1	chr3:113415577-113416782	GM12878	blood:	n/a	n/a
21	ARID3A	chr3:113416102-113416874	HepG2	liver:	n/a	n/a
22	KAP1	chr3:113415652-113416868	HEK293	kidney:	n/a	n/a
23	POLR2A	chr3:113416310-113416737	HepG2	liver:	n/a	n/a
24	NFYA	chr3:113415470-113416716	Hela-S3	cervix:	n/a	chr3:113415623-113415633 chr3:113415621-113415636 chr3:113415621-113415636 chr3:113415591-113415601 chr3:113415621-113415634 chr3:113415621-113415635
25	RFX5	chr3:113415447-113416905	Hela-S3	cervix:	n/a	n/a
26	POLR2A	chr3:113414481-113416784	GM19099	blood:	n/a	n/a
27	POLR2A	chr3:113416414-113416917	HepG2	liver:	n/a	n/a
28	CEBPB	chr3:113416189-113416805	HepG2	liver:	n/a	chr3:113416483-113416496
29	FOXA2	chr3:113416455-113416750	HepG2	liver:	n/a	n/a
30	POLR2A	chr3:113414131-113416896	GM12891	blood:	n/a	n/a
31	TCF12	chr3:113415429-113416703	A549	lung:	n/a	n/a
32	POLR2A	chr3:113414736-113416907	GM18951	blood:	n/a	n/a
33	MXI1	chr3:113414365-113416857	GM12878	blood:	n/a	n/a
34	TCF7L2	chr3:113416108-113416822	PANC-1	pancreas:	n/a	chr3:113416769-113416776
35	FOXA1	chr3:113416254-113416768	HepG2	liver:	n/a	n/a
36	POLR2A	chr3:113414216-113416718	HepG2	liver:	n/a	n/a
37	RUNX3	chr3:113414782-113416679	GM12878	blood:	n/a	chr3:113416448-113416457
38	POLR2A	chr3:113414712-113416772	GM18505	blood:	n/a	n/a
39	POLR2A	chr3:113416656-113416676	Hela-S3	cervix:	n/a	n/a
40	MTA3	chr3:113415656-113416742	GM12878	blood:	n/a	n/a
41	POLR2A	chr3:113414281-113416885	MCF10A-Er-Src	breast:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr3:113415039..113416819-chr5:179245947..179248252,2	MCF-7	breast:
2	chr3:113414100..113416894-chr3:113456404..113459311,4	K562	blood:
3	chr3:113415334..113416894-chr3:113456404..113458988,2	K562	blood:
4	chr3:113392230..113394314-chr3:113415307..113418198,2	MCF-7	breast:
5	chr3:113416571..113418073-chr3:113464513..113466698,2	MCF-7	breast:

Variant related genes	Relation type
KIAA2018	TF binding region
ENSG00000242659	Chromatin interaction
ENSG00000161011	Chromatin interaction
ENSG00000114573	Chromatin interaction
ENSG00000121579	Chromatin interaction
ENSG00000176542	Chromatin interaction

Extended variants
information (count: 6 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:4)

rs_ID	r²[population]
rs55868922	1.00[AMR][1000 genomes]
rs57010522	1.00[EUR][1000 genomes]
rs73854819	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs9839237	1.00[EUR][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	nsv1013506	chr3:112890608-113680951	Weak transcription Bivalent/Poised TSS Enhancers Strong transcription ZNF genes & repeats Genic enhancers Active TSS Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	51 gene(s)	inside rSNPs	diseases
2	nsv1004000	chr3:113116778-113513899	Weak transcription Strong transcription ZNF genes & repeats Active TSS Enhancers Flanking Active TSS Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	34 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:126 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:113413600-113416800	Active TSS	Pancreatic Islets	Pancreatic Islet
2	chr3:113413600-113417200	Active TSS	GM12878-XiMat	blood
3	chr3:113413800-113416800	Active TSS	Fetal Intestine Large	intestine
4	chr3:113413800-113416800	Active TSS	Small Intestine	intestine
5	chr3:113413800-113417200	Active TSS	Fetal Intestine Small	intestine
6	chr3:113414000-113416800	Active TSS	Fetal Muscle Trunk	muscle
7	chr3:113414000-113416800	Active TSS	Sigmoid Colon	Sigmoid Colon
8	chr3:113414000-113417000	Active TSS	Foreskin Fibroblast Primary Cells skin02	Skin
9	chr3:113414000-113417000	Active TSS	K562	blood
10	chr3:113414000-113417200	Active TSS	IMR90 fetal lung fibroblasts Cell Line	lung
11	chr3:113414200-113416800	Active TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
12	chr3:113414200-113416800	Active TSS	Foreskin Melanocyte Primary Cells skin01	Skin
13	chr3:113414200-113416800	Active TSS	Aorta	Aorta
14	chr3:113414200-113416800	Active TSS	Psoas Muscle	Psoas
15	chr3:113414200-113416800	Active TSS	HepG2	liver
16	chr3:113414200-113417000	Active TSS	H1 Cell Line	embryonic stem cell
17	chr3:113414200-113417000	Active TSS	HMEC	breast
18	chr3:113414200-113417200	Active TSS	Right Atrium	heart
19	chr3:113414200-113418200	Active TSS	NHLF	lung
20	chr3:113414400-113416800	Active TSS	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
21	chr3:113414400-113416800	Active TSS	iPS DF 6.9 Cell Line	embryonic stem cell
22	chr3:113414400-113416800	Active TSS	Primary T cells fromperipheralblood	blood
23	chr3:113414400-113416800	Active TSS	Primary T killer memory cells from peripheral blood	blood
24	chr3:113414400-113416800	Active TSS	Fetal Kidney	kidney
25	chr3:113414400-113416800	Active TSS	Left Ventricle	heart
26	chr3:113414400-113416800	Active TSS	Ovary	ovary
27	chr3:113414400-113416800	Active TSS	Pancreas	Pancrea
28	chr3:113414400-113416800	Active TSS	Placenta Amnion	Placenta Amnion
29	chr3:113414400-113416800	Active TSS	Right Ventricle	heart
30	chr3:113414400-113416800	Active TSS	HSMMtube	muscle
31	chr3:113414400-113416800	Active TSS	NHDF-Ad	bronchial
32	chr3:113414400-113417000	Active TSS	Stomach Smooth Muscle	stomach
33	chr3:113414400-113417200	Active TSS	Skeletal Muscle Male	skeletal muscle
34	chr3:113414400-113417600	Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
35	chr3:113414400-113418400	Active TSS	HUES6 Cell Line	embryonic stem cell
36	chr3:113414600-113416800	Active TSS	H9 Cell Line	embryonic stem cell
37	chr3:113414600-113416800	Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
38	chr3:113414600-113416800	Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
39	chr3:113414600-113416800	Active TSS	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
40	chr3:113414600-113416800	Active TSS	Fetal Muscle Leg	muscle
41	chr3:113414600-113416800	Active TSS	HSMM	muscle
42	chr3:113414600-113417000	Active TSS	Primary T cells effector/memory enriched fromperipheralblood	blood
43	chr3:113414600-113417000	Active TSS	Fetal Lung	lung
44	chr3:113414600-113417200	Active TSS	Rectal Mucosa Donor 29	rectum
45	chr3:113414600-113417600	Active TSS	iPS-15b Cell Line	embryonic stem cell
46	chr3:113414600-113417800	Active TSS	HUES64 Cell Line	embryonic stem cell
47	chr3:113414600-113418400	Active TSS	ES-I3 Cell Line	embryonic stem cell
48	chr3:113414800-113416800	Active TSS	iPS-18 Cell Line	embryonic stem cell
49	chr3:113414800-113416800	Active TSS	Hela-S3	cervix
50	chr3:113415000-113417200	Active TSS	Foreskin Keratinocyte Primary Cells skin03	Skin

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