Variant report

Variant	rs10415257
Chromosome Location	chr19:18699489-18699490
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:528)
CpG islands
(count:61)
Chromatin interactive
region (count:17)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:528 , 50 per page) page: 1 2 3 4 5 6 7 ... 11

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	CTCF	chr19:18699480-18699630	GM12867	blood:	n/a	chr19:18699546-18699562 chr19:18699545-18699563
3	POLR2A	chr19:18698432-18704772	HepG2	liver:	n/a	n/a
4	CTCF	chr19:18699387-18699723	NHEK	skin:	n/a	chr19:18699546-18699562 chr19:18699545-18699563
5	CTCF	chr19:18699305-18699775	K562	blood:	n/a	chr19:18699546-18699562 chr19:18699545-18699563
6	CEBPD	chr19:18699371-18700588	HepG2	liver:	n/a	n/a
7	CTCF	chr19:18699480-18699630	Caco-2	colon:	n/a	chr19:18699546-18699562 chr19:18699545-18699563
8	MXI1	chr19:18699464-18700802	Hela-S3	cervix:	n/a	n/a
9	CTCF	chr19:18699292-18699877	MCF-7	breast:	n/a	chr19:18699546-18699562 chr19:18699545-18699563
10	CTCF	chr19:18699446-18699678	MCF-7	breast:	n/a	chr19:18699546-18699562 chr19:18699545-18699563
11	MAX	chr19:18698458-18701025	HepG2	liver:	n/a	chr19:18699922-18699932 chr19:18699937-18699946
12	POLR2A	chr19:18699333-18700873	Hela-S3	cervix:	n/a	n/a
13	CTCF	chr19:18699412-18699687	Medullo	brain:	n/a	chr19:18699546-18699562 chr19:18699545-18699563
14	CTCF	chr19:18699347-18699949	H1-hESC	embryonic stem cell:	n/a	chr19:18699925-18699938 chr19:18699546-18699562 chr19:18699545-18699563
15	EP300	chr19:18699339-18700171	GM12878	blood:	n/a	n/a
16	POLR2A	chr19:18699287-18700931	K562	blood:	n/a	n/a
17	ELF1	chr19:18698919-18700973	GM12878	blood:	n/a	n/a
18	POLR2A	chr19:18699241-18700733	HUVEC	blood vessel:	n/a	n/a
19	CTCF	chr19:18699440-18699590	GM12865	blood:	n/a	chr19:18699546-18699562 chr19:18699545-18699563
20	MAX	chr19:18698953-18700664	NB4	blood:	n/a	chr19:18699922-18699932 chr19:18699937-18699946
21	PML	chr19:18699332-18699903	GM12878	blood:	n/a	n/a
22	POU2F2	chr19:18699387-18699807	GM12878	blood:	n/a	n/a
23	NFIC	chr19:18699296-18699985	ECC-1	luminal epithelium:	n/a	n/a
24	CTCF	chr19:18699419-18699699	LNCaP	prostate:	n/a	chr19:18699546-18699562 chr19:18699545-18699563
25	MYC	chr19:18699341-18699670	H1-hESC	embryonic stem cell:	n/a	n/a
26	MAFK	chr19:18699458-18699834	Hela-S3	cervix:	n/a	n/a
27	EP300	chr19:18699402-18699597	K562	blood:	n/a	n/a
28	TBL1XR1	chr19:18699301-18700392	K562	blood:	n/a	n/a
29	SMC3	chr19:18699380-18699624	HepG2	liver:	n/a	n/a
30	CTCF	chr19:18699480-18699630	GM12868	blood:	n/a	chr19:18699546-18699562 chr19:18699545-18699563
31	HDAC2	chr19:18699319-18700747	HepG2	liver:	n/a	n/a
32	POLR2A	chr19:18699435-18700507	GM12892	blood:	n/a	n/a
33	POLR2A	chr19:18699468-18700085	K562	blood:	n/a	n/a
34	POLR2A	chr19:18699316-18700031	GM12891	blood:	n/a	n/a
35	ELF1	chr19:18699396-18699774	HepG2	liver:	n/a	n/a
36	FOXM1	chr19:18699069-18700111	GM12878	blood:	n/a	n/a
37	CTCF	chr19:18699480-18699630	BE2_C	brain:	n/a	chr19:18699546-18699562 chr19:18699545-18699563
38	CTCF	chr19:18699480-18699630	HPAF	blood vessel:	n/a	chr19:18699546-18699562 chr19:18699545-18699563
39	POLR2A	chr19:18699398-18700524	MCF-7	breast:	n/a	n/a
40	POLR2A	chr19:18699344-18700583	GM12892	blood:	n/a	n/a
41	TBL1XR1	chr19:18699360-18699971	GM12878	blood:	n/a	n/a
42	POLR2A	chr19:18699434-18700548	Gliobla	brain:	n/a	n/a
43	POLR2A	chr19:18699190-18700536	GM12878	blood:	n/a	n/a
44	RFX5	chr19:18699450-18700084	Hela-S3	cervix:	n/a	n/a
45	MAX	chr19:18699250-18701052	MCF-7	breast:	n/a	chr19:18699922-18699932 chr19:18699937-18699946
46	YY1	chr19:18699424-18699713	HCT-116	colon:	n/a	n/a
47	CTCF	chr19:18699480-18699630	AG04449	skin:	n/a	chr19:18699546-18699562 chr19:18699545-18699563
48	JUN	chr19:18699423-18699965	K562	blood:	n/a	n/a
49	CTCF	chr19:18699411-18699709	MCF-7	breast:	n/a	chr19:18699546-18699562 chr19:18699545-18699563
50	BACH1	chr19:18699284-18699762	K562	blood:	n/a	n/a

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

No.	Chromosome Location	Cell Line	Cell type	Cell Stage
1	chr19:18699444-18699494	HNPCEpiC	eye:	n/a
2	chr19:18699444-18699494	H1-hESC	embryonic stem cell:	embryo
3	chr19:18699444-18699494	HIPEpiC	eye:	n/a
4	chr19:18699444-18699494	HRCEpiC	kidney:	n/a
5	chr19:18699444-18699494	GM12892	blood:	n/a
6	chr19:18699444-18699494	SK-N-SH	brain:	n/a
7	chr19:18699444-18699494	HCF	heart:	n/a
8	chr19:18699444-18699494	AG09319	gingival:	n/a
9	chr19:18699444-18699494	NH-A	brain:	n/a
10	chr19:18699444-18699494	HCM	heart:	n/a
11	chr19:18699444-18699494	MCF-7	breast:	n/a
12	chr19:18699444-18699494	RPTEC	kidney:	n/a
13	chr19:18699444-18699494	ECC-1	luminal epithelium:	n/a
14	chr19:18699444-18699494	BJ	skin:	n/a
15	chr19:18699444-18699494	NHBE	bronchial:	n/a
16	chr19:18699444-18699494	K562	blood:	n/a
17	chr19:18699444-18699494	NB4	blood:	n/a
18	chr19:18699444-18699494	PrEC	prostate:	n/a
19	chr19:18699444-18699494	AoSMC	blood vessel:	n/a
20	chr19:18699444-18699494	HepG2	liver:	n/a
21	chr19:18699444-18699494	PANC-1	pancreas:	n/a
22	chr19:18699444-18699494	NHDF-neo	bronchial:	n/a
23	chr19:18699444-18699494	HL-60	blood:	n/a
24	chr19:18699444-18699494	HMEC	breast:	n/a
25	chr19:18699444-18699494	HEK293	kidney:	embryo
26	chr19:18699444-18699494	SK-N-SH_RA	brain:	n/a
27	chr19:18699444-18699494	MCF10A-Er-Src	breast:	n/a
28	chr19:18699444-18699494	HUVEC	blood vessel:	n/a
29	chr19:18699444-18699494	Caco-2	colon:	n/a
30	chr19:18699444-18699494	CMK	blood:	n/a
31	chr19:18699444-18699494	BE2_C	brain:	n/a
32	chr19:18699444-18699494	ovcar-3	ovarian:	n/a
33	chr19:18699444-18699494	HPAEpiC	pulmonary alveolar:	n/a
34	chr19:18699444-18699494	AG09309	skin:	n/a
35	chr19:18699444-18699494	AG04449	skin:	fetal
36	chr19:18699444-18699494	GM19239	blood:	n/a
37	chr19:18699444-18699494	SAEC	small airway:	n/a
38	chr19:18699444-18699494	SKMC	muscle:	n/a
39	chr19:18699444-18699494	A549	lung:	n/a
40	chr19:18699444-18699494	LNCaP	prostate:	n/a
41	chr19:18699444-18699494	AG10803	skin:	n/a
42	chr19:18699444-18699494	IMR90	lung:	fetal
43	chr19:18699444-18699494	SK-N-MC	brain:	n/a
44	chr19:18699444-18699494	HCPEpiC	choroid plexus:	n/a
45	chr19:18699444-18699494	GM06990	blood:	n/a
46	chr19:18699444-18699494	Hela-S3	cervix:	n/a
47	chr19:18699444-18699494	HAEpiC	amniotic membrane:	n/a
48	chr19:18699444-18699494	Jurkat	blood:	n/a
49	chr19:18699444-18699494	NT2-D1	testis:	n/a
50	chr19:18699444-18699494	GM12878	blood:	n/a

(count:17 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr19:18667424..18670168-chr19:18699281..18701481,3	MCF-7	breast:
2	chr19:18699463..18701468-chr19:19028694..19031158,3	K562	blood:
3	chr19:18698544..18700812-chr19:18957924..18960532,2	MCF-7	breast:
4	chr19:18698512..18700358-chr19:18745222..18750244,4	K562	blood:
5	chr19:18669154..18672917-chr19:18697910..18700793,4	K562	blood:
6	chr19:18699463..18701468-chr19:19028694..19031158,2	K562	blood:
7	chr19:18681312..18685117-chr19:18698049..18701447,5	MCF-7	breast:
8	chr19:18653459..18656385-chr19:18699225..18703130,9	K562	blood:
9	chr19:18678376..18688390-chr19:18697032..18707656,34	K562	blood:
10	chr19:18495663..18499199-chr19:18698556..18701601,3	K562	blood:
11	chr19:18672789..18675551-chr19:18697478..18700004,2	MCF-7	breast:
12	chr19:18631688..18633803-chr19:18698894..18701519,3	MCF-7	breast:
13	chr19:18631032..18633728-chr19:18697675..18701681,7	MCF-7	breast:
14	chr19:18630919..18637145-chr19:18698949..18704438,10	K562	blood:
15	chr19:18698708..18701515-chr19:18746316..18749182,4	MCF-7	breast:
16	chr19:18629422..18634718-chr19:18699285..18702887,8	K562	blood:
17	chr19:18527544..18530023-chr19:18699407..18700970,2	K562	blood:

No data

Variant related genes	Relation type
C19orf60	TF binding region
C19orf60	CpG island
ENSG00000130511	Chromatin interaction
ENSG00000105656	Chromatin interaction
ENSG00000105671	Chromatin interaction
ENSG00000105701	Chromatin interaction
ENSG00000005007	Chromatin interaction
ENSG00000268030	Chromatin interaction
ENSG00000268983	Chromatin interaction
ENSG00000105669	Chromatin interaction
ENSG00000221983	Chromatin interaction
ENSG00000130513	Chromatin interaction
ENSG00000167487	Chromatin interaction
ENSG00000105700	Chromatin interaction
ENSG00000264175	Chromatin interaction

Extended variants
information (count: 18 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:10)

rs_ID	r²[population]
rs10407212	0.85[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2074174	0.91[AMR][1000 genomes];0.85[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2074175	0.91[AMR][1000 genomes];0.86[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs3170474	0.91[ASN][1000 genomes]
rs4808823	0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6417264	0.91[ASN][1000 genomes]
rs7250623	0.81[ASN][1000 genomes]
rs7252198	0.91[ASN][1000 genomes]
rs7256319	0.89[ASN][1000 genomes]
rs886242	0.80[AMR][1000 genomes];0.82[EUR][1000 genomes];0.87[ASN][1000 genomes]

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

No data

Chromatin state (count:127 , 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	chr19:18698600-18699600	Flanking Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
3	chr19:18698600-18699600	Flanking Active TSS	Rectal Mucosa Donor 29	rectum
4	chr19:18698600-18699600	Enhancers	Sigmoid Colon	Sigmoid Colon
5	chr19:18698600-18700800	Flanking Active TSS	Colonic Mucosa	Colon
6	chr19:18698600-18701200	Flanking Active TSS	Primary hematopoietic stem cells short term culture	blood
7	chr19:18698600-18701200	Flanking Active TSS	Stomach Smooth Muscle	stomach
8	chr19:18698600-18701200	Flanking Active TSS	Monocytes-CD14+_RO01746	blood
9	chr19:18698800-18699600	Flanking Active TSS	Primary monocytes fromperipheralblood	blood
10	chr19:18698800-18699600	Flanking Active TSS	Primary T helper naive cells fromperipheralblood	blood
11	chr19:18698800-18699600	Flanking Active TSS	Primary T regulatory cells fromperipheralblood	blood
12	chr19:18698800-18699600	Flanking Active TSS	Brain Cingulate Gyrus	brain
13	chr19:18698800-18699600	Flanking Active TSS	Rectal Mucosa Donor 31	rectum
14	chr19:18698800-18699600	Flanking Active TSS	Skeletal Muscle Male	skeletal muscle
15	chr19:18698800-18699800	Flanking Active TSS	Foreskin Keratinocyte Primary Cells skin03	Skin
16	chr19:18698800-18700000	Active TSS	Foreskin Melanocyte Primary Cells skin01	Skin
17	chr19:18698800-18700200	Enhancers	Fetal Heart	heart
18	chr19:18698800-18700400	Active TSS	Rectal Smooth Muscle	rectum
19	chr19:18698800-18701000	Flanking Active TSS	Skeletal Muscle Female	skeletal muscle
20	chr19:18698800-18701400	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Female	--
21	chr19:18698800-18701800	Active TSS	Fetal Brain Female	brain
22	chr19:18699000-18699600	Flanking Active TSS	Primary B cells from peripheral blood	blood
23	chr19:18699000-18699600	Flanking Active TSS	Primary Natural Killer cells fromperipheralblood	blood
24	chr19:18699000-18699600	Active TSS	Foreskin Keratinocyte Primary Cells skin02	Skin
25	chr19:18699000-18699600	Flanking Active TSS	Brain Germinal Matrix	brain
26	chr19:18699000-18699600	Flanking Active TSS	Brain Inferior Temporal Lobe	brain
27	chr19:18699000-18699600	Flanking Active TSS	Fetal Adrenal Gland	Adrenal Gland
28	chr19:18699000-18699600	Flanking Active TSS	Fetal Stomach	stomach
29	chr19:18699000-18699600	Flanking Active TSS	Fetal Thymus	thymus
30	chr19:18699000-18699600	Flanking Active TSS	Thymus	Thymus
31	chr19:18699000-18699600	Flanking Active TSS	HMEC	breast
32	chr19:18699000-18700000	Active TSS	H9 Derived Neuron Cultured Cells	ES cell derived
33	chr19:18699000-18700000	Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
34	chr19:18699000-18700400	Flanking Active TSS	Liver	Liver
35	chr19:18699000-18700800	Flanking Active TSS	Primary mononuclear cells fromperipheralblood	Blood
36	chr19:18699000-18701000	Flanking Active TSS	Primary B cells from cord blood	blood
37	chr19:18699000-18701000	Flanking Active TSS	Adipose Nuclei	Adipose
38	chr19:18699000-18701400	Active TSS	ES-WA7 Cell Line	embryonic stem cell
39	chr19:18699000-18701600	Active TSS	iPS DF 6.9 Cell Line	embryonic stem cell
40	chr19:18699000-18701600	Active TSS	A549	lung
41	chr19:18699000-18701800	Active TSS	HUES48 Cell Line	embryonic stem cell
42	chr19:18699000-18701800	Active TSS	Fetal Kidney	kidney
43	chr19:18699200-18699600	Flanking Active TSS	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
44	chr19:18699200-18699600	Flanking Active TSS	IMR90 fetal lung fibroblasts Cell Line	lung
45	chr19:18699200-18699600	Flanking Active TSS	Ganglion Eminence derived primary cultured neurospheres	brain
46	chr19:18699200-18699600	Flanking Active TSS	Fetal Muscle Leg	muscle
47	chr19:18699200-18699600	Flanking Active TSS	Placenta	Placenta
48	chr19:18699200-18699600	Flanking Active TSS	Pancreas	Pancrea
49	chr19:18699200-18699600	Flanking Active TSS	Right Ventricle	heart
50	chr19:18699200-18699600	Flanking Active TSS	NHEK	skin

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