Variant report

Variant	rs12144178
Chromosome Location	chr1:241804700-241804701
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	EP300	chr1:241803745-241806107	A549	lung:	n/a	chr1:241804139-241804149 chr1:241804154-241804164 chr1:241803841-241803857 chr1:241804622-241804636
2	NR3C1	chr1:241804385-241804945	A549	lung:	n/a	n/a
3	E2F4	chr1:241803201-241804785	K562	blood:	n/a	chr1:241803839-241803848 chr1:241804035-241804044
4	NR3C1	chr1:241804320-241804907	A549	lung:	n/a	n/a
5	MAX	chr1:241803269-241805364	A549	lung:	n/a	chr1:241804047-241804056 chr1:241803840-241803850 chr1:241804048-241804055 chr1:241804047-241804056 chr1:241804047-241804057
6	JUND	chr1:241803958-241805583	Hela-S3	cervix:	n/a	chr1:241805169-241805180
7	BCL3	chr1:241803712-241804889	A549	lung:	n/a	n/a
8	MAX	chr1:241803199-241805449	Hela-S3	cervix:	n/a	chr1:241804047-241804056 chr1:241803840-241803850 chr1:241804048-241804055 chr1:241804047-241804056 chr1:241804047-241804057
9	RPC155	chr1:241804694-241805774	Hela-S3	cervix:	n/a	n/a
10	FOSL2	chr1:241803746-241805666	A549	lung:	n/a	n/a
11	CHD2	chr1:241803105-241805505	Hela-S3	cervix:	n/a	chr1:241803837-241803847
12	JUN	chr1:241804122-241805483	Hela-S3	cervix:	n/a	n/a
13	MAFK	chr1:241803857-241805405	Hela-S3	cervix:	n/a	chr1:241804877-241804892 chr1:241805164-241805179
14	TBP	chr1:241803265-241804928	HepG2	liver:	n/a	n/a
15	POLR2A	chr1:241802347-241805302	MCF10A-Er-Src	breast:	n/a	n/a
16	STAT3	chr1:241804030-241805438	MCF10A-Er-Src	breast:	n/a	chr1:241804179-241804199 chr1:241804951-241804958
17	CEBPB	chr1:241803232-241805865	Hela-S3	cervix:	n/a	chr1:241804623-241804634 chr1:241804621-241804632 chr1:241804621-241804634 chr1:241804623-241804632
18	MXI1	chr1:241803216-241805469	Hela-S3	cervix:	n/a	n/a
19	RAD21	chr1:241804066-241805453	Hela-S3	cervix:	n/a	n/a
20	HEY1	chr1:241804469-241804849	HepG2	liver:	n/a	n/a
21	SP1	chr1:241803416-241806004	A549	lung:	n/a	chr1:241803838-241803852 chr1:241803942-241803956 chr1:241803838-241803848 chr1:241803839-241803848 chr1:241803837-241803849 chr1:241803707-241803718 chr1:241803838-241803847 chr1:241803740-241803751 chr1:241803838-241803848 chr1:241803696-241803707 chr1:241803838-241803847 chr1:241803837-241803849
22	ELK1	chr1:241803629-241805441	Hela-S3	cervix:	n/a	n/a
23	TAF1	chr1:241804440-241804943	Hela-S3	cervix:	n/a	n/a
24	FOS	chr1:241803948-241805396	Hela-S3	cervix:	n/a	chr1:241805169-241805180
25	FOXA2	chr1:241804413-241804907	A549	lung:	n/a	n/a
26	E2F6	chr1:241803579-241805120	A549	lung:	n/a	chr1:241803839-241803848 chr1:241804035-241804044
27	EP300	chr1:241804568-241805418	HepG2	liver:	n/a	chr1:241804622-241804636
28	POLR2A	chr1:241802710-241804788	HepG2	liver:	n/a	n/a
29	POLR2A	chr1:241804278-241804964	Hela-S3	cervix:	n/a	n/a
30	TFAP2C	chr1:241803198-241805402	Hela-S3	cervix:	n/a	chr1:241803895-241803910
31	BCL3	chr1:241804258-241805505	A549	lung:	n/a	n/a
32	SMC3	chr1:241803172-241805588	Hela-S3	cervix:	n/a	n/a
33	NR3C1	chr1:241804595-241804766	A549	lung:	n/a	n/a
34	FOS	chr1:241804418-241805407	MCF10A-Er-Src	breast:	n/a	chr1:241805169-241805180
35	CEBPB	chr1:241804396-241804789	MCF-7	breast:	n/a	chr1:241804623-241804634 chr1:241804621-241804632 chr1:241804621-241804634 chr1:241804623-241804632
36	FOS	chr1:241804392-241805437	MCF10A-Er-Src	breast:	n/a	chr1:241805169-241805180
37	MAFK	chr1:241804107-241805353	HepG2	liver:	n/a	chr1:241804877-241804892 chr1:241805164-241805179
38	STAT3	chr1:241804011-241805462	MCF10A-Er-Src	breast:	n/a	chr1:241804179-241804199 chr1:241804951-241804958
39	CEBPB	chr1:241804433-241804825	K562	blood:	n/a	chr1:241804623-241804634 chr1:241804621-241804632 chr1:241804621-241804634 chr1:241804623-241804632
40	POLR2A	chr1:241801599-241805416	Hela-S3	cervix:	n/a	n/a
41	MYBL2	chr1:241804394-241805533	HepG2	liver:	n/a	n/a
42	POLR2A	chr1:241802932-241804993	HepG2	liver:	n/a	n/a
43	ARID3A	chr1:241804647-241805695	HepG2	liver:	n/a	n/a
44	CEBPB	chr1:241804401-241804949	A549	lung:	n/a	chr1:241804623-241804634 chr1:241804621-241804632 chr1:241804621-241804634 chr1:241804623-241804632
45	POLR2A	chr1:241802948-241804992	HepG2	liver:	n/a	n/a
46	ELK4	chr1:241803831-241804905	Hela-S3	cervix:	n/a	n/a
47	CREB1	chr1:241804376-241804958	A549	lung:	n/a	n/a
48	POLR2A	chr1:241804645-241804709	MCF-7	breast:	n/a	n/a
49	SMARCB1	chr1:241802469-241805865	Hela-S3	cervix:	n/a	n/a
50	MAX	chr1:241803261-241804856	HepG2	liver:	n/a	chr1:241804047-241804056 chr1:241803840-241803850 chr1:241804048-241804055 chr1:241804047-241804056 chr1:241804047-241804057

No.	Distal block	Cell Line	Cell type
1	chr1:241693526..241696085-chr1:241801417..241805051,3	MCF-7	breast:
2	chr1:241799844..241805446-chr1:241909864..241915090,9	MCF-7	breast:
3	chr1:241801200..241805205-chr1:241910998..241914529,7	MCF-7	breast:
4	chr1:241802310..241805173-chr1:241993132..241995327,2	K562	blood:
5	chr1:241804081..241806043-chr1:241997998..241999955,2	MCF-7	breast:
6	chr1:241796724..241805103-chr1:242008052..242013159,15	K562	blood:
7	chr1:241799658..241805161-chr1:242010004..242013743,14	K562	blood:
8	chr1:241799429..241802453-chr1:241804405..241808572,4	MCF-7	breast:
9	chr1:241801957..241807032-chr1:241808533..241817679,11	K562	blood:

Variant related genes	Relation type
OPN3	TF binding region
ENSG00000174371	Chromatin interaction
ENSG00000162843	Chromatin interaction
ENSG00000229022	Chromatin interaction
ENSG00000117009	Chromatin interaction

Extended variants
information (count: 16 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:6)

rs_ID	r²[population]
rs12141288	0.85[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs12141693	0.89[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs3753223	0.85[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs3765822	0.85[AMR][1000 genomes]
rs3765827	0.85[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs73139033	0.85[AMR][1000 genomes];0.82[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:10 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv918034	chr1:241072791-242005532	Weak transcription Enhancers Active TSS Bivalent/Poised TSS Strong transcription Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	32 gene(s)	inside rSNPs	diseases
2	nsv997966	chr1:241100739-242087629	Active TSS Genic enhancers Flanking Active TSS Strong transcription Enhancers Weak transcription Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	40 gene(s)	inside rSNPs	diseases
3	nsv1002214	chr1:241458939-242099790	Active TSS Weak transcription Enhancers Strong transcription Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	37 gene(s)	inside rSNPs	diseases
4	nsv549460	chr1:241494578-241833287	Genic enhancers Enhancers Weak transcription Flanking Bivalent TSS/Enh Active TSS Strong transcription Flanking Active TSS Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	27 gene(s)	inside rSNPs	diseases
5	nsv1009579	chr1:241499537-241824631	Bivalent/Poised TSS Enhancers Weak transcription Flanking Bivalent TSS/Enh Bivalent Enhancer Strong transcription Active TSS Genic enhancers Flanking Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	27 gene(s)	inside rSNPs	diseases
6	nsv530112	chr1:241522031-241840269	Strong transcription Enhancers Flanking Active TSS Weak transcription Flanking Bivalent TSS/Enh Active TSS Bivalent/Poised TSS Bivalent Enhancer Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	25 gene(s)	inside rSNPs	diseases
7	nsv873368	chr1:241533392-242195928	Weak transcription Active TSS Transcr. at gene 5' and 3' Enhancers Strong transcription Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer Flanking Active TSS Genic enhancers Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	36 gene(s)	inside rSNPs	diseases
8	nsv873372	chr1:241690554-242438293	Enhancers Strong transcription Weak transcription Flanking Active TSS Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Genic enhancers Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	40 gene(s)	inside rSNPs	diseases
9	nsv427963	chr1:241718799-241832833	Weak transcription Strong transcription Flanking Active TSS Enhancers Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	21 gene(s)	inside rSNPs	diseases
10	esv3399692	chr1:241802554-241805102	Flanking Active TSS Enhancers Active TSS Weak transcription Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region	20 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs12144178	CHML	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:40 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:241803600-241804800	Enhancers	Spleen	Spleen
2	chr1:241803800-241806200	Flanking Active TSS	Hela-S3	cervix
3	chr1:241804000-241804800	Enhancers	Gastric	stomach
4	chr1:241804000-241805000	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
5	chr1:241804000-241805600	Flanking Active TSS	HepG2	liver
6	chr1:241804000-241806200	Flanking Active TSS	A549	lung
7	chr1:241804200-241804800	ZNF genes & repeats	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
8	chr1:241804200-241804800	Enhancers	Primary monocytes fromperipheralblood	blood
9	chr1:241804200-241804800	Enhancers	Fetal Thymus	thymus
10	chr1:241804200-241805000	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
11	chr1:241804200-241805000	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
12	chr1:241804200-241805000	Enhancers	HMEC	breast
13	chr1:241804200-241805000	ZNF genes & repeats	K562	blood
14	chr1:241804200-241805000	Enhancers	NH-A	brain
15	chr1:241804200-241805200	Weak transcription	Liver	Liver
16	chr1:241804200-241805400	ZNF genes & repeats	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
17	chr1:241804200-241805400	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
18	chr1:241804200-241805400	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
19	chr1:241804200-241805600	Enhancers	Muscle Satellite Cultured Cells	--
20	chr1:241804200-241805600	Enhancers	Foreskin Fibroblast Primary Cells skin02	Skin
21	chr1:241804200-241805600	Enhancers	Stomach Mucosa	stomach
22	chr1:241804200-241805600	Enhancers	HUVEC	blood vessel
23	chr1:241804200-241805600	Enhancers	NHDF-Ad	bronchial
24	chr1:241804200-241805600	Enhancers	Osteobl	bone
25	chr1:241804200-241805800	Enhancers	Placenta	Placenta
26	chr1:241804200-241805800	Enhancers	NHEK	skin
27	chr1:241804200-241806800	Enhancers	Fetal Intestine Large	intestine
28	chr1:241804200-241808600	Weak transcription	Ovary	ovary
29	chr1:241804200-241809600	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
30	chr1:241804400-241804800	Enhancers	Brain Inferior Temporal Lobe	brain
31	chr1:241804400-241805000	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
32	chr1:241804400-241805800	Enhancers	Rectal Mucosa Donor 31	rectum
33	chr1:241804400-241809400	Weak transcription	Placenta Amnion	Placenta Amnion
34	chr1:241804400-241809600	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
35	chr1:241804600-241804800	Flanking Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
36	chr1:241804600-241804800	Flanking Active TSS	Foreskin Melanocyte Primary Cells skin03	Skin
37	chr1:241804600-241804800	Active TSS	Skeletal Muscle Female	skeletal muscle
38	chr1:241804600-241805000	Enhancers	Lung	lung
39	chr1:241804600-241805400	Weak transcription	Rectal Mucosa Donor 29	rectum
40	chr1:241804600-241805600	Enhancers	NHLF	lung

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