Variant report

Variant	rs62119686
Chromosome Location	chr19:39842332-39842333
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:83)
CpG islands
(count:0)
Chromatin interactive
region (count:2)
LncRNA
region (count:1)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:83 , 50 per page) page: 1 2

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	CTCF	chr19:39842240-39842390	NHLF	lung:	n/a	n/a
2	USF1	chr19:39841974-39842534	K562	blood:	n/a	n/a
3	CTCF	chr19:39842220-39842370	Caco-2	colon:	n/a	n/a
4	NFIC	chr19:39842133-39842578	GM12878	blood:	n/a	n/a
5	CTCF	chr19:39842220-39842370	GM12870	blood:	n/a	n/a
6	RAD21	chr19:39842076-39842372	GM12878	blood:	n/a	n/a
7	JUND	chr19:39842105-39842524	K562	blood:	n/a	n/a
8	MAX	chr19:39842177-39842413	K562	blood:	n/a	n/a
9	MAZ	chr19:39842155-39842492	GM12878	blood:	n/a	n/a
10	CHD1	chr19:39842263-39842363	GM12878	blood:	n/a	n/a
11	CTCF	chr19:39842260-39842410	NHDF-neo	bronchial:	n/a	n/a
12	FOXM1	chr19:39841952-39842596	GM12878	blood:	n/a	n/a
13	IRF4	chr19:39841932-39842569	GM12878	blood:	n/a	n/a
14	BHLHE40	chr19:39842112-39842513	GM12878	blood:	n/a	n/a
15	MXI1	chr19:39842222-39842438	GM12878	blood:	n/a	n/a
16	RFX5	chr19:39842142-39842818	GM12878	blood:	n/a	n/a
17	TBL1XR1	chr19:39842154-39842502	GM12878	blood:	n/a	n/a
18	PML	chr19:39842144-39842443	GM12878	blood:	n/a	n/a
19	RFX5	chr19:39842228-39842560	Hela-S3	cervix:	n/a	n/a
20	BATF	chr19:39842057-39842586	GM12878	blood:	n/a	n/a
21	CTCF	chr19:39842220-39842370	AoAF	blood vessel:	n/a	n/a
22	CTCF	chr19:39842074-39842437	GM12878	blood:	n/a	n/a
23	POU2F2	chr19:39842058-39842488	GM12891	blood:	n/a	n/a
24	POU2F2	chr19:39842099-39842414	GM12878	blood:	n/a	n/a
25	STAT1	chr19:39842199-39842399	GM12878	blood:	n/a	n/a
26	EBF1	chr19:39842203-39842363	GM12878	blood:	n/a	n/a
27	RUNX3	chr19:39842028-39842483	GM12878	blood:	n/a	n/a
28	STAT5A	chr19:39841863-39842674	GM12878	blood:	n/a	n/a
29	PAX5	chr19:39842056-39842617	GM12878	blood:	n/a	n/a
30	ATF2	chr19:39842027-39842566	GM12878	blood:	n/a	n/a
31	SMC3	chr19:39842049-39842450	GM12878	blood:	n/a	n/a
32	CTCF	chr19:39842219-39842350	GM19238	blood:	n/a	n/a
33	TBP	chr19:39842195-39842397	GM12878	blood:	n/a	n/a
34	ZNF143	chr19:39842122-39842435	GM12878	blood:	n/a	n/a
35	CUX1	chr19:39842274-39842445	GM12878	blood:	n/a	n/a
36	CTCF	chr19:39842200-39842350	AG04449	skin:	n/a	n/a
37	CHD2	chr19:39842187-39842457	GM12878	blood:	n/a	n/a
38	CTCF	chr19:39842200-39842350	GM12871	blood:	n/a	n/a
39	CREB1	chr19:39842026-39842671	GM12878	blood:	n/a	n/a
40	RAD21	chr19:39842178-39842351	K562	blood:	n/a	n/a
41	RFX5	chr19:39841953-39842764	SK-N-SH	brain:	n/a	n/a
42	MAX	chr19:39842205-39842392	K562	blood:	n/a	n/a
43	CTCF	chr19:39842165-39842364	GM10266	blood:	n/a	n/a
44	SREBP1	chr19:39841939-39843251	GM12878	blood:	n/a	n/a
45	EP300	chr19:39842171-39842477	GM12878	blood:	n/a	n/a
46	MAZ	chr19:39842143-39842459	K562	blood:	n/a	n/a
47	RFX5	chr19:39842207-39842641	K562	blood:	n/a	n/a
48	CTCF	chr19:39842220-39842370	GM12872	blood:	n/a	n/a
49	CREB1	chr19:39841958-39842684	GM12878	blood:	n/a	n/a
50	RFX5	chr19:39842313-39842505	HepG2	liver:	n/a	n/a

No data

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

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr19:39840535..39845164-chr19:39896257..39899085,6	K562	blood:
2	chr19:39841107..39843356-chr19:39881795..39884514,2	MCF-7	breast:

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

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-MED29-3	chr19:39840440-39843129	NONHSAT066282

No data

Variant related genes	Relation type
SAMD4B	TF binding region
ENSG00000006712	Chromatin interaction
ENSG00000063322	Chromatin interaction
ENSG00000128016	Chromatin interaction

Extended variants
information (count: 39 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:32)

rs_ID	r²[population]
rs40469	0.82[EUR][1000 genomes]
rs45591338	1.00[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs45613331	1.00[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs61736260	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs62119672	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs62119675	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs62119676	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs62119678	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs62119679	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs62119680	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs62119682	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs62119685	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs62119687	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs62119688	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs62119689	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs62119690	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs62119692	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs62119693	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs62119695	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs62119697	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs62119698	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs62119699	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs62119700	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs62119702	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs62119721	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs62119722	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs62119723	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs62122887	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs62122888	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs62122889	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs62122891	1.00[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs62122892	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.93[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:7 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv432048	chr19:39572060-39850060	Bivalent/Poised TSS Bivalent Enhancer Weak transcription Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Active TSS Strong transcription Enhancers Flanking Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	42 gene(s)	inside rSNPs	diseases
2	nsv911679	chr19:39735106-39924129	Active TSS Flanking Active TSS Weak transcription Enhancers Strong transcription Bivalent Enhancer Transcr. at gene 5' and 3' Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	198 gene(s)	inside rSNPs	diseases
3	nsv1058514	chr19:39744112-39902580	Flanking Active TSS Enhancers Active TSS Bivalent/Poised TSS Weak transcription Genic enhancers Strong transcription Transcr. at gene 5' and 3' Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	187 gene(s)	inside rSNPs	diseases
4	nsv911680	chr19:39792460-39924129	Enhancers Flanking Active TSS Weak transcription Strong transcription Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	194 gene(s)	inside rSNPs	diseases
5	nsv911681	chr19:39797716-39856246	Strong transcription Weak transcription Genic enhancers Bivalent/Poised TSS Flanking Active TSS Active TSS Bivalent Enhancer Enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	29 gene(s)	inside rSNPs	diseases
6	esv10629	chr19:39811570-39886212	Flanking Active TSS Strong transcription Weak transcription Enhancers Transcr. at gene 5' and 3' Genic enhancers Active TSS Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	34 gene(s)	inside rSNPs	diseases
7	nsv870133	chr19:39822160-39938468	Weak transcription Strong transcription Flanking Active TSS Enhancers Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	233 gene(s)	inside rSNPs	diseases

No data

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr19:39834000-39842400	Weak transcription	Gastric	stomach
2	chr19:39834200-39846600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
3	chr19:39834200-39859200	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
4	chr19:39834400-39842400	Weak transcription	Rectal Mucosa Donor 31	rectum
5	chr19:39834400-39844600	Weak transcription	ES-I3 Cell Line	embryonic stem cell
6	chr19:39834400-39845400	Weak transcription	Fetal Kidney	kidney
7	chr19:39834400-39849200	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
8	chr19:39834600-39842400	Weak transcription	Colonic Mucosa	Colon
9	chr19:39834600-39842400	Weak transcription	HMEC	breast
10	chr19:39834800-39842400	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
11	chr19:39834800-39847400	Weak transcription	Small Intestine	intestine
12	chr19:39834800-39852800	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
13	chr19:39834800-39852800	Strong transcription	Fetal Muscle Trunk	muscle
14	chr19:39834800-39880000	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
15	chr19:39835000-39844600	Weak transcription	Stomach Mucosa	stomach
16	chr19:39835000-39846000	Weak transcription	Primary T helper naive cells from peripheral blood	blood
17	chr19:39835600-39853600	Strong transcription	Placenta	Placenta
18	chr19:39835800-39880200	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
19	chr19:39835800-39880200	Strong transcription	Monocytes-CD14+_RO01746	blood
20	chr19:39836000-39847600	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
21	chr19:39836200-39842400	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
22	chr19:39836200-39842800	Weak transcription	Placenta Amnion	Placenta Amnion
23	chr19:39836200-39880400	Strong transcription	Primary T cells from cord blood	blood
24	chr19:39836400-39862600	Strong transcription	Duodenum Mucosa	Duodenum
25	chr19:39836600-39845600	Weak transcription	Aorta	Aorta
26	chr19:39836600-39845800	Weak transcription	Rectal Smooth Muscle	rectum
27	chr19:39836600-39864000	Strong transcription	HUES48 Cell Line	embryonic stem cell
28	chr19:39836600-39880400	Strong transcription	Primary monocytes fromperipheralblood	blood
29	chr19:39836600-39880400	Strong transcription	Fetal Brain Female	brain
30	chr19:39836800-39846000	Weak transcription	Pancreas	Pancrea
31	chr19:39836800-39852000	Strong transcription	HUES64 Cell Line	embryonic stem cell
32	chr19:39836800-39852600	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
33	chr19:39837200-39842600	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
34	chr19:39837400-39842400	Enhancers	Brain Cingulate Gyrus	brain
35	chr19:39837400-39842400	Weak transcription	Fetal Brain Male	brain
36	chr19:39837400-39846400	Weak transcription	Pancreatic Islets	Pancreatic Islet
37	chr19:39837400-39880000	Strong transcription	Primary T helper cells fromperipheralblood	blood
38	chr19:39837600-39863600	Strong transcription	Fetal Intestine Small	intestine
39	chr19:39837800-39854400	Strong transcription	Fetal Stomach	stomach
40	chr19:39837800-39855400	Strong transcription	Sigmoid Colon	Sigmoid Colon
41	chr19:39838000-39851800	Strong transcription	Liver	Liver
42	chr19:39838000-39880000	Strong transcription	Brain Germinal Matrix	brain
43	chr19:39838200-39858200	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
44	chr19:39838200-39858200	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
45	chr19:39838200-39862600	Strong transcription	Rectal Mucosa Donor 29	rectum
46	chr19:39838400-39843200	Strong transcription	Ovary	ovary
47	chr19:39838400-39843800	Enhancers	Brain Inferior Temporal Lobe	brain
48	chr19:39838400-39853200	Strong transcription	A549	lung
49	chr19:39838600-39852600	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
50	chr19:39838600-39880400	Strong transcription	HUES6 Cell Line	embryonic stem cell

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