Variant report

Variant	rs12462203
Chromosome Location	chr19:41732423-41732424
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	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	CTCF	chr19:41732360-41732510	MCF-7	breast:	n/a	n/a
6	CHD2	chr19:41731704-41732573	K562	blood:	n/a	chr19:41732045-41732055 chr19:41732249-41732259
7	POLR2A	chr19:41732165-41732766	HepG2	liver:	n/a	n/a
8	CTCF	chr19:41732420-41732570	AG09319	gingival:	n/a	n/a
9	SMARCC1	chr19:41731299-41732741	Hela-S3	cervix:	n/a	chr19:41732095-41732104
10	EP300	chr19:41731029-41733372	A549	lung:	n/a	chr19:41732177-41732186 chr19:41732179-41732188 chr19:41732175-41732191 chr19:41732187-41732203 chr19:41731857-41731873
11	CEBPB	chr19:41731444-41732538	Hela-S3	cervix:	n/a	n/a
12	TBP	chr19:41731712-41732540	H1-hESC	embryonic stem cell:	n/a	n/a
13	MAX	chr19:41731440-41732897	HepG2	liver:	n/a	chr19:41732217-41732226 chr19:41732252-41732262 chr19:41732215-41732224 chr19:41732218-41732225
14	USF1	chr19:41731983-41732524	SK-N-SH	brain:	n/a	chr19:41732180-41732196 chr19:41732355-41732366
15	EGR1	chr19:41731549-41732462	K562	blood:	n/a	chr19:41732102-41732115 chr19:41732048-41732061 chr19:41732252-41732265 chr19:41732252-41732262
16	FOXP2	chr19:41731201-41732816	PFSK-1	brain:	n/a	chr19:41731516-41731528
17	CEBPB	chr19:41731308-41732660	A549	lung:	n/a	n/a
18	CTCF	chr19:41732360-41732510	AoAF	blood vessel:	n/a	n/a
19	MYC	chr19:41732025-41732656	HepG2	liver:	n/a	chr19:41732217-41732226 chr19:41732252-41732262 chr19:41732215-41732224 chr19:41732218-41732225
20	TCF12	chr19:41731355-41732571	ECC-1	luminal epithelium:	n/a	chr19:41732002-41732009
21	REST	chr19:41731206-41733199	A549	lung:	n/a	chr19:41733063-41733076 chr19:41732188-41732198
22	CBX3	chr19:41731407-41732712	K562	blood:	n/a	n/a
23	POLR2A	chr19:41731729-41732809	A549	lung:	n/a	n/a
24	JUND	chr19:41731290-41732491	SK-N-SH	brain:	n/a	chr19:41731564-41731576 chr19:41732094-41732106 chr19:41732267-41732276 chr19:41732097-41732108 chr19:41732095-41732104 chr19:41731853-41731867 chr19:41731605-41731616
25	NFIC	chr19:41731250-41732808	SK-N-SH	brain:	n/a	n/a
26	FOXA2	chr19:41731218-41732928	A549	lung:	n/a	chr19:41731516-41731528
27	HNF4A	chr19:41732255-41732580	HepG2	liver:	n/a	chr19:41732434-41732449 chr19:41732434-41732449 chr19:41732434-41732449
28	ZBTB7A	chr19:41731598-41732588	K562	blood:	n/a	n/a
29	UBTF	chr19:41731599-41732638	K562	blood:	n/a	n/a
30	CTCF	chr19:41732360-41732510	Caco-2	colon:	n/a	n/a
31	MAX	chr19:41731852-41732954	HepG2	liver:	n/a	chr19:41732217-41732226 chr19:41732252-41732262 chr19:41732215-41732224 chr19:41732218-41732225
32	HEY1	chr19:41731626-41732537	K562	blood:	n/a	chr19:41732217-41732226
33	POLR2A	chr19:41731760-41732524	H1-hESC	embryonic stem cell:	n/a	n/a
34	GTF2F1	chr19:41731634-41732598	H1-hESC	embryonic stem cell:	n/a	n/a
35	MYC	chr19:41731483-41732632	HUVEC	blood vessel:	n/a	chr19:41732217-41732226 chr19:41732252-41732262 chr19:41732215-41732224 chr19:41732218-41732225
36	MAX	chr19:41729124-41733421	A549	lung:	n/a	chr19:41732217-41732226 chr19:41729661-41729670 chr19:41732252-41732262 chr19:41732215-41732224 chr19:41732218-41732225
37	HEY1	chr19:41732277-41732780	K562	blood:	n/a	n/a
38	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
39	MYC	chr19:41731533-41732596	K562	blood:	n/a	chr19:41732217-41732226 chr19:41732252-41732262 chr19:41732215-41732224 chr19:41732218-41732225
40	E2F6	chr19:41731655-41732732	A549	lung:	n/a	chr19:41732047-41732056 chr19:41732248-41732260 chr19:41732251-41732260 chr19:41732181-41732191 chr19:41732105-41732115
41	CTCF	chr19:41732340-41732490	Hela-S3	cervix:	n/a	n/a
42	TBP	chr19:41731525-41732619	HepG2	liver:	n/a	n/a
43	HNF4A	chr19:41732013-41732565	HepG2	liver:	n/a	chr19:41732434-41732449 chr19:41732434-41732449 chr19:41732434-41732449
44	MAX	chr19:41731398-41732653	NB4	blood:	n/a	chr19:41732217-41732226 chr19:41732252-41732262 chr19:41732215-41732224 chr19:41732218-41732225
45	EGR1	chr19:41731349-41732547	HCT-116	colon:	n/a	chr19:41732102-41732115 chr19:41732538-41732547 chr19:41732048-41732061 chr19:41732252-41732265 chr19:41732252-41732262
46	POLR2A	chr19:41731038-41732909	HUVEC	blood vessel:	n/a	n/a
47	SIN3AK20	chr19:41731135-41733273	A549	lung:	n/a	n/a
48	PBX3	chr19:41731112-41733271	A549	lung:	n/a	n/a
49	TCF7L2	chr19:41731578-41732632	Hela-S3	cervix:	n/a	chr19:41732095-41732104
50	POLR2A	chr19:41731657-41732904	K562	blood:	n/a	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
AXL	TF binding region
ENSG00000269652	TF binding region
ENSG00000269652	Chromatin interaction
ENSG00000136997	Chromatin interaction
ENSG00000105323	Chromatin interaction
ENSG00000173068	Chromatin interaction
ENSG00000131653	Chromatin interaction
ENSG00000167601	Chromatin interaction
ENSG00000206630	Chromatin interaction
ENSG00000260260	Chromatin interaction

Extended variants
information (count: 37 )
Associated
traits (count: 5 )

rSNPs within LD-proxies of this variant (count:36)

rs_ID	r²[population]
rs10421990	0.90[CHB][hapmap]
rs11879562	0.90[CHB][hapmap]
rs11882467	0.95[CHB][hapmap];0.83[JPT][hapmap]
rs12327659	0.90[CHB][hapmap]
rs12975585	0.95[CHB][hapmap]
rs12978098	0.93[AFR][1000 genomes];0.97[ASN][1000 genomes]
rs12978323	0.85[CHB][hapmap]
rs12979764	0.88[AFR][1000 genomes];0.96[ASN][1000 genomes]
rs12980248	0.97[AFR][1000 genomes];0.97[ASN][1000 genomes]
rs12980480	0.90[CHB][hapmap]
rs12983047	0.85[CHB][hapmap]
rs12984621	0.95[AFR][1000 genomes];0.97[ASN][1000 genomes]
rs1865051	0.85[CHB][hapmap]
rs1865053	0.90[CHB][hapmap]
rs2304230	0.90[CHB][hapmap]
rs2304234	0.90[CHB][hapmap];0.83[JPT][hapmap]
rs3745295	0.90[CHB][hapmap]
rs3752705	0.90[CHB][hapmap]
rs3816052	0.90[CHB][hapmap]
rs3826714	0.85[CHB][hapmap]
rs4456618	0.90[CHB][hapmap]
rs4802111	1.00[ASW][hapmap];0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.88[GIH][hapmap];0.94[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];0.95[YRI][hapmap];0.97[AFR][1000 genomes];0.87[AMR][1000 genomes];0.99[ASN][1000 genomes]
rs4802112	0.95[CHB][hapmap];0.84[JPT][hapmap];0.84[ASN][1000 genomes]
rs4802113	0.94[ASW][hapmap];0.96[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];0.83[GIH][hapmap];0.94[JPT][hapmap];0.98[LWK][hapmap];0.95[MEX][hapmap];1.00[MKK][hapmap];0.95[YRI][hapmap];0.90[AFR][1000 genomes];0.88[ASN][1000 genomes]
rs4803448	1.00[ASW][hapmap];0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.88[GIH][hapmap];0.94[JPT][hapmap];1.00[LWK][hapmap];0.95[MEX][hapmap];1.00[MKK][hapmap];0.95[YRI][hapmap];0.97[AFR][1000 genomes];0.97[ASN][1000 genomes]
rs4803449	1.00[CHB][hapmap];1.00[CHD][hapmap];0.94[JPT][hapmap];0.82[MEX][hapmap];0.97[ASN][1000 genomes]
rs6508974	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.94[JPT][hapmap];0.95[MEX][hapmap];0.92[MKK][hapmap];0.84[TSI][hapmap];0.93[AMR][1000 genomes];0.88[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs67033402	0.94[AFR][1000 genomes];0.93[ASN][1000 genomes]
rs6957	0.85[CHB][hapmap]
rs7245398	0.90[CHB][hapmap]
rs7246525	0.94[ASW][hapmap];0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.83[GIH][hapmap];0.94[JPT][hapmap];1.00[LWK][hapmap];0.95[MEX][hapmap];1.00[MKK][hapmap];0.95[YRI][hapmap];0.94[AFR][1000 genomes];0.93[ASN][1000 genomes]
rs7248164	0.90[CHB][hapmap]
rs7257310	0.85[CHB][hapmap]
rs7258749	0.90[CHB][hapmap]
rs8109167	0.85[CHB][hapmap]
rs8109627	0.85[CHB][hapmap];0.84[JPT][hapmap]

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

mRNA abundance (count:5)

SNP	Gene	Cis/trans	Tissue	Source
rs12462203	ZNF155	cis	parietal	SCAN
rs12462203	FOSB	cis	parietal	SCAN
rs12462203	ZNF226	cis	cerebellum	SCAN
rs12462203	BAX	cis	cerebellum	SCAN
rs12462203	ERF	cis	cerebellum	SCAN

Chromatin state (count:125 , 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	chr19:41731200-41732600	Flanking Active TSS	Adipose Nuclei	Adipose
7	chr19:41731200-41732800	Transcr. at gene 5' and 3'	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
8	chr19:41731200-41732800	Transcr. at gene 5' and 3'	NH-A	brain
9	chr19:41731200-41732800	Transcr. at gene 5' and 3'	NHEK	skin
10	chr19:41731200-41733000	Flanking Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
11	chr19:41731400-41732800	Flanking Active TSS	Cortex derived primary cultured neurospheres	brain
12	chr19:41731600-41732800	Flanking Active TSS	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
13	chr19:41731600-41732800	Flanking Bivalent TSS/Enh	Fetal Brain Female	brain
14	chr19:41731600-41732800	Flanking Active TSS	Fetal Muscle Trunk	muscle
15	chr19:41731600-41733000	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Female	--
16	chr19:41731600-41733000	Flanking Active TSS	Fetal Muscle Leg	muscle
17	chr19:41731600-41733000	Flanking Active TSS	Stomach Smooth Muscle	stomach
18	chr19:41731600-41733200	Flanking Active TSS	Primary T helper cells PMA-I stimulated	--
19	chr19:41731600-41733200	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
20	chr19:41731800-41732600	Active TSS	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
21	chr19:41731800-41732600	Flanking Active TSS	ES-UCSF4 Cell Line	embryonic stem cell
22	chr19:41731800-41732600	Flanking Active TSS	Ganglion Eminence derived primary cultured neurospheres	brain
23	chr19:41731800-41732600	Active TSS	Colon Smooth Muscle	Colon
24	chr19:41731800-41732600	Active TSS	Rectal Smooth Muscle	rectum
25	chr19:41731800-41732800	Flanking Active TSS	H9 Derived Neuron Cultured Cells	ES cell derived
26	chr19:41731800-41732800	Flanking Active TSS	Primary hematopoietic stem cells	blood
27	chr19:41731800-41732800	Flanking Active TSS	Foreskin Melanocyte Primary Cells skin01	Skin
28	chr19:41731800-41732800	Flanking Bivalent TSS/Enh	Primary mononuclear cells fromperipheralblood	Blood
29	chr19:41731800-41732800	Flanking Active TSS	Pancreas	Pancrea
30	chr19:41731800-41733000	Flanking Bivalent TSS/Enh	Primary T regulatory cells fromperipheralblood	blood
31	chr19:41731800-41733000	Flanking Active TSS	Foreskin Melanocyte Primary Cells skin03	Skin
32	chr19:41731800-41733000	Flanking Active TSS	Liver	Liver
33	chr19:41731800-41733000	Flanking Active TSS	Colonic Mucosa	Colon
34	chr19:41731800-41733000	Flanking Bivalent TSS/Enh	Monocytes-CD14+_RO01746	blood
35	chr19:41732000-41732600	Active TSS	Primary T helper memory cells from peripheral blood 2	blood
36	chr19:41732000-41732600	Active TSS	Primary T killer memory cells from peripheral blood	blood
37	chr19:41732000-41732600	Active TSS	Fetal Intestine Large	intestine
38	chr19:41732000-41732600	Active TSS	Fetal Intestine Small	intestine
39	chr19:41732000-41732600	Bivalent/Poised TSS	Pancreatic Islets	Pancreatic Islet
40	chr19:41732000-41732800	Flanking Active TSS	Primary hematopoietic stem cells short term culture	blood
41	chr19:41732000-41732800	Active TSS	Aorta	Aorta
42	chr19:41732000-41733000	Flanking Active TSS	Primary T helper cells fromperipheralblood	blood
43	chr19:41732200-41732600	Flanking Active TSS	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
44	chr19:41732200-41732600	Active TSS	Primary T helper naive cells from peripheral blood	blood
45	chr19:41732200-41732600	Active TSS	Primary T cells effector/memory enriched fromperipheralblood	blood
46	chr19:41732200-41732600	Active TSS	Small Intestine	intestine
47	chr19:41732200-41732600	Bivalent/Poised TSS	Thymus	Thymus
48	chr19:41732200-41732800	Flanking Active TSS	Primary T killer naive cells fromperipheralblood	blood
49	chr19:41732200-41732800	Bivalent Enhancer	Spleen	Spleen
50	chr19:41732200-41733000	Transcr. at gene 5' and 3'	Muscle Satellite Cultured Cells	--

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