Variant report

Variant	rs12459929
Chromosome Location	chr19:41732610-41732611
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	ATF3	chr19:41731186-41733152	A549	lung:	n/a	chr19:41731637-41731650 chr19:41732251-41732260
2	SIN3AK20	chr19:41731178-41732786	HCT-116	colon:	n/a	n/a
3	MAZ	chr19:41731596-41732610	HepG2	liver:	n/a	chr19:41732217-41732226 chr19:41732252-41732262 chr19:41732215-41732224 chr19:41732218-41732225
4	SIN3AK20	chr19:41731231-41732772	HCT-116	colon:	n/a	n/a
5	POLR2A	chr19:41732165-41732766	HepG2	liver:	n/a	n/a
6	SMARCC1	chr19:41731299-41732741	Hela-S3	cervix:	n/a	chr19:41732095-41732104
7	EP300	chr19:41731029-41733372	A549	lung:	n/a	chr19:41732177-41732186 chr19:41732179-41732188 chr19:41732175-41732191 chr19:41732187-41732203 chr19:41731857-41731873
8	MAX	chr19:41731440-41732897	HepG2	liver:	n/a	chr19:41732217-41732226 chr19:41732252-41732262 chr19:41732215-41732224 chr19:41732218-41732225
9	FOXP2	chr19:41731201-41732816	PFSK-1	brain:	n/a	chr19:41731516-41731528
10	CEBPB	chr19:41731308-41732660	A549	lung:	n/a	n/a
11	MYC	chr19:41732025-41732656	HepG2	liver:	n/a	chr19:41732217-41732226 chr19:41732252-41732262 chr19:41732215-41732224 chr19:41732218-41732225
12	REST	chr19:41731206-41733199	A549	lung:	n/a	chr19:41733063-41733076 chr19:41732188-41732198
13	CBX3	chr19:41731407-41732712	K562	blood:	n/a	n/a
14	POLR2A	chr19:41731729-41732809	A549	lung:	n/a	n/a
15	NFIC	chr19:41731250-41732808	SK-N-SH	brain:	n/a	n/a
16	FOXA2	chr19:41731218-41732928	A549	lung:	n/a	chr19:41731516-41731528
17	UBTF	chr19:41731599-41732638	K562	blood:	n/a	n/a
18	MAX	chr19:41731852-41732954	HepG2	liver:	n/a	chr19:41732217-41732226 chr19:41732252-41732262 chr19:41732215-41732224 chr19:41732218-41732225
19	MYC	chr19:41731483-41732632	HUVEC	blood vessel:	n/a	chr19:41732217-41732226 chr19:41732252-41732262 chr19:41732215-41732224 chr19:41732218-41732225
20	MAX	chr19:41729124-41733421	A549	lung:	n/a	chr19:41732217-41732226 chr19:41729661-41729670 chr19:41732252-41732262 chr19:41732215-41732224 chr19:41732218-41732225
21	HEY1	chr19:41732277-41732780	K562	blood:	n/a	n/a
22	FOSL2	chr19:41731180-41732778	A549	lung:	n/a	chr19:41731564-41731576 chr19:41732094-41732106 chr19:41732267-41732276 chr19:41732097-41732108 chr19:41732095-41732104 chr19:41731853-41731867
23	E2F6	chr19:41731655-41732732	A549	lung:	n/a	chr19:41732047-41732056 chr19:41732248-41732260 chr19:41732251-41732260 chr19:41732181-41732191 chr19:41732105-41732115
24	TBP	chr19:41731525-41732619	HepG2	liver:	n/a	n/a
25	MAX	chr19:41731398-41732653	NB4	blood:	n/a	chr19:41732217-41732226 chr19:41732252-41732262 chr19:41732215-41732224 chr19:41732218-41732225
26	POLR2A	chr19:41731038-41732909	HUVEC	blood vessel:	n/a	n/a
27	SIN3AK20	chr19:41731135-41733273	A549	lung:	n/a	n/a
28	PBX3	chr19:41731112-41733271	A549	lung:	n/a	n/a
29	TCF7L2	chr19:41731578-41732632	Hela-S3	cervix:	n/a	chr19:41732095-41732104
30	POLR2A	chr19:41731657-41732904	K562	blood:	n/a	n/a
31	E2F6	chr19:41731518-41732754	K562	blood:	n/a	chr19:41732047-41732056 chr19:41732248-41732260 chr19:41732251-41732260 chr19:41732181-41732191 chr19:41732105-41732115
32	TFAP2C	chr19:41731324-41732824	Hela-S3	cervix:	n/a	chr19:41732155-41732170
33	TCF12	chr19:41731354-41732643	SK-N-SH	brain:	n/a	chr19:41732002-41732009
34	POLR2A	chr19:41731726-41732906	A549	lung:	n/a	n/a
35	TEAD4	chr19:41731321-41732917	A549	lung:	n/a	n/a
36	TCF12	chr19:41731404-41732668	ECC-1	luminal epithelium:	n/a	chr19:41732002-41732009
37	SP1	chr19:41731941-41732805	HepG2	liver:	n/a	chr19:41732250-41732264 chr19:41732250-41732259 chr19:41732074-41732085 chr19:41732250-41732259 chr19:41732251-41732260 chr19:41732249-41732261
38	FOSL2	chr19:41731411-41732834	HepG2	liver:	n/a	chr19:41731564-41731576 chr19:41732094-41732106 chr19:41732267-41732276 chr19:41732097-41732108 chr19:41732095-41732104 chr19:41731853-41731867
39	USF1	chr19:41731386-41732700	A549	lung:	n/a	chr19:41732180-41732196 chr19:41732355-41732366
40	ELF1	chr19:41731843-41732626	K562	blood:	n/a	chr19:41732177-41732186 chr19:41732064-41732073
41	HEY1	chr19:41732032-41732662	HepG2	liver:	n/a	chr19:41732217-41732226
42	MAZ	chr19:41731016-41733348	IMR90	lung:	n/a	chr19:41732217-41732226 chr19:41732252-41732262 chr19:41732215-41732224 chr19:41732218-41732225
43	MAX	chr19:41731392-41732715	SK-N-SH	brain:	n/a	chr19:41732217-41732226 chr19:41732252-41732262 chr19:41732215-41732224 chr19:41732218-41732225
44	POLR2A	chr19:41731080-41732633	PANC-1	pancreas:	n/a	n/a
45	BHLHE40	chr19:41731356-41732770	A549	lung:	n/a	chr19:41732180-41732196
46	ATF3	chr19:41731184-41733132	A549	lung:	n/a	chr19:41731637-41731650 chr19:41732251-41732260
47	FOSL1	chr19:41731203-41732738	HCT-116	colon:	n/a	chr19:41731564-41731576 chr19:41732094-41732106 chr19:41732267-41732276 chr19:41732097-41732108 chr19:41732095-41732104 chr19:41731853-41731867
48	POLR2A	chr19:41731212-41733160	HepG2	liver:	n/a	n/a
49	EP300	chr19:41731294-41732819	SK-N-SH	brain:	n/a	chr19:41732177-41732186 chr19:41732179-41732188 chr19:41732175-41732191 chr19:41732187-41732203 chr19:41731857-41731873
50	SMC3	chr19:41731538-41732610	Hela-S3	cervix:	n/a	n/a

No.	Chromosome Location	Cell Line	Cell type	Cell Stage
1	chr19:41732589-41732639	HEK293	kidney:	embryo
2	chr19:41732589-41732639	RPTEC	kidney:	n/a
3	chr19:41732589-41732639	K562	blood:	n/a
4	chr19:41732589-41732639	AG09309	skin:	n/a
5	chr19:41732589-41732639	Hela-S3	cervix:	n/a
6	chr19:41732589-41732639	HRE	kidney:	n/a
7	chr19:41732589-41732639	HNPCEpiC	eye:	n/a
8	chr19:41732589-41732639	HCT-116	colon:	n/a
9	chr19:41732589-41732639	Caco-2	colon:	n/a
10	chr19:41732589-41732639	SK-N-MC	brain:	n/a
11	chr19:41732589-41732639	ProgFib	skin:	n/a
12	chr19:41732589-41732639	ECC-1	luminal epithelium:	n/a
13	chr19:41732589-41732639	HPAEpiC	pulmonary alveolar:	n/a
14	chr19:41732589-41732639	HepG2	liver:	n/a
15	chr19:41732589-41732639	GM12892	blood:	n/a
16	chr19:41732589-41732639	SK-N-SH	brain:	n/a
17	chr19:41732589-41732639	SKMC	muscle:	n/a
18	chr19:41732589-41732639	A549	lung:	n/a
19	chr19:41732589-41732639	HCPEpiC	choroid plexus:	n/a
20	chr19:41732589-41732639	PrEC	prostate:	n/a
21	chr19:41732589-41732639	IMR90	lung:	fetal
22	chr19:41732589-41732639	HEEpiC	esophagus:	n/a
23	chr19:41732589-41732639	NHBE	bronchial:	n/a
24	chr19:41732589-41732639	AG10803	skin:	n/a
25	chr19:41732589-41732639	Jurkat	blood:	n/a
26	chr19:41732589-41732639	T-47D	breast:	n/a
27	chr19:41732589-41732639	CMK	blood:	n/a
28	chr19:41732589-41732639	H1-hESC	embryonic stem cell:	embryo
29	chr19:41732589-41732639	LNCaP	prostate:	n/a
30	chr19:41732589-41732639	HRPEpiC	eye:	n/a
31	chr19:41732589-41732639	AG09319	gingival:	n/a
32	chr19:41732589-41732639	GM12891	blood:	n/a
33	chr19:41732589-41732639	NHDF-neo	bronchial:	n/a
34	chr19:41732589-41732639	HIPEpiC	eye:	n/a
35	chr19:41732589-41732639	MCF10A-Er-Src	breast:	n/a
36	chr19:41732589-41732639	MCF-7	breast:	n/a
37	chr19:41732589-41732639	BJ	skin:	n/a
38	chr19:41732589-41732639	GM06990	blood:	n/a
39	chr19:41732589-41732639	U87	brain:	n/a
40	chr19:41732589-41732639	PANC-1	pancreas:	n/a
41	chr19:41732589-41732639	HRCEpiC	kidney:	n/a
42	chr19:41732589-41732639	NT2-D1	testis:	n/a
43	chr19:41732589-41732639	NH-A	brain:	n/a
44	chr19:41732589-41732639	HL-60	blood:	n/a
45	chr19:41732589-41732639	NB4	blood:	n/a
46	chr19:41732589-41732639	SAEC	small airway:	n/a
47	chr19:41732589-41732639	BE2_C	brain:	n/a
48	chr19:41732589-41732639	ovcar-3	ovarian:	n/a
49	chr19:41732589-41732639	GM12878	blood:	n/a
50	chr19:41732589-41732639	PFSK-1	brain:	n/a

No.	Distal block	Cell Line	Cell type
1	chr19:41731896..41732688-chr9:16704803..16705712,2	Hela-S3	cervix:
2	chr19:41729266..41732729-chr19:41766701..41770009,7	K562	blood:
3	chr16:2205027..2205724-chr19:41732119..41732657,2	Hela-S3	cervix:
4	chr19:41732172..41733076-chr8:128747187..128747713,2	Hela-S3	cervix:
5	chr19:41725446..41729347-chr19:41729788..41733704,5	K562	blood:
6	chr19:41730545..41733193-chr19:41768273..41769945,2	MCF-7	breast:
7	chr19:41726271..41727956-chr19:41730948..41733143,2	MCF-7	breast:

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-TGFB1-3	chr19:41732389-41732667	expReg_chr19_5280_-

Variant related genes	Relation type
ENSG00000269652	TF binding region
AXL	TF binding region
ENSG00000269652	CpG island
AXL	CpG island
ENSG00000167601	Chromatin interaction
ENSG00000260260	Chromatin interaction
ENSG00000136997	Chromatin interaction
ENSG00000105323	Chromatin interaction
ENSG00000206630	Chromatin interaction
ENSG00000269652	Chromatin interaction
ENSG00000173068	Chromatin interaction
ENSG00000131653	Chromatin interaction

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

rSNPs within LD-proxies of this variant (count:14)

rs_ID	r²[population]
rs12459996	0.80[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12461203	0.80[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs15052	1.00[ASN][1000 genomes]
rs17251589	0.80[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4803447	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs55841050	0.80[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs55994820	0.80[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs56254331	1.00[ASN][1000 genomes]
rs73043273	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73045223	0.80[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73045226	0.80[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73045231	0.80[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73045269	1.00[ASN][1000 genomes]
rs8109440	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[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	nsv911768	chr19:41680424-41748753	Flanking Bivalent TSS/Enh Active TSS Enhancers Strong transcription Genic enhancers Transcr. at gene 5' and 3' Flanking Active TSS Bivalent/Poised TSS Bivalent Enhancer Weak transcription ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	16 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:122 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr19:41724400-41733200	Transcr. at gene 5' and 3'	Foreskin Fibroblast Primary Cells skin02	Skin
2	chr19:41726000-41733200	Transcr. at gene 5' and 3'	Foreskin Fibroblast Primary Cells skin01	Skin
3	chr19:41729200-41732800	Transcr. at gene 5' and 3'	NHLF	lung
4	chr19:41730200-41762600	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
5	chr19:41731000-41732800	Enhancers	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
6	chr19:41731200-41732800	Transcr. at gene 5' and 3'	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
7	chr19:41731200-41732800	Transcr. at gene 5' and 3'	NH-A	brain
8	chr19:41731200-41732800	Transcr. at gene 5' and 3'	NHEK	skin
9	chr19:41731200-41733000	Flanking Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
10	chr19:41731400-41732800	Flanking Active TSS	Cortex derived primary cultured neurospheres	brain
11	chr19:41731600-41732800	Flanking Active TSS	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
12	chr19:41731600-41732800	Flanking Bivalent TSS/Enh	Fetal Brain Female	brain
13	chr19:41731600-41732800	Flanking Active TSS	Fetal Muscle Trunk	muscle
14	chr19:41731600-41733000	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Female	--
15	chr19:41731600-41733000	Flanking Active TSS	Fetal Muscle Leg	muscle
16	chr19:41731600-41733000	Flanking Active TSS	Stomach Smooth Muscle	stomach
17	chr19:41731600-41733200	Flanking Active TSS	Primary T helper cells PMA-I stimulated	--
18	chr19:41731600-41733200	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
19	chr19:41731800-41732800	Flanking Active TSS	H9 Derived Neuron Cultured Cells	ES cell derived
20	chr19:41731800-41732800	Flanking Active TSS	Primary hematopoietic stem cells	blood
21	chr19:41731800-41732800	Flanking Active TSS	Foreskin Melanocyte Primary Cells skin01	Skin
22	chr19:41731800-41732800	Flanking Bivalent TSS/Enh	Primary mononuclear cells fromperipheralblood	Blood
23	chr19:41731800-41732800	Flanking Active TSS	Pancreas	Pancrea
24	chr19:41731800-41733000	Flanking Bivalent TSS/Enh	Primary T regulatory cells fromperipheralblood	blood
25	chr19:41731800-41733000	Flanking Active TSS	Foreskin Melanocyte Primary Cells skin03	Skin
26	chr19:41731800-41733000	Flanking Active TSS	Liver	Liver
27	chr19:41731800-41733000	Flanking Active TSS	Colonic Mucosa	Colon
28	chr19:41731800-41733000	Flanking Bivalent TSS/Enh	Monocytes-CD14+_RO01746	blood
29	chr19:41732000-41732800	Flanking Active TSS	Primary hematopoietic stem cells short term culture	blood
30	chr19:41732000-41732800	Active TSS	Aorta	Aorta
31	chr19:41732000-41733000	Flanking Active TSS	Primary T helper cells fromperipheralblood	blood
32	chr19:41732200-41732800	Flanking Active TSS	Primary T killer naive cells fromperipheralblood	blood
33	chr19:41732200-41732800	Bivalent Enhancer	Spleen	Spleen
34	chr19:41732200-41733000	Transcr. at gene 5' and 3'	Muscle Satellite Cultured Cells	--
35	chr19:41732200-41733200	Genic enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
36	chr19:41732400-41732800	Flanking Active TSS	ES-I3 Cell Line	embryonic stem cell
37	chr19:41732400-41732800	Flanking Active TSS	H1 Cell Line	embryonic stem cell
38	chr19:41732400-41732800	Transcr. at gene 5' and 3'	H1 Derived Mesenchymal Stem Cells	ES cell derived
39	chr19:41732400-41732800	Flanking Active TSS	H9 Cell Line	embryonic stem cell
40	chr19:41732400-41732800	Flanking Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
41	chr19:41732400-41732800	Transcr. at gene 5' and 3'	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
42	chr19:41732400-41732800	Flanking Active TSS	HUES48 Cell Line	embryonic stem cell
43	chr19:41732400-41732800	Transcr. at gene 5' and 3'	HUES6 Cell Line	embryonic stem cell
44	chr19:41732400-41732800	Flanking Active TSS	HUES64 Cell Line	embryonic stem cell
45	chr19:41732400-41732800	Transcr. at gene 5' and 3'	IMR90 fetal lung fibroblasts Cell Line	lung
46	chr19:41732400-41732800	Flanking Active TSS	iPS-15b Cell Line	embryonic stem cell
47	chr19:41732400-41732800	Transcr. at gene 5' and 3'	iPS DF 6.9 Cell Line	embryonic stem cell
48	chr19:41732400-41732800	Flanking Active TSS	iPS DF 19.11 Cell Line	embryonic stem cell
49	chr19:41732400-41732800	Flanking Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
50	chr19:41732400-41732800	Flanking Bivalent TSS/Enh	Primary monocytes fromperipheralblood	blood

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