Variant report

Variant	rs10409392
Chromosome Location	chr19:18699333-18699334
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:246)
CpG islands
(count:61)
Chromatin interactive
region (count:15)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:246 , 50 per page) page: 1 2 3 4 5

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	HDAC2	chr19:18699301-18699819	K562	blood:	n/a	n/a
2	POLR2A	chr19:18698432-18704772	HepG2	liver:	n/a	n/a
3	CTCF	chr19:18699305-18699775	K562	blood:	n/a	chr19:18699546-18699562 chr19:18699545-18699563
4	CTCF	chr19:18699292-18699877	MCF-7	breast:	n/a	chr19:18699546-18699562 chr19:18699545-18699563
5	MAX	chr19:18698458-18701025	HepG2	liver:	n/a	chr19:18699922-18699932 chr19:18699937-18699946
6	POLR2A	chr19:18699333-18700873	Hela-S3	cervix:	n/a	n/a
7	POLR2A	chr19:18699287-18700931	K562	blood:	n/a	n/a
8	ELF1	chr19:18698919-18700973	GM12878	blood:	n/a	n/a
9	POLR2A	chr19:18699241-18700733	HUVEC	blood vessel:	n/a	n/a
10	MAX	chr19:18698953-18700664	NB4	blood:	n/a	chr19:18699922-18699932 chr19:18699937-18699946
11	PML	chr19:18699332-18699903	GM12878	blood:	n/a	n/a
12	NFIC	chr19:18699296-18699985	ECC-1	luminal epithelium:	n/a	n/a
13	TBL1XR1	chr19:18699301-18700392	K562	blood:	n/a	n/a
14	HDAC2	chr19:18699319-18700747	HepG2	liver:	n/a	n/a
15	POLR2A	chr19:18699316-18700031	GM12891	blood:	n/a	n/a
16	FOXM1	chr19:18699069-18700111	GM12878	blood:	n/a	n/a
17	POLR2A	chr19:18699190-18700536	GM12878	blood:	n/a	n/a
18	MAX	chr19:18699250-18701052	MCF-7	breast:	n/a	chr19:18699922-18699932 chr19:18699937-18699946
19	BACH1	chr19:18699284-18699762	K562	blood:	n/a	n/a
20	TCF12	chr19:18699233-18700737	ECC-1	luminal epithelium:	n/a	n/a
21	SP2	chr19:18699287-18700045	H1-hESC	embryonic stem cell:	n/a	n/a
22	TAF1	chr19:18699269-18700182	K562	blood:	n/a	n/a
23	POLR2A	chr19:18698422-18702101	K562	blood:	n/a	n/a
24	KAP1	chr19:18699051-18700904	HEK293	kidney:	n/a	n/a
25	CTCF	chr19:18699329-18699775	IMR90	lung:	n/a	chr19:18699546-18699562 chr19:18699545-18699563
26	TAF1	chr19:18699322-18700357	PFSK-1	brain:	n/a	n/a
27	ZBTB7A	chr19:18699187-18700809	ECC-1	luminal epithelium:	n/a	chr19:18699893-18699902
28	SIN3AK20	chr19:18699251-18699750	A549	lung:	n/a	n/a
29	POLR2A	chr19:18699298-18701733	H1-hESC	embryonic stem cell:	n/a	n/a
30	FOXA1	chr19:18699311-18700808	HepG2	liver:	n/a	n/a
31	NFATC1	chr19:18699164-18700187	GM12878	blood:	n/a	n/a
32	BCLAF1	chr19:18699207-18700633	GM12878	blood:	n/a	chr19:18699897-18699906
33	POLR2A	chr19:18699269-18701040	HCT-116	colon:	n/a	n/a
34	PAX5	chr19:18699273-18700218	GM12878	blood:	n/a	n/a
35	JUND	chr19:18699306-18700561	K562	blood:	n/a	n/a
36	POLR2A	chr19:18699208-18700179	HUVEC	blood vessel:	n/a	n/a
37	MAX	chr19:18699272-18700647	K562	blood:	n/a	chr19:18699922-18699932 chr19:18699937-18699946
38	CTCF	chr19:18699283-18699986	HCT-116	colon:	n/a	chr19:18699925-18699938 chr19:18699546-18699562 chr19:18699545-18699563
39	ELK1	chr19:18699195-18700255	GM12878	blood:	n/a	n/a
40	POLR2A	chr19:18699232-18700527	K562	blood:	n/a	n/a
41	MAFK	chr19:18699141-18699741	K562	blood:	n/a	n/a
42	ATF2	chr19:18699251-18699853	H1-hESC	embryonic stem cell:	n/a	n/a
43	HEY1	chr19:18698550-18701536	K562	blood:	n/a	n/a
44	PML	chr19:18699075-18700578	GM12878	blood:	n/a	n/a
45	MTA3	chr19:18698687-18700702	GM12878	blood:	n/a	n/a
46	TAF1	chr19:18699321-18700029	GM12892	blood:	n/a	n/a
47	POLR2A	chr19:18699241-18701902	K562	blood:	n/a	n/a
48	YY1	chr19:18699159-18700000	GM12878	blood:	n/a	n/a
49	MYBL2	chr19:18699251-18700653	HepG2	liver:	n/a	n/a
50	MAX	chr19:18699096-18700857	ECC-1	luminal epithelium:	n/a	chr19:18699922-18699932 chr19:18699937-18699946

(count:61 , 50 per page) page: 1 2

No.	Chromosome Location	Cell Line	Cell type	Cell Stage
1	chr19:18699326-18699376	Caco-2	colon:	n/a
2	chr19:18699326-18699376	AoSMC	blood vessel:	n/a
3	chr19:18699326-18699376	HEK293	kidney:	embryo
4	chr19:18699326-18699376	HRE	kidney:	n/a
5	chr19:18699326-18699376	ECC-1	luminal epithelium:	n/a
6	chr19:18699326-18699376	NT2-D1	testis:	n/a
7	chr19:18699326-18699376	IMR90	lung:	fetal
8	chr19:18699326-18699376	PANC-1	pancreas:	n/a
9	chr19:18699326-18699376	SK-N-MC	brain:	n/a
10	chr19:18699326-18699376	BE2_C	brain:	n/a
11	chr19:18699326-18699376	AG04449	skin:	fetal
12	chr19:18699326-18699376	NB4	blood:	n/a
13	chr19:18699326-18699376	HRPEpiC	eye:	n/a
14	chr19:18699326-18699376	HRCEpiC	kidney:	n/a
15	chr19:18699326-18699376	HCF	heart:	n/a
16	chr19:18699326-18699376	GM12878	blood:	n/a
17	chr19:18699326-18699376	HCPEpiC	choroid plexus:	n/a
18	chr19:18699326-18699376	GM06990	blood:	n/a
19	chr19:18699326-18699376	HIPEpiC	eye:	n/a
20	chr19:18699326-18699376	GM19239	blood:	n/a
21	chr19:18699326-18699376	PFSK-1	brain:	n/a
22	chr19:18699326-18699376	CMK	blood:	n/a
23	chr19:18699326-18699376	NHBE	bronchial:	n/a
24	chr19:18699326-18699376	RPTEC	kidney:	n/a
25	chr19:18699326-18699376	HNPCEpiC	eye:	n/a
26	chr19:18699326-18699376	Hepatocyte	liver:	n/a
27	chr19:18699326-18699376	K562	blood:	n/a
28	chr19:18699326-18699376	Hela-S3	cervix:	n/a
29	chr19:18699326-18699376	NHDF-neo	bronchial:	n/a
30	chr19:18699326-18699376	HepG2	liver:	n/a
31	chr19:18699326-18699376	GM12892	blood:	n/a
32	chr19:18699326-18699376	NH-A	brain:	n/a
33	chr19:18699326-18699376	MCF10A-Er-Src	breast:	n/a
34	chr19:18699326-18699376	HUVEC	blood vessel:	n/a
35	chr19:18699326-18699376	AG09309	skin:	n/a
36	chr19:18699326-18699376	LNCaP	prostate:	n/a
37	chr19:18699326-18699376	T-47D	breast:	n/a
38	chr19:18699326-18699376	AG10803	skin:	n/a
39	chr19:18699326-18699376	SK-N-SH	brain:	n/a
40	chr19:18699326-18699376	SAEC	small airway:	n/a
41	chr19:18699326-18699376	SKMC	muscle:	n/a
42	chr19:18699326-18699376	SK-N-SH_RA	brain:	n/a
43	chr19:18699326-18699376	H1-hESC	embryonic stem cell:	embryo
44	chr19:18699326-18699376	HPAEpiC	pulmonary alveolar:	n/a
45	chr19:18699326-18699376	PrEC	prostate:	n/a
46	chr19:18699326-18699376	HCT-116	colon:	n/a
47	chr19:18699326-18699376	HMEC	breast:	n/a
48	chr19:18699326-18699376	HAEpiC	amniotic membrane:	n/a
49	chr19:18699326-18699376	MCF-7	breast:	n/a
50	chr19:18699326-18699376	A549	lung:	n/a

(count:15 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr19:18667424..18670168-chr19:18699281..18701481,3	MCF-7	breast:
2	chr19:18698544..18700812-chr19:18957924..18960532,2	MCF-7	breast:
3	chr19:18698512..18700358-chr19:18745222..18750244,4	K562	blood:
4	chr19:18669154..18672917-chr19:18697910..18700793,4	K562	blood:
5	chr19:18681312..18685117-chr19:18698049..18701447,5	MCF-7	breast:
6	chr19:18653459..18656385-chr19:18699225..18703130,9	K562	blood:
7	chr19:18678376..18688390-chr19:18697032..18707656,34	K562	blood:
8	chr19:18495663..18499199-chr19:18698556..18701601,3	K562	blood:
9	chr19:18672789..18675551-chr19:18697478..18700004,2	MCF-7	breast:
10	chr19:18631688..18633803-chr19:18698894..18701519,3	MCF-7	breast:
11	chr19:18631032..18633728-chr19:18697675..18701681,7	MCF-7	breast:
12	chr19:18630919..18637145-chr19:18698949..18704438,10	K562	blood:
13	chr19:18698708..18701515-chr19:18746316..18749182,4	MCF-7	breast:
14	chr19:18629422..18634718-chr19:18699285..18702887,8	K562	blood:
15	chr19:18560428..18562290-chr19:18697928..18699471,2	K562	blood:

No data

Variant related genes	Relation type
C19orf60	TF binding region
C19orf60	CpG island
ENSG00000268983	Chromatin interaction
ENSG00000130513	Chromatin interaction
ENSG00000264175	Chromatin interaction
ENSG00000167487	Chromatin interaction
ENSG00000005007	Chromatin interaction
ENSG00000105701	Chromatin interaction
ENSG00000221983	Chromatin interaction
ENSG00000105656	Chromatin interaction
ENSG00000268030	Chromatin interaction
ENSG00000105700	Chromatin interaction

Extended variants
information (count: 50 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:42)

rs_ID	r²[population]
rs10419226	0.80[MEX][hapmap]
rs1043192	0.81[JPT][hapmap]
rs11667551	0.83[EUR][1000 genomes]
rs12150991	0.83[EUR][1000 genomes]
rs12608925	0.83[EUR][1000 genomes]
rs12609505	0.80[CEU][hapmap];0.86[CHB][hapmap];0.81[CHD][hapmap];0.84[GIH][hapmap];0.80[TSI][hapmap]
rs1468475	0.80[CEU][hapmap];0.85[CHB][hapmap];0.81[CHD][hapmap];0.84[GIH][hapmap];0.80[TSI][hapmap];0.83[EUR][1000 genomes]
rs1862645	0.81[JPT][hapmap]
rs2057649	0.84[CEU][hapmap];0.86[CHB][hapmap];0.89[CHD][hapmap];0.85[GIH][hapmap];0.90[JPT][hapmap];0.82[TSI][hapmap];0.84[EUR][1000 genomes]
rs2074175	0.90[JPT][hapmap];0.85[TSI][hapmap]
rs2079015	0.84[CEU][hapmap];0.86[CHB][hapmap];0.86[CHD][hapmap];0.89[GIH][hapmap];0.90[JPT][hapmap];0.82[TSI][hapmap];0.84[EUR][1000 genomes]
rs2079016	0.84[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs2238650	0.81[JPT][hapmap]
rs2283616	0.86[CHB][hapmap];1.00[YRI][hapmap]
rs2302055	0.86[CHB][hapmap];0.81[CHD][hapmap];0.82[GIH][hapmap];0.82[EUR][1000 genomes]
rs2314664	0.86[CHB][hapmap];0.92[CHD][hapmap];0.89[GIH][hapmap];0.90[JPT][hapmap];0.85[MEX][hapmap]
rs2314665	0.84[CEU][hapmap];0.86[CHB][hapmap];0.92[CHD][hapmap];0.89[GIH][hapmap];0.90[JPT][hapmap];0.82[TSI][hapmap];0.84[EUR][1000 genomes]
rs2314666	0.86[CHB][hapmap];0.87[CHD][hapmap];0.87[GIH][hapmap];0.84[JPT][hapmap];0.85[MEX][hapmap]
rs28711754	0.81[EUR][1000 genomes]
rs3170474	0.85[JPT][hapmap]
rs35867875	0.82[EUR][1000 genomes]
rs35875334	0.82[EUR][1000 genomes]
rs3761032	0.81[JPT][hapmap]
rs3761034	0.80[CEU][hapmap];0.81[CHB][hapmap];0.84[GIH][hapmap];0.80[TSI][hapmap];0.83[EUR][1000 genomes]
rs3795028	1.00[YRI][hapmap]
rs4629093	0.84[EUR][1000 genomes]
rs4808137	0.80[CEU][hapmap];0.86[CHB][hapmap];0.81[CHD][hapmap];0.80[GIH][hapmap];0.82[TSI][hapmap];0.83[EUR][1000 genomes]
rs4808823	0.90[JPT][hapmap]
rs4808839	0.81[JPT][hapmap]
rs55888366	0.83[EUR][1000 genomes]
rs58782998	0.82[EUR][1000 genomes]
rs62137086	0.82[EUR][1000 genomes]
rs6554	0.86[CHB][hapmap];0.81[CHD][hapmap];0.84[GIH][hapmap];0.90[MEX][hapmap];0.91[MKK][hapmap];1.00[YRI][hapmap]
rs709679	0.81[JPT][hapmap]
rs7247346	0.82[ASN][1000 genomes]
rs7250192	0.81[JPT][hapmap]
rs7250623	0.90[JPT][hapmap]
rs7254004	0.83[EUR][1000 genomes]
rs7256319	0.85[JPT][hapmap]
rs7648	0.86[CHB][hapmap];0.83[EUR][1000 genomes]
rs8109364	0.81[CHB][hapmap];0.88[GIH][hapmap];0.90[MEX][hapmap]
rs916791	0.81[JPT][hapmap]

Variant overlapped rSNPs/rCNVs (count:8 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1057795	chr19:18453362-18883844	Active TSS Enhancers Weak transcription Bivalent Enhancer Flanking Active TSS Genic enhancers Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	92 gene(s)	inside rSNPs	diseases
2	nsv543925	chr19:18453362-18883844	Weak transcription Genic enhancers Strong transcription Enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS Flanking Active TSS Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	92 gene(s)	inside rSNPs	diseases
3	nsv532615	chr19:18534867-18796031	Enhancers Flanking Active TSS Weak transcription Bivalent Enhancer Strong transcription Flanking Bivalent TSS/Enh Genic enhancers Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	71 gene(s)	inside rSNPs	diseases
4	nsv911281	chr19:18613917-18758255	Enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Weak transcription Bivalent/Poised TSS Active TSS Flanking Active TSS Strong transcription Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	51 gene(s)	inside rSNPs	diseases
5	nsv911282	chr19:18624964-18928480	ZNF genes & repeats Weak transcription Enhancers Flanking Active TSS Genic enhancers Active TSS Strong transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	60 gene(s)	inside rSNPs	diseases
6	nsv833776	chr19:18638028-18782264	Flanking Active TSS Enhancers ZNF genes & repeats Bivalent Enhancer Active TSS Strong transcription Weak transcription Bivalent/Poised TSS Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	44 gene(s)	inside rSNPs	diseases
7	nsv911286	chr19:18652844-18811112	Active TSS Flanking Active TSS Enhancers Strong transcription Weak transcription Transcr. at gene 5' and 3' Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	50 gene(s)	inside rSNPs	diseases
8	nsv911287	chr19:18699333-18727913	Genic enhancers Enhancers Flanking Active TSS Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Weak transcription Strong transcription Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region	18 gene(s)	inside rSNPs	diseases

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs10409392	UBA52	cis	lymphoblastoid	seeQTL
rs10409392	GATAD2A	cis	cerebellum	SCAN
rs10409392	NDUFA13	cis	parietal	SCAN
rs10409392	UBA52	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:126 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr19:18686800-18699600	Weak transcription	Small Intestine	intestine
2	chr19:18687200-18699400	Weak transcription	Ovary	ovary
3	chr19:18698400-18699400	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
4	chr19:18698400-18699400	Flanking Active TSS	Dnd41	blood
5	chr19:18698600-18699400	Flanking Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
6	chr19:18698600-18699400	Flanking Active TSS	Primary T helper naive cells from peripheral blood	blood
7	chr19:18698600-18699400	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
8	chr19:18698600-18699400	Flanking Active TSS	Brain Anterior Caudate	brain
9	chr19:18698600-18699400	Flanking Active TSS	GM12878-XiMat	blood
10	chr19:18698600-18699600	Flanking Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
11	chr19:18698600-18699600	Flanking Active TSS	Rectal Mucosa Donor 29	rectum
12	chr19:18698600-18699600	Enhancers	Sigmoid Colon	Sigmoid Colon
13	chr19:18698600-18700800	Flanking Active TSS	Colonic Mucosa	Colon
14	chr19:18698600-18701200	Flanking Active TSS	Primary hematopoietic stem cells short term culture	blood
15	chr19:18698600-18701200	Flanking Active TSS	Stomach Smooth Muscle	stomach
16	chr19:18698600-18701200	Flanking Active TSS	Monocytes-CD14+_RO01746	blood
17	chr19:18698800-18699400	Flanking Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
18	chr19:18698800-18699400	Flanking Active TSS	HUES6 Cell Line	embryonic stem cell
19	chr19:18698800-18699400	Flanking Active TSS	iPS-15b Cell Line	embryonic stem cell
20	chr19:18698800-18699400	Flanking Active TSS	iPS DF 19.11 Cell Line	embryonic stem cell
21	chr19:18698800-18699400	Flanking Active TSS	Primary neutrophils fromperipheralblood	blood
22	chr19:18698800-18699400	Flanking Active TSS	Primary T cells fromperipheralblood	blood
23	chr19:18698800-18699400	Flanking Active TSS	Primary T helper cells PMA-I stimulated	--
24	chr19:18698800-18699400	Flanking Active TSS	Primary T helper cells fromperipheralblood	blood
25	chr19:18698800-18699400	Flanking Active TSS	Primary T killer naive cells fromperipheralblood	blood
26	chr19:18698800-18699400	Flanking Active TSS	Primary T killer memory cells from peripheral blood	blood
27	chr19:18698800-18699400	Flanking Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
28	chr19:18698800-18699400	Flanking Active TSS	Muscle Satellite Cultured Cells	--
29	chr19:18698800-18699400	Flanking Active TSS	Foreskin Fibroblast Primary Cells skin02	Skin
30	chr19:18698800-18699400	Flanking Active TSS	Brain Dorsolateral Prefrontal Cortex	brain
31	chr19:18698800-18699400	Flanking Active TSS	Duodenum Mucosa	Duodenum
32	chr19:18698800-18699400	Enhancers	Fetal Brain Male	brain
33	chr19:18698800-18699400	Enhancers	Gastric	stomach
34	chr19:18698800-18699400	Enhancers	Placenta Amnion	Placenta Amnion
35	chr19:18698800-18699400	Flanking Active TSS	Hela-S3	cervix
36	chr19:18698800-18699400	Flanking Active TSS	NHDF-Ad	bronchial
37	chr19:18698800-18699400	Flanking Active TSS	Osteobl	bone
38	chr19:18698800-18699600	Flanking Active TSS	Primary monocytes fromperipheralblood	blood
39	chr19:18698800-18699600	Flanking Active TSS	Primary T helper naive cells fromperipheralblood	blood
40	chr19:18698800-18699600	Flanking Active TSS	Primary T regulatory cells fromperipheralblood	blood
41	chr19:18698800-18699600	Flanking Active TSS	Brain Cingulate Gyrus	brain
42	chr19:18698800-18699600	Flanking Active TSS	Rectal Mucosa Donor 31	rectum
43	chr19:18698800-18699600	Flanking Active TSS	Skeletal Muscle Male	skeletal muscle
44	chr19:18698800-18699800	Flanking Active TSS	Foreskin Keratinocyte Primary Cells skin03	Skin
45	chr19:18698800-18700000	Active TSS	Foreskin Melanocyte Primary Cells skin01	Skin
46	chr19:18698800-18700200	Enhancers	Fetal Heart	heart
47	chr19:18698800-18700400	Active TSS	Rectal Smooth Muscle	rectum
48	chr19:18698800-18701000	Flanking Active TSS	Skeletal Muscle Female	skeletal muscle
49	chr19:18698800-18701400	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Female	--
50	chr19:18698800-18701800	Active TSS	Fetal Brain Female	brain

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