Variant report

Variant	rs6540558
Chromosome Location	chr1:209981778-209981779
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	GATA2	chr1:209981419-209981841	SH-SY5Y	brain:	n/a	n/a
2	ZNF143	chr1:209981250-209981834	K562	blood:	n/a	chr1:209981755-209981774
3	MYC	chr1:209981392-209981811	MCF10A-Er-Src	breast:	n/a	n/a
4	KAP1	chr1:209981201-209981864	HEK293	kidney:	n/a	n/a
5	REST	chr1:209981423-209981788	SK-N-SH	brain:	n/a	n/a
6	BHLHE40	chr1:209981377-209981913	K562	blood:	n/a	n/a
7	EP300	chr1:209981293-209981829	SK-N-SH_RA	brain:	n/a	n/a
8	KAP1	chr1:209981188-209981961	U2OS	brain:	n/a	n/a
9	CUX1	chr1:209981330-209981873	K562	blood:	n/a	n/a
10	RCOR1	chr1:209981424-209981782	K562	blood:	n/a	n/a
11	STAT3	chr1:209981364-209981842	MCF10A-Er-Src	breast:	n/a	n/a
12	MAZ	chr1:209981375-209981839	K562	blood:	n/a	n/a
13	FOS	chr1:209981301-209981877	HUVEC	blood vessel:	n/a	chr1:209981571-209981582 chr1:209981572-209981583
14	FOSL2	chr1:209981448-209981816	A549	lung:	n/a	chr1:209981572-209981583
15	EP300	chr1:209981372-209981822	K562	blood:	n/a	n/a
16	FOXP2	chr1:209981415-209981851	PFSK-1	brain:	n/a	n/a
17	TCF7L2	chr1:209981483-209981824	Hela-S3	cervix:	n/a	n/a
18	ATF1	chr1:209981388-209981796	K562	blood:	n/a	n/a
19	GATA2	chr1:209981346-209981811	HUVEC	blood vessel:	n/a	n/a
20	RCOR1	chr1:209981362-209981882	K562	blood:	n/a	n/a
21	SIN3AK20	chr1:209981327-209981936	MCF-7	breast:	n/a	n/a
22	TEAD4	chr1:209981276-209981839	K562	blood:	n/a	n/a
23	FOSL2	chr1:209981352-209981821	SK-N-SH	brain:	n/a	chr1:209981572-209981583
24	REST	chr1:209981354-209981800	PFSK-1	brain:	n/a	n/a
25	TCF12	chr1:209981148-209982027	SK-N-SH	brain:	n/a	n/a
26	FOXA2	chr1:209981390-209981828	A549	lung:	n/a	n/a
27	FOSL2	chr1:209981215-209981956	SK-N-SH	brain:	n/a	chr1:209981572-209981583
28	ZNF263	chr1:209981357-209981885	HEK293-T-REx	kidney:	n/a	n/a
29	EP300	chr1:209981379-209981797	SK-N-SH_RA	brain:	n/a	n/a
30	MAX	chr1:209981406-209981804	K562	blood:	n/a	n/a
31	HCFC1	chr1:209981385-209981854	K562	blood:	n/a	n/a
32	CEBPB	chr1:209981424-209981789	K562	blood:	n/a	n/a
33	MEF2A	chr1:209981168-209981959	SK-N-SH	brain:	n/a	n/a
34	MYC	chr1:209981341-209981865	MCF10A-Er-Src	breast:	n/a	chr1:209981853-209981862
35	TBL1XR1	chr1:209981394-209981795	K562	blood:	n/a	n/a
36	JUN	chr1:209981354-209981823	HUVEC	blood vessel:	n/a	chr1:209981572-209981583
37	FOXP2	chr1:209981420-209981782	PFSK-1	brain:	n/a	n/a
38	POLR2A	chr1:209975033-209981799	MCF10A-Er-Src	breast:	n/a	n/a
39	CEBPB	chr1:209981406-209981802	IMR90	lung:	n/a	n/a
40	POLR2A	chr1:209981344-209981797	PFSK-1	brain:	n/a	n/a
41	CHD2	chr1:209981423-209981806	Hela-S3	cervix:	n/a	n/a
42	RAD21	chr1:209981392-209981793	SK-N-SH_RA	brain:	n/a	chr1:209981599-209981611 chr1:209981714-209981727
43	RCOR1	chr1:209981137-209982147	IMR90	lung:	n/a	n/a
44	STAT3	chr1:209981314-209981962	MCF10A-Er-Src	breast:	n/a	n/a
45	STAT3	chr1:209981363-209981995	MCF10A-Er-Src	breast:	n/a	n/a
46	PBX3	chr1:209981281-209981970	SK-N-SH	brain:	n/a	n/a
47	JUN	chr1:209981354-209981839	K562	blood:	n/a	chr1:209981572-209981583
48	JUND	chr1:209981205-209981958	SK-N-SH	brain:	n/a	chr1:209981572-209981583
49	SIN3AK20	chr1:209981321-209981785	SK-N-SH	brain:	n/a	n/a
50	STAT3	chr1:209981381-209981809	MCF10A-Er-Src	breast:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr1:209979052..209983681-chr1:210545344..210549112,5	K562	blood:
2	chr1:209981459..209983151-chr1:209995817..209998034,2	MCF-7	breast:
3	chr1:209981422..209983543-chr1:209995395..209998153,2	K562	blood:
4	chr1:209977871..209984485-chr1:209998424..210002427,6	K562	blood:
5	chr1:209980787..209983095-chr1:209985152..209988028,2	K562	blood:
6	chr1:209955520..209962214-chr1:209976009..209982555,8	K562	blood:
7	chr1:209968649..209970778-chr1:209979506..209982286,2	K562	blood:
8	chr1:209970799..209973393-chr1:209981570..209983608,2	K562	blood:
9	chr1:209979780..209981458-chr1:209981509..209984915,3	K562	blood:

Variant related genes	Relation type
IRF6	TF binding region
ENSG00000117597	Chromatin interaction
ENSG00000232222	Chromatin interaction
ENSG00000200972	Chromatin interaction
ENSG00000162757	Chromatin interaction

Extended variants
information (count: 15 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:12)

rs_ID	r²[population]
rs11806020	1.00[EUR][1000 genomes]
rs17015326	1.00[EUR][1000 genomes]
rs56655983	1.00[EUR][1000 genomes]
rs57139400	1.00[EUR][1000 genomes]
rs60014300	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs60079073	1.00[EUR][1000 genomes]
rs6540562	1.00[EUR][1000 genomes]
rs6684236	0.83[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs6692359	1.00[EUR][1000 genomes]
rs74156256	0.83[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs74156257	1.00[EUR][1000 genomes]
rs7550222	1.00[EUR][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	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
2	nsv1014034	chr1:209759648-210501731	Enhancers Weak transcription Flanking Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer Strong transcription Active TSS Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	45 gene(s)	inside rSNPs	diseases
3	nsv873139	chr1:209828955-210050794	Active TSS Enhancers Weak transcription Bivalent Enhancer Genic enhancers Strong transcription Flanking Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	27 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:54 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:209979600-209985000	Weak transcription	Gastric	stomach
2	chr1:209979800-209989200	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
3	chr1:209980000-209982000	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
4	chr1:209980000-209982000	Enhancers	Fetal Adrenal Gland	Adrenal Gland
5	chr1:209980000-209982200	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
6	chr1:209980000-209982200	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
7	chr1:209980000-209982200	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
8	chr1:209980000-209982200	Enhancers	Foreskin Fibroblast Primary Cells skin02	Skin
9	chr1:209980000-209982200	Enhancers	Stomach Mucosa	stomach
10	chr1:209980000-209982400	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
11	chr1:209980000-209982600	Enhancers	Breast Myoepithelial Primary Cells	Breast
12	chr1:209980000-209983600	Enhancers	Fetal Intestine Large	intestine
13	chr1:209980000-209983600	Enhancers	Fetal Intestine Small	intestine
14	chr1:209980200-209981800	Enhancers	Duodenum Mucosa	Duodenum
15	chr1:209980200-209982200	Enhancers	HUVEC	blood vessel
16	chr1:209980200-209982400	Enhancers	K562	blood
17	chr1:209980600-209981800	Flanking Active TSS	Foreskin Keratinocyte Primary Cells skin03	Skin
18	chr1:209980600-209982000	Enhancers	NH-A	brain
19	chr1:209980600-209982200	Enhancers	NHLF	lung
20	chr1:209980600-209982200	Enhancers	Osteobl	bone
21	chr1:209980800-209981800	Enhancers	Pancreas	Pancrea
22	chr1:209980800-209982000	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
23	chr1:209980800-209984400	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
24	chr1:209980800-209985600	Enhancers	HMEC	breast
25	chr1:209981000-209982000	Enhancers	ES-I3 Cell Line	embryonic stem cell
26	chr1:209981000-209982000	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
27	chr1:209981000-209982000	Enhancers	Muscle Satellite Cultured Cells	--
28	chr1:209981000-209982000	Enhancers	Foreskin Melanocyte Primary Cells skin01	Skin
29	chr1:209981000-209982000	Enhancers	HSMM	muscle
30	chr1:209981000-209982200	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
31	chr1:209981000-209982200	Enhancers	NHDF-Ad	bronchial
32	chr1:209981000-209982400	Enhancers	Placenta	Placenta
33	chr1:209981000-209985800	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
34	chr1:209981200-209982000	Enhancers	Hela-S3	cervix
35	chr1:209981200-209984400	Enhancers	NHEK	skin
36	chr1:209981400-209981800	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
37	chr1:209981400-209981800	Enhancers	Esophagus	oesophagus
38	chr1:209981400-209981800	Enhancers	Fetal Muscle Trunk	muscle
39	chr1:209981400-209981800	Enhancers	Sigmoid Colon	Sigmoid Colon
40	chr1:209981400-209981800	Enhancers	Skeletal Muscle Male	skeletal muscle
41	chr1:209981400-209981800	Enhancers	Stomach Smooth Muscle	stomach
42	chr1:209981400-209981800	Enhancers	Spleen	Spleen
43	chr1:209981400-209982000	Weak transcription	Right Ventricle	heart
44	chr1:209981600-209981800	Enhancers	iPS-20b Cell Line	embryonic stem cell
45	chr1:209981600-209981800	Enhancers	Adipose Nuclei	Adipose
46	chr1:209981600-209981800	Flanking Active TSS	Fetal Heart	heart
47	chr1:209981600-209981800	Enhancers	Fetal Lung	lung
48	chr1:209981600-209981800	Enhancers	Placenta Amnion	Placenta Amnion
49	chr1:209981600-209981800	Enhancers	Rectal Mucosa Donor 31	rectum
50	chr1:209981600-209981800	Enhancers	Right Atrium	heart

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