Variant report

Variant	rs58568360
Chromosome Location	chr3:119041825-119041826
allele	C/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	EP300	chr3:119041781-119042646	GM12878	blood:	n/a	chr3:119041973-119041987 chr3:119042149-119042165 chr3:119041956-119041972
2	POLR2A	chr3:119041258-119042260	A549	lung:	n/a	n/a
3	CTCF	chr3:119041558-119042073	K562	blood:	n/a	chr3:119041959-119041972 chr3:119041729-119041750 chr3:119041736-119041749 chr3:119041676-119041689 chr3:119042028-119042041 chr3:119041734-119041752 chr3:119041676-119041685
4	POLR2A	chr3:119041212-119042480	GM18951	blood:	n/a	n/a
5	TCF3	chr3:119041664-119042320	GM12878	blood:	n/a	n/a
6	HDAC2	chr3:119041299-119041988	H1-hESC	embryonic stem cell:	n/a	n/a
7	CREB1	chr3:119041780-119042047	A549	lung:	n/a	n/a
8	RAD21	chr3:119041630-119042023	SK-N-SH_RA	brain:	n/a	chr3:119041734-119041746 chr3:119041732-119041751 chr3:119041735-119041748
9	THAP1	chr3:119041755-119041973	K562	blood:	n/a	n/a
10	CTCF	chr3:119041511-119042007	MCF-7	breast:	n/a	chr3:119041959-119041972 chr3:119041729-119041750 chr3:119041736-119041749 chr3:119041676-119041689 chr3:119041734-119041752 chr3:119041676-119041685
11	PAX5	chr3:119041744-119042292	GM12892	blood:	n/a	n/a
12	E2F4	chr3:119041803-119042134	MCF10A-Er-Src	breast:	n/a	chr3:119042026-119042035
13	IKZF1	chr3:119041801-119042634	GM12878	blood:	n/a	n/a
14	ELF1	chr3:119041705-119042225	MCF-7	breast:	n/a	n/a
15	SP1	chr3:119041198-119042184	A549	lung:	n/a	chr3:119041681-119041693 chr3:119041678-119041692 chr3:119041684-119041698 chr3:119041795-119041807 chr3:119041293-119041307 chr3:119041682-119041691 chr3:119041797-119041806 chr3:119041419-119041429 chr3:119041795-119041807 chr3:119041796-119041805
16	ETS1	chr3:119041611-119042352	GM12878	blood:	n/a	chr3:119042196-119042213 chr3:119041680-119041691 chr3:119041791-119041802
17	YY1	chr3:119041674-119042262	HepG2	liver:	n/a	chr3:119041719-119041728 chr3:119042153-119042167 chr3:119042080-119042094 chr3:119042024-119042038 chr3:119042081-119042095 chr3:119041788-119041799
18	RELA	chr3:119041704-119042771	GM19099	blood:	n/a	chr3:119042019-119042028 chr3:119042019-119042028
19	POLR2A	chr3:119041767-119042124	Hela-S3	cervix:	n/a	n/a
20	CTCF	chr3:119041450-119042046	MCF-7	breast:	n/a	chr3:119041959-119041972 chr3:119041729-119041750 chr3:119041736-119041749 chr3:119041676-119041689 chr3:119042028-119042041 chr3:119041734-119041752 chr3:119041676-119041685
21	POU2F2	chr3:119041689-119042282	GM12891	blood:	n/a	n/a
22	POLR2A	chr3:119041571-119042301	HL-60	blood:	n/a	n/a
23	TAF1	chr3:119041437-119042291	ECC-1	luminal epithelium:	n/a	n/a
24	POLR2A	chr3:119040718-119042639	IMR90	lung:	n/a	n/a
25	GABPA	chr3:119041679-119042179	K562	blood:	n/a	chr3:119042026-119042035
26	MYC	chr3:119041317-119042420	NB4	blood:	n/a	chr3:119042031-119042041
27	MAZ	chr3:119041256-119042179	K562	blood:	n/a	chr3:119042031-119042041
28	JUND	chr3:119041478-119042397	K562	blood:	n/a	chr3:119042065-119042075 chr3:119042065-119042075 chr3:119041798-119041807 chr3:119042066-119042074 chr3:119042065-119042075
29	ZNF263	chr3:119041262-119042548	HEK293-T-REx	kidney:	n/a	chr3:119041626-119041635
30	MAFK	chr3:119041817-119042100	K562	blood:	n/a	chr3:119041919-119041935 chr3:119041920-119041934
31	EP300	chr3:119041750-119042179	A549	lung:	n/a	chr3:119041973-119041987 chr3:119042149-119042165 chr3:119041956-119041972
32	MAX	chr3:119041682-119042323	A549	lung:	n/a	chr3:119042031-119042041
33	MAX	chr3:119041694-119042551	GM12878	blood:	n/a	chr3:119042031-119042041
34	FOXP2	chr3:119041715-119042128	PFSK-1	brain:	n/a	n/a
35	MEF2A	chr3:119041663-119042297	GM12878	blood:	n/a	n/a
36	ATF2	chr3:119041645-119042605	GM12878	blood:	n/a	n/a
37	ZNF143	chr3:119041582-119042398	GM12878	blood:	n/a	chr3:119041792-119041802
38	ZNF143	chr3:119041598-119042043	H1-hESC	embryonic stem cell:	n/a	chr3:119041792-119041802
39	YY1	chr3:119041667-119042595	GM12891	blood:	n/a	chr3:119041719-119041728 chr3:119042153-119042167 chr3:119042080-119042094 chr3:119042024-119042038 chr3:119042081-119042095 chr3:119041788-119041799
40	ZBTB7A	chr3:119041279-119042418	ECC-1	luminal epithelium:	n/a	n/a
41	POU2F2	chr3:119041747-119042275	GM12878	blood:	n/a	n/a
42	POLR2A	chr3:119041260-119042608	GM18526	blood:	n/a	n/a
43	NFIC	chr3:119041685-119042531	GM12878	blood:	n/a	n/a
44	RELA	chr3:119041715-119042803	GM10847	blood:	n/a	chr3:119042019-119042028 chr3:119042019-119042028
45	MYC	chr3:119041806-119042191	MCF10A-Er-Src	breast:	n/a	chr3:119042031-119042041
46	EP300	chr3:119041789-119042352	GM12878	blood:	n/a	chr3:119041973-119041987 chr3:119042149-119042165 chr3:119041956-119041972
47	MEF2C	chr3:119041731-119042337	GM12878	blood:	n/a	n/a
48	RELA	chr3:119040978-119042718	GM15510	blood:	n/a	chr3:119042019-119042028 chr3:119042019-119042028
49	E2F6	chr3:119041728-119042105	K562	blood:	n/a	chr3:119041792-119041802 chr3:119042026-119042035
50	CTCF	chr3:119041680-119041830	GM12867	blood:	n/a	chr3:119041729-119041750 chr3:119041736-119041749 chr3:119041734-119041752

No.	Distal block	Cell Line	Cell type
1	chr3:119040381..119043387-chr3:119393976..119396207,3	K562	blood:
2	chr3:119039655..119042714-chr3:119058706..119061390,3	MCF-7	breast:
3	chr15:101817168..101817800-chr3:119041367..119041890,2	NB4	blood:
4	chr3:119016211..119028042-chr3:119037960..119043695,12	MCF-7	breast:
5	chr3:119041713..119043287-chr3:119530571..119533210,2	MCF-7	breast:
6	chr3:119012312..119014941-chr3:119040203..119043471,4	MCF-7	breast:
7	chr3:119011662..119015799-chr3:119040784..119043293,4	MCF-7	breast:
8	chr3:119041710..119043371-chr3:119051543..119054199,2	K562	blood:
9	chr3:119040625..119043456-chr3:119181021..119182647,3	MCF-7	breast:
10	chr3:119040520..119043561-chr3:119060040..119062334,3	MCF-7	breast:

Variant related genes	Relation type
ARHGAP31-AS1	TF binding region
ARHGAP31	TF binding region
ENSG00000242829	Chromatin interaction
ENSG00000131871	Chromatin interaction
ENSG00000176142	Chromatin interaction
ENSG00000207310	Chromatin interaction
ENSG00000031081	Chromatin interaction
ENSG00000138495	Chromatin interaction

Extended variants
information (count: 36 )
Associated
traits (count: 0)

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

rs_ID	r²[population]
rs10511386	0.90[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs10934490	0.89[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12497738	0.90[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13314464	0.90[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1375135	0.85[AFR][1000 genomes];0.90[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1448434	0.90[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs2278781	0.90[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs4687994	0.80[EUR][1000 genomes]
rs62265236	0.89[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs62265237	0.84[AMR][1000 genomes];0.94[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs6438518	0.81[AMR][1000 genomes];0.94[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs6438519	0.81[AMR][1000 genomes];0.94[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs6438520	0.90[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs6438521	0.90[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs6438522	0.84[AMR][1000 genomes];0.94[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs6438523	0.90[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs6762580	0.90[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs6785727	0.88[AFR][1000 genomes];0.90[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6786522	0.88[AFR][1000 genomes];0.90[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6789881	0.86[AFR][1000 genomes];0.90[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6799733	0.88[AFR][1000 genomes];0.90[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7610546	0.84[AMR][1000 genomes];0.94[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs7611832	0.90[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs7644570	0.84[AMR][1000 genomes];0.94[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs7649480	0.89[EUR][1000 genomes]
rs7649930	0.88[AFR][1000 genomes];0.90[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9822211	0.88[AFR][1000 genomes];0.90[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9825078	0.87[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs9834750	0.88[AFR][1000 genomes];0.90[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9847963	0.88[AFR][1000 genomes];0.90[AMR][1000 genomes];0.94[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs9861372	0.88[AFR][1000 genomes];0.90[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9861688	0.89[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9877740	0.88[AFR][1000 genomes];0.90[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv3487859	chr3:118570588-119419623	Weak transcription Active TSS Strong transcription Enhancers Flanking Active TSS ZNF genes & repeats Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	61 gene(s)	inside rSNPs	diseases
2	esv3487860	chr3:118570588-119419623	Strong transcription Enhancers Active TSS Weak transcription ZNF genes & repeats Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	61 gene(s)	inside rSNPs	diseases
3	nsv829694	chr3:119011488-119153579	Enhancers Strong transcription Weak transcription Active TSS Flanking Active TSS Flanking Bivalent TSS/Enh Genic enhancers ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	14 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	chr3:119040600-119042400	Active TSS	H9 Derived Neuron Cultured Cells	ES cell derived
2	chr3:119040600-119042400	Active TSS	iPS-15b Cell Line	embryonic stem cell
3	chr3:119040600-119042600	Flanking Active TSS	HUVEC	blood vessel
4	chr3:119040600-119043000	Active TSS	ES-I3 Cell Line	embryonic stem cell
5	chr3:119040600-119043000	Active TSS	iPS-20b Cell Line	embryonic stem cell
6	chr3:119040800-119042200	Active TSS	HUES64 Cell Line	embryonic stem cell
7	chr3:119040800-119042400	Active TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
8	chr3:119040800-119042400	Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
9	chr3:119040800-119042600	Flanking Active TSS	Dnd41	blood
10	chr3:119040800-119042800	Flanking Active TSS	Primary hematopoietic stem cells short term culture	blood
11	chr3:119041000-119042200	Active TSS	Fetal Brain Female	brain
12	chr3:119041000-119042400	Active TSS	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
13	chr3:119041000-119042400	Active TSS	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
14	chr3:119041000-119042400	Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
15	chr3:119041000-119042400	Active TSS	Breast Myoepithelial Primary Cells	Breast
16	chr3:119041000-119042400	Active TSS	Brain Germinal Matrix	brain
17	chr3:119041000-119042400	Active TSS	Brain Substantia Nigra	brain
18	chr3:119041000-119042400	Active TSS	Colon Smooth Muscle	Colon
19	chr3:119041000-119042400	Active TSS	Duodenum Smooth Muscle	Duodenum
20	chr3:119041000-119042400	Active TSS	Fetal Intestine Large	intestine
21	chr3:119041000-119042400	Active TSS	Fetal Lung	lung
22	chr3:119041000-119042400	Active TSS	NHLF	lung
23	chr3:119041000-119042600	Active TSS	H9 Cell Line	embryonic stem cell
24	chr3:119041000-119042600	Flanking Active TSS	Foreskin Fibroblast Primary Cells skin02	Skin
25	chr3:119041000-119042600	Active TSS	Rectal Mucosa Donor 29	rectum
26	chr3:119041000-119042800	Active TSS	Pancreatic Islets	Pancreatic Islet
27	chr3:119041000-119042800	Active TSS	K562	blood
28	chr3:119041200-119042200	Active TSS	GM12878-XiMat	blood
29	chr3:119041200-119042400	Active TSS	iPS-18 Cell Line	embryonic stem cell
30	chr3:119041200-119042400	Active TSS	iPS DF 6.9 Cell Line	embryonic stem cell
31	chr3:119041200-119042400	Flanking Active TSS	Foreskin Melanocyte Primary Cells skin03	Skin
32	chr3:119041200-119042400	Active TSS	Aorta	Aorta
33	chr3:119041200-119042400	Active TSS	Liver	Liver
34	chr3:119041200-119042400	Active TSS	Brain Cingulate Gyrus	brain
35	chr3:119041200-119042400	Active TSS	Brain Dorsolateral Prefrontal Cortex	brain
36	chr3:119041200-119042400	Active TSS	Left Ventricle	heart
37	chr3:119041200-119042400	Active TSS	Sigmoid Colon	Sigmoid Colon
38	chr3:119041200-119042400	Active TSS	Spleen	Spleen
39	chr3:119041200-119042400	Active TSS	Hela-S3	cervix
40	chr3:119041200-119042600	Active TSS	Ovary	ovary
41	chr3:119041200-119042800	Active TSS	Fetal Kidney	kidney
42	chr3:119041200-119042800	Flanking Active TSS	HMEC	breast
43	chr3:119041400-119042000	Active TSS	ES-UCSF4 Cell Line	embryonic stem cell
44	chr3:119041400-119042000	Transcr. at gene 5' and 3'	Primary T helper 17 cells PMA-I stimulated	--
45	chr3:119041400-119042200	Active TSS	HUES48 Cell Line	embryonic stem cell
46	chr3:119041400-119042200	Active TSS	Primary neutrophils fromperipheralblood	blood
47	chr3:119041400-119042200	Active TSS	Brain Hippocampus Middle	brain
48	chr3:119041400-119042200	Active TSS	Brain Inferior Temporal Lobe	brain
49	chr3:119041400-119042200	Enhancers	Fetal Brain Male	brain
50	chr3:119041400-119042200	Active TSS	Small Intestine	intestine

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