Variant report

Variant	rs4239516
Chromosome Location	chr19:38398590-38398591
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	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	HA-E2F1	chr19:38397141-38398596	MCF-7	breast:	n/a	chr19:38397794-38397804 chr19:38398036-38398048 chr19:38398113-38398123 chr19:38398119-38398129 chr19:38397864-38397875 chr19:38397430-38397439
24	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
25	SMC3	chr19:38396793-38399215	GM12878	blood:	n/a	n/a
26	RELA	chr19:38397080-38398673	GM15510	blood:	n/a	n/a
27	SIN3AK20	chr19:38396486-38398590	MCF-7	breast:	n/a	n/a
28	SIN3A	chr19:38397372-38398626	GM12878	blood:	n/a	chr19:38397770-38397781
29	SIX5	chr19:38396323-38398939	A549	lung:	n/a	chr19:38397652-38397661 chr19:38397845-38397854 chr19:38397847-38397856 chr19:38397843-38397857
30	EBF1	chr19:38398272-38399082	GM12878	blood:	n/a	n/a
31	HCFC1	chr19:38396984-38398989	Hela-S3	cervix:	n/a	n/a
32	SIN3AK20	chr19:38398177-38398752	A549	lung:	n/a	n/a
33	FOSL2	chr19:38396783-38398945	A549	lung:	n/a	chr19:38397812-38397824 chr19:38398111-38398120
34	SREBP1	chr19:38397066-38399311	GM12878	blood:	n/a	n/a
35	SMARCC1	chr19:38397308-38399022	Hela-S3	cervix:	n/a	chr19:38397652-38397661 chr19:38397845-38397854
36	RUNX3	chr19:38396945-38398670	GM12878	blood:	n/a	n/a
37	POLR2A	chr19:38396802-38398791	GM12878	blood:	n/a	n/a
38	MAX	chr19:38396733-38398729	HepG2	liver:	n/a	chr19:38398162-38398171 chr19:38397081-38397090 chr19:38397082-38397089
39	POLR2A	chr19:38396847-38398644	Raji	blood:	n/a	n/a
40	WRNIP1	chr19:38398209-38399718	GM12878	blood:	n/a	n/a
41	GATA3	chr19:38396607-38398961	A549	lung:	n/a	n/a
42	RAD21	chr19:38396375-38398813	A549	lung:	n/a	chr19:38397076-38397090 chr19:38397691-38397704
43	BHLHE40	chr19:38396962-38398592	GM12878	blood:	n/a	chr19:38397785-38397801
44	ZNF263	chr19:38396853-38398737	HEK293-T-REx	kidney:	n/a	chr19:38397585-38397594
45	SIN3A	chr19:38396676-38398782	H1-hESC	embryonic stem cell:	n/a	chr19:38397770-38397781
46	MAFK	chr19:38398544-38399043	Hela-S3	cervix:	n/a	n/a
47	MXI1	chr19:38396594-38399000	IMR90	lung:	n/a	n/a
48	POLR2A	chr19:38396652-38400700	IMR90	lung:	n/a	n/a
49	RAD21	chr19:38397493-38399099	IMR90	lung:	n/a	chr19:38397691-38397704
50	MAX	chr19:38398450-38398605	H1-hESC	embryonic stem cell:	n/a	n/a

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:

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-ZNF540-1	chr19:38398184-38398614	NONHSAT066181

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

Extended variants
information (count: 62 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:59)

rs_ID	r²[population]
rs10404159	0.93[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs10404567	0.87[CEU][hapmap]
rs10415399	0.89[AFR][1000 genomes];0.93[AMR][1000 genomes];0.91[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs10415548	1.00[CEU][hapmap];0.95[CHB][hapmap];0.94[JPT][hapmap];1.00[YRI][hapmap];0.92[AFR][1000 genomes];0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs10420746	0.83[CEU][hapmap]
rs11083441	0.92[AFR][1000 genomes];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs1119229	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.82[EUR][1000 genomes]
rs12608883	0.95[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1291	0.87[CEU][hapmap]
rs12973580	0.89[AMR][1000 genomes];0.96[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs12974225	0.87[CEU][hapmap]
rs1643460	0.82[EUR][1000 genomes]
rs1643461	0.86[EUR][1000 genomes]
rs1643466	0.82[CEU][hapmap]
rs1643467	0.82[CEU][hapmap]
rs1643468	0.82[CEU][hapmap]
rs1725481	0.83[CEU][hapmap]
rs1725482	0.87[CEU][hapmap]
rs1725499	1.00[CEU][hapmap];0.95[CHB][hapmap];0.94[JPT][hapmap];1.00[YRI][hapmap];0.91[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2075281	0.83[CEU][hapmap]
rs241932	0.87[CEU][hapmap]
rs28460297	0.88[AFR][1000 genomes];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2909093	0.81[CEU][hapmap]
rs2909098	0.87[CEU][hapmap]
rs2972437	0.87[CEU][hapmap]
rs2972438	0.87[CEU][hapmap]
rs2972439	0.87[CEU][hapmap]
rs353410	1.00[CEU][hapmap];0.91[CHB][hapmap];0.94[JPT][hapmap];0.83[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs353411	1.00[CEU][hapmap];0.91[CHB][hapmap];0.94[JPT][hapmap];0.85[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs353414	0.82[CEU][hapmap]
rs353415	0.83[CEU][hapmap]
rs353423	0.82[CEU][hapmap]
rs3786869	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3865514	1.00[YRI][hapmap]
rs4802144	0.87[AFR][1000 genomes];0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs4802147	0.95[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4802151	0.83[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs4803524	0.87[CEU][hapmap]
rs4803551	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4803573	1.00[CEU][hapmap];0.95[CHB][hapmap];0.94[JPT][hapmap];1.00[YRI][hapmap];0.92[AFR][1000 genomes];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs705491	1.00[CEU][hapmap];0.95[CHB][hapmap];0.94[JPT][hapmap];0.84[AMR][1000 genomes];0.91[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs705492	0.83[CEU][hapmap]
rs705493	1.00[CEU][hapmap];0.95[CHB][hapmap];0.94[JPT][hapmap];0.84[AMR][1000 genomes];0.91[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs705494	0.87[CEU][hapmap]
rs705495	1.00[CEU][hapmap];0.95[CHB][hapmap];0.94[JPT][hapmap];1.00[YRI][hapmap];0.92[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs705499	0.86[AFR][1000 genomes];0.90[AMR][1000 genomes];0.88[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs7250409	0.87[CEU][hapmap]
rs8102579	0.87[CEU][hapmap]
rs8108434	0.95[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs8109053	0.95[AFR][1000 genomes];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs8109835	0.93[AFR][1000 genomes];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs8110284	0.82[CEU][hapmap]
rs8112706	0.82[CEU][hapmap]
rs8113273	0.97[AFR][1000 genomes];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs8113521	1.00[CEU][hapmap];0.95[CHB][hapmap];0.94[JPT][hapmap];0.85[YRI][hapmap];0.91[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs833895	0.83[CEU][hapmap]
rs833926	0.83[CEU][hapmap]
rs856300	0.81[CEU][hapmap]
rs856304	0.87[CEU][hapmap]

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

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs4239516	AC012309.5	cis	Artery Tibial	GTEx

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr19:38396400-38398600	Active TSS	Spleen	Spleen
2	chr19:38396400-38398800	Active TSS	ES-I3 Cell Line	embryonic stem cell
3	chr19:38396400-38400600	Active TSS	Foreskin Fibroblast Primary Cells skin02	Skin
4	chr19:38396600-38398600	Active TSS	H9 Cell Line	embryonic stem cell
5	chr19:38396600-38398800	Active TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
6	chr19:38396600-38398800	Active TSS	iPS DF 6.9 Cell Line	embryonic stem cell
7	chr19:38396600-38399000	Active TSS	ES-WA7 Cell Line	embryonic stem cell
8	chr19:38396600-38399200	Active TSS	HUES64 Cell Line	embryonic stem cell
9	chr19:38396800-38398600	Active TSS	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
10	chr19:38396800-38398600	Active TSS	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
11	chr19:38396800-38398600	Active TSS	Primary T cells effector/memory enriched fromperipheralblood	blood
12	chr19:38396800-38398600	Active TSS	Foreskin Melanocyte Primary Cells skin01	Skin
13	chr19:38396800-38398800	Active TSS	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
14	chr19:38396800-38398800	Active TSS	IMR90 fetal lung fibroblasts Cell Line	lung
15	chr19:38396800-38398800	Active TSS	Muscle Satellite Cultured Cells	--
16	chr19:38396800-38399000	Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
17	chr19:38396800-38399000	Active TSS	iPS DF 19.11 Cell Line	embryonic stem cell
18	chr19:38396800-38399000	Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
19	chr19:38397000-38398600	Active TSS	H1 Cell Line	embryonic stem cell
20	chr19:38397000-38398600	Active TSS	iPS-18 Cell Line	embryonic stem cell
21	chr19:38397000-38398600	Active TSS	iPS-20b Cell Line	embryonic stem cell
22	chr19:38397000-38398600	Active TSS	ES-UCSF4 Cell Line	embryonic stem cell
23	chr19:38397000-38398600	Active TSS	Primary T helper naive cells from peripheral blood	blood
24	chr19:38397000-38398600	Active TSS	Aorta	Aorta
25	chr19:38397000-38398600	Active TSS	Esophagus	oesophagus
26	chr19:38397000-38398600	Active TSS	Gastric	stomach
27	chr19:38397000-38398600	Active TSS	Pancreas	Pancrea
28	chr19:38397000-38398600	Active TSS	Psoas Muscle	Psoas
29	chr19:38397000-38398600	Active TSS	Right Atrium	heart
30	chr19:38397000-38398600	Active TSS	Sigmoid Colon	Sigmoid Colon
31	chr19:38397000-38398600	Active TSS	HSMMtube	muscle
32	chr19:38397000-38398800	Active TSS	HUES48 Cell Line	embryonic stem cell
33	chr19:38397000-38398800	Active TSS	Ovary	ovary
34	chr19:38397000-38398800	Active TSS	Small Intestine	intestine
35	chr19:38397000-38398800	Active TSS	NHDF-Ad	bronchial
36	chr19:38397000-38399000	Flanking Active TSS	Primary mononuclear cells fromperipheralblood	Blood
37	chr19:38397000-38399400	Active TSS	HSMM	muscle
38	chr19:38397000-38401000	Active TSS	Pancreatic Islets	Pancreatic Islet
39	chr19:38397200-38398600	Active TSS	Foreskin Melanocyte Primary Cells skin03	Skin
40	chr19:38397200-38398600	Active TSS	Stomach Mucosa	stomach
41	chr19:38397200-38398600	Active TSS	Thymus	Thymus
42	chr19:38397200-38398600	Active TSS	A549	lung
43	chr19:38397200-38398600	Active TSS	NH-A	brain
44	chr19:38397200-38398600	Active TSS	NHLF	lung
45	chr19:38397200-38398800	Active TSS	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
46	chr19:38397200-38398800	Active TSS	Fetal Intestine Large	intestine
47	chr19:38397200-38399000	Active TSS	H1 Derived Mesenchymal Stem Cells	ES cell derived
48	chr19:38397200-38399000	Active TSS	Fetal Intestine Small	intestine
49	chr19:38397200-38399400	Active TSS	GM12878-XiMat	blood
50	chr19:38397400-38398600	Bivalent/Poised TSS	HepG2	liver

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