Variant report

Variant	rs62112275
Chromosome Location	chr19:38398635-38398636
allele	G/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	ZNF143	chr19:38397488-38398786	Hela-S3	cervix:	n/a	chr19:38397847-38397856 chr19:38397748-38397766 chr19:38397781-38397799 chr19:38397845-38397863 chr19:38397845-38397854 chr19:38397794-38397804
2	SP1	chr19:38396870-38398870	A549	lung:	n/a	chr19:38397677-38397691
3	TCF12	chr19:38396474-38399045	A549	lung:	n/a	chr19:38397051-38397058
4	POLR2A	chr19:38396879-38398820	HUVEC	blood vessel:	n/a	n/a
5	POLR2A	chr19:38396943-38398925	GM12891	blood:	n/a	n/a
6	MAFK	chr19:38398421-38399162	IMR90	lung:	n/a	n/a
7	MAX	chr19:38396546-38398638	A549	lung:	n/a	chr19:38398162-38398171 chr19:38397081-38397090 chr19:38397082-38397089
8	MAFF	chr19:38398580-38399099	HepG2	liver:	n/a	chr19:38398947-38398965
9	MAFK	chr19:38398395-38399101	HepG2	liver:	n/a	n/a
10	RCOR1	chr19:38398399-38398831	K562	blood:	n/a	n/a
11	MAX	chr19:38396868-38398859	GM12878	blood:	n/a	chr19:38398162-38398171 chr19:38397081-38397090 chr19:38397082-38397089
12	MTA3	chr19:38396725-38398718	GM12878	blood:	n/a	n/a
13	SIN3AK20	chr19:38396454-38398869	A549	lung:	n/a	n/a
14	GATA2	chr19:38397312-38398639	SH-SY5Y	brain:	n/a	n/a
15	ZNF143	chr19:38397236-38398796	GM12878	blood:	n/a	chr19:38397847-38397856 chr19:38397748-38397766 chr19:38397781-38397799 chr19:38397845-38397863 chr19:38397845-38397854 chr19:38397794-38397804 chr19:38397462-38397472
16	SP1	chr19:38396918-38399144	A549	lung:	n/a	chr19:38397677-38397691
17	RUNX3	chr19:38396890-38398785	GM12878	blood:	n/a	n/a
18	RCOR1	chr19:38398471-38398781	K562	blood:	n/a	n/a
19	RELA	chr19:38397055-38398848	GM10847	blood:	n/a	n/a
20	ZNF143	chr19:38397495-38398766	K562	blood:	n/a	chr19:38397847-38397856 chr19:38397748-38397766 chr19:38397781-38397799 chr19:38397845-38397863 chr19:38397845-38397854 chr19:38397794-38397804
21	MXI1	chr19:38396945-38399356	GM12878	blood:	n/a	n/a
22	SMC3	chr19:38397563-38398708	Hela-S3	cervix:	n/a	n/a
23	ZNF143	chr19:38396963-38398763	H1-hESC	embryonic stem cell:	n/a	chr19:38397847-38397856 chr19:38397748-38397766 chr19:38397781-38397799 chr19:38397845-38397863 chr19:38397845-38397854 chr19:38397794-38397804 chr19:38397462-38397472
24	SMC3	chr19:38396793-38399215	GM12878	blood:	n/a	n/a
25	RELA	chr19:38397080-38398673	GM15510	blood:	n/a	n/a
26	SIX5	chr19:38396323-38398939	A549	lung:	n/a	chr19:38397652-38397661 chr19:38397845-38397854 chr19:38397847-38397856 chr19:38397843-38397857
27	EBF1	chr19:38398272-38399082	GM12878	blood:	n/a	n/a
28	HCFC1	chr19:38396984-38398989	Hela-S3	cervix:	n/a	n/a
29	SIN3AK20	chr19:38398177-38398752	A549	lung:	n/a	n/a
30	FOSL2	chr19:38396783-38398945	A549	lung:	n/a	chr19:38397812-38397824 chr19:38398111-38398120
31	SREBP1	chr19:38397066-38399311	GM12878	blood:	n/a	n/a
32	SMARCC1	chr19:38397308-38399022	Hela-S3	cervix:	n/a	chr19:38397652-38397661 chr19:38397845-38397854
33	RUNX3	chr19:38396945-38398670	GM12878	blood:	n/a	n/a
34	POLR2A	chr19:38396802-38398791	GM12878	blood:	n/a	n/a
35	MAX	chr19:38396733-38398729	HepG2	liver:	n/a	chr19:38398162-38398171 chr19:38397081-38397090 chr19:38397082-38397089
36	POLR2A	chr19:38396847-38398644	Raji	blood:	n/a	n/a
37	WRNIP1	chr19:38398209-38399718	GM12878	blood:	n/a	n/a
38	GATA3	chr19:38396607-38398961	A549	lung:	n/a	n/a
39	RAD21	chr19:38396375-38398813	A549	lung:	n/a	chr19:38397076-38397090 chr19:38397691-38397704
40	ZNF263	chr19:38396853-38398737	HEK293-T-REx	kidney:	n/a	chr19:38397585-38397594
41	SIN3A	chr19:38396676-38398782	H1-hESC	embryonic stem cell:	n/a	chr19:38397770-38397781
42	MAFK	chr19:38398544-38399043	Hela-S3	cervix:	n/a	n/a
43	MAFK	chr19:38398632-38399098	HepG2	liver:	n/a	n/a
44	MXI1	chr19:38396594-38399000	IMR90	lung:	n/a	n/a
45	POLR2A	chr19:38396652-38400700	IMR90	lung:	n/a	n/a
46	RAD21	chr19:38397493-38399099	IMR90	lung:	n/a	chr19:38397691-38397704
47	REST	chr19:38396460-38398775	A549	lung:	n/a	n/a
48	MAX	chr19:38396216-38399888	A549	lung:	n/a	chr19:38398162-38398171 chr19:38399338-38399348 chr19:38397081-38397090 chr19:38397082-38397089
49	BCL3	chr19:38396275-38399254	A549	lung:	n/a	chr19:38398115-38398128 chr19:38398114-38398127 chr19:38398116-38398125 chr19:38398111-38398124 chr19:38397977-38397990 chr19:38398005-38398018 chr19:38398113-38398122

No.	Distal block	Cell Line	Cell type
1	chr19:38395556..38401665-chr19:38419693..38425913,12	MCF-7	breast:
2	chr19:38396344..38398889-chr19:38454374..38457525,4	MCF-7	breast:
3	chr19:38395370..38399266-chr19:38452571..38456602,5	MCF-7	breast:
4	chr19:38393450..38400778-chr19:38419865..38427350,17	MCF-7	breast:

Variant related genes	Relation type
WDR87	TF binding region
ENSG00000105738	Chromatin interaction
ENSG00000268051	Chromatin interaction

Extended variants
information (count: 27 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:24)

rs_ID	r²[population]
rs62110229	0.81[ASN][1000 genomes]
rs62110230	0.80[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs62110232	0.80[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs62112272	0.86[AMR][1000 genomes];0.93[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs62112273	0.86[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62112274	0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs62112277	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62112279	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs62112280	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62112282	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62112285	1.00[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62112286	1.00[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62112287	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62112288	0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62112289	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62112290	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62112291	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs62120128	0.93[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs62120129	0.93[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs62120130	0.93[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs62120131	0.93[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs7257838	0.93[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs7258680	0.86[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs8105754	0.80[EUR][1000 genomes];0.81[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	nsv949296	chr19:38034722-38763140	Weak transcription Enhancers ZNF genes & repeats Flanking Active TSS Strong transcription Active TSS Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	58 gene(s)	inside rSNPs	diseases
2	nsv833820	chr19:38190721-38414049	Flanking Active TSS Weak transcription ZNF genes & repeats Strong transcription Active TSS Enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	27 gene(s)	inside rSNPs	diseases
3	nsv1064401	chr19:38387797-38427984	Enhancers Weak transcription Active TSS Flanking Active TSS Strong transcription ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:127 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr19:38396400-38398800	Active TSS	ES-I3 Cell Line	embryonic stem cell
2	chr19:38396400-38400600	Active TSS	Foreskin Fibroblast Primary Cells skin02	Skin
3	chr19:38396600-38398800	Active TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
4	chr19:38396600-38398800	Active TSS	iPS DF 6.9 Cell Line	embryonic stem cell
5	chr19:38396600-38399000	Active TSS	ES-WA7 Cell Line	embryonic stem cell
6	chr19:38396600-38399200	Active TSS	HUES64 Cell Line	embryonic stem cell
7	chr19:38396800-38398800	Active TSS	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
8	chr19:38396800-38398800	Active TSS	IMR90 fetal lung fibroblasts Cell Line	lung
9	chr19:38396800-38398800	Active TSS	Muscle Satellite Cultured Cells	--
10	chr19:38396800-38399000	Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
11	chr19:38396800-38399000	Active TSS	iPS DF 19.11 Cell Line	embryonic stem cell
12	chr19:38396800-38399000	Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
13	chr19:38397000-38398800	Active TSS	HUES48 Cell Line	embryonic stem cell
14	chr19:38397000-38398800	Active TSS	Ovary	ovary
15	chr19:38397000-38398800	Active TSS	Small Intestine	intestine
16	chr19:38397000-38398800	Active TSS	NHDF-Ad	bronchial
17	chr19:38397000-38399000	Flanking Active TSS	Primary mononuclear cells fromperipheralblood	Blood
18	chr19:38397000-38399400	Active TSS	HSMM	muscle
19	chr19:38397000-38401000	Active TSS	Pancreatic Islets	Pancreatic Islet
20	chr19:38397200-38398800	Active TSS	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
21	chr19:38397200-38398800	Active TSS	Fetal Intestine Large	intestine
22	chr19:38397200-38399000	Active TSS	H1 Derived Mesenchymal Stem Cells	ES cell derived
23	chr19:38397200-38399000	Active TSS	Fetal Intestine Small	intestine
24	chr19:38397200-38399400	Active TSS	GM12878-XiMat	blood
25	chr19:38397400-38398800	Active TSS	Placenta	Placenta
26	chr19:38398000-38399000	Flanking Active TSS	Skeletal Muscle Female	skeletal muscle
27	chr19:38398000-38399200	Flanking Active TSS	Primary hematopoietic stem cells	blood
28	chr19:38398200-38398800	Flanking Active TSS	Primary monocytes fromperipheralblood	blood
29	chr19:38398200-38398800	Flanking Active TSS	Primary T cells fromperipheralblood	blood
30	chr19:38398200-38398800	Flanking Active TSS	Primary T regulatory cells fromperipheralblood	blood
31	chr19:38398200-38398800	Flanking Active TSS	Primary T killer naive cells fromperipheralblood	blood
32	chr19:38398200-38399000	Flanking Active TSS	Primary T helper cells fromperipheralblood	blood
33	chr19:38398200-38399000	Flanking Active TSS	Primary Natural Killer cells fromperipheralblood	blood
34	chr19:38398200-38399000	Flanking Active TSS	Fetal Stomach	stomach
35	chr19:38398200-38399200	Flanking Active TSS	Primary hematopoietic stem cells short term culture	blood
36	chr19:38398200-38399200	Flanking Active TSS	Stomach Smooth Muscle	stomach
37	chr19:38398200-38399200	Flanking Active TSS	Monocytes-CD14+_RO01746	blood
38	chr19:38398200-38399600	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
39	chr19:38398200-38399800	Flanking Active TSS	Primary B cells from cord blood	blood
40	chr19:38398400-38398800	Flanking Active TSS	iPS-15b Cell Line	embryonic stem cell
41	chr19:38398400-38398800	Flanking Active TSS	Primary T helper memory cells from peripheral blood 2	blood
42	chr19:38398400-38398800	Flanking Active TSS	Primary T helper naive cells fromperipheralblood	blood
43	chr19:38398400-38398800	Flanking Active TSS	Primary T helper cells PMA-I stimulated	--
44	chr19:38398400-38398800	Flanking Active TSS	Primary T killer memory cells from peripheral blood	blood
45	chr19:38398400-38398800	Flanking Active TSS	Liver	Liver
46	chr19:38398400-38398800	Flanking Active TSS	Brain Substantia Nigra	brain
47	chr19:38398400-38398800	Flanking Active TSS	Colon Smooth Muscle	Colon
48	chr19:38398400-38398800	Flanking Active TSS	Fetal Adrenal Gland	Adrenal Gland
49	chr19:38398400-38398800	Flanking Active TSS	Fetal Lung	lung
50	chr19:38398400-38398800	Flanking Active TSS	Fetal Muscle Leg	muscle

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