Variant report

Variant	rs62119676
Chromosome Location	chr19:39833662-39833663
allele	C/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	CTCF	chr19:39833620-39833770	A549	lung:	n/a	n/a
2	POLR2A	chr19:39833267-39834007	K562	blood:	n/a	n/a
3	ZBTB7A	chr19:39833248-39833970	ECC-1	luminal epithelium:	n/a	n/a
4	ZBTB7A	chr19:39833459-39833794	HepG2	liver:	n/a	n/a
5	E2F6	chr19:39833329-39833849	K562	blood:	n/a	n/a
6	JUN	chr19:39831847-39833851	K562	blood:	n/a	chr19:39832793-39832802
7	SIN3A	chr19:39833483-39834101	H1-hESC	embryonic stem cell:	n/a	chr19:39833520-39833533
8	MXI1	chr19:39831704-39834033	SK-N-SH	brain:	n/a	n/a
9	POLR2A	chr19:39833571-39833934	IMR90	lung:	n/a	n/a
10	ZBTB7A	chr19:39833248-39833884	K562	blood:	n/a	n/a
11	ZBTB7A	chr19:39833211-39833948	ECC-1	luminal epithelium:	n/a	n/a
12	ZBTB7A	chr19:39833499-39833744	HepG2	liver:	n/a	n/a
13	MAX	chr19:39831278-39833917	A549	lung:	n/a	chr19:39832865-39832875 chr19:39833668-39833678 chr19:39832862-39832872 chr19:39832756-39832765 chr19:39832838-39832847
14	ZBTB7A	chr19:39832435-39833860	K562	blood:	n/a	chr19:39832625-39832632 chr19:39832784-39832791
15	MAX	chr19:39833338-39833952	K562	blood:	n/a	chr19:39833668-39833678
16	MAZ	chr19:39831350-39834239	IMR90	lung:	n/a	chr19:39832865-39832875 chr19:39833668-39833678 chr19:39832862-39832872 chr19:39832756-39832765 chr19:39832838-39832847
17	JUND	chr19:39831794-39833840	A549	lung:	n/a	chr19:39832793-39832802
18	REST	chr19:39831318-39834372	PANC-1	pancreas:	n/a	chr19:39832957-39832970 chr19:39833520-39833533
19	CHD1	chr19:39831630-39834716	IMR90	lung:	n/a	chr19:39832940-39832950 chr19:39832779-39832789
20	SIN3AK20	chr19:39831291-39835344	PANC-1	pancreas:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr19:39831356..39834540-chr19:39880141..39881911,4	MCF-7	breast:
2	chr19:39832559..39836457-chr19:39880660..39884768,5	MCF-7	breast:
3	chr19:39833435..39835021-chr19:39840872..39844768,3	MCF-7	breast:
4	chr19:39831465..39834764-chr19:39935836..39937934,3	K562	blood:
5	chr19:39614928..39617634-chr19:39831535..39834253,2	K562	blood:
6	chr19:39831462..39833819-chr19:39895852..39900331,6	MCF-7	breast:
7	chr19:39833451..39835275-chr19:39876704..39878338,2	MCF-7	breast:
8	chr19:39831269..39834563-chr19:39900586..39904953,4	MCF-7	breast:
9	chr17:58602101..58603865-chr19:39833012..39834515,2	MCF-7	breast:
10	chr19:39829936..39834375-chr19:39901478..39904741,5	MCF-7	breast:
11	chr19:39830889..39835466-chr19:39836647..39841099,6	MCF-7	breast:
12	chr19:39832709..39837239-chr19:39925090..39928725,4	K562	blood:
13	chr19:39830669..39836861-chr19:39895802..39900887,6	MCF-7	breast:
14	chr19:39811372..39812878-chr19:39831167..39833886,2	MCF-7	breast:
15	chr19:39828912..39834348-chr19:39896525..39904623,14	K562	blood:
16	chr19:39826340..39829691-chr19:39831267..39834495,5	K562	blood:
17	chr19:39809900..39813494-chr19:39831059..39834441,3	MCF-7	breast:
18	chr19:39832183..39834517-chr19:39925160..39926923,2	MCF-7	breast:
19	chr19:39727142..39728696-chr19:39832975..39834941,2	K562	blood:

Variant related genes	Relation type
GMFG	TF binding region
ENSG00000269246	TF binding region
ENSG00000105193	Chromatin interaction
ENSG00000006712	Chromatin interaction
ENSG00000196235	Chromatin interaction
ENSG00000268262	Chromatin interaction
ENSG00000179134	Chromatin interaction
ENSG00000259349	Chromatin interaction
ENSG00000130755	Chromatin interaction
ENSG00000130669	Chromatin interaction
ENSG00000090924	Chromatin interaction
ENSG00000063322	Chromatin interaction
ENSG00000268510	Chromatin interaction
ENSG00000062725	Chromatin interaction
ENSG00000266559	Chromatin interaction
ENSG00000128016	Chromatin interaction

Extended variants
information (count: 43 )
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]
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]
rs62119686	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:11 , 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	nsv833830	chr19:39709538-39837846	Enhancers Bivalent Enhancer Genic enhancers Strong transcription Bivalent/Poised TSS Active TSS Flanking Active TSS Weak transcription Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	32 gene(s)	inside rSNPs	diseases
3	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
4	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
5	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
6	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
7	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
8	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
9	esv3322501	chr19:39831637-39834485	Flanking Active TSS Enhancers Active TSS ZNF genes & repeats Weak transcription Bivalent/Poised TSS Transcr. at gene 5' and 3' Genic enhancers Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region	21 gene(s)	inside rSNPs	diseases
10	esv3350319	chr19:39831712-39835310	Enhancers Flanking Active TSS Active TSS Weak transcription Genic enhancers Strong transcription Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region	21 gene(s)	inside rSNPs	diseases
11	esv3359345	chr19:39832262-39834360	Flanking Active TSS Active TSS Weak transcription Enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh Genic enhancers	TF binding region CpG island Chromatin interactive region	21 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	chr19:39831400-39834200	Active TSS	iPS DF 6.9 Cell Line	embryonic stem cell
2	chr19:39831400-39834400	Active TSS	HUES48 Cell Line	embryonic stem cell
3	chr19:39831600-39834000	Active TSS	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
4	chr19:39831600-39834000	Active TSS	NHLF	lung
5	chr19:39831600-39834400	Active TSS	H9 Cell Line	embryonic stem cell
6	chr19:39831800-39833800	Active TSS	H9 Derived Neuron Cultured Cells	ES cell derived
7	chr19:39831800-39833800	Active TSS	HUES6 Cell Line	embryonic stem cell
8	chr19:39831800-39833800	Active TSS	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
9	chr19:39831800-39833800	Active TSS	Aorta	Aorta
10	chr19:39831800-39833800	Active TSS	Fetal Intestine Large	intestine
11	chr19:39831800-39833800	Active TSS	Small Intestine	intestine
12	chr19:39831800-39833800	Active TSS	Dnd41	blood
13	chr19:39831800-39833800	Active TSS	GM12878-XiMat	blood
14	chr19:39831800-39833800	Active TSS	HSMMtube	muscle
15	chr19:39831800-39833800	Active TSS	K562	blood
16	chr19:39831800-39833800	Active TSS	NH-A	brain
17	chr19:39831800-39833800	Active TSS	NHEK	skin
18	chr19:39831800-39834000	Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
19	chr19:39831800-39834000	Active TSS	IMR90 fetal lung fibroblasts Cell Line	lung
20	chr19:39831800-39834000	Active TSS	iPS-15b Cell Line	embryonic stem cell
21	chr19:39831800-39834000	Active TSS	Foreskin Melanocyte Primary Cells skin03	Skin
22	chr19:39831800-39834000	Active TSS	Brain Dorsolateral Prefrontal Cortex	brain
23	chr19:39831800-39834000	Active TSS	Fetal Stomach	stomach
24	chr19:39831800-39834000	Active TSS	Ovary	ovary
25	chr19:39831800-39834000	Active TSS	Osteobl	bone
26	chr19:39831800-39834200	Active TSS	HUES64 Cell Line	embryonic stem cell
27	chr19:39831800-39834200	Active TSS	iPS-20b Cell Line	embryonic stem cell
28	chr19:39831800-39834200	Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
29	chr19:39831800-39834200	Active TSS	HMEC	breast
30	chr19:39831800-39834400	Active TSS	H1 Cell Line	embryonic stem cell
31	chr19:39831800-39834400	Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
32	chr19:39831800-39834400	Active TSS	Pancreatic Islets	Pancreatic Islet
33	chr19:39831800-39834600	Active TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
34	chr19:39832000-39833800	Active TSS	ES-UCSF4 Cell Line	embryonic stem cell
35	chr19:39832000-39833800	Active TSS	Primary T killer naive cells fromperipheralblood	blood
36	chr19:39832000-39833800	Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
37	chr19:39832000-39833800	Active TSS	Muscle Satellite Cultured Cells	--
38	chr19:39832000-39833800	Active TSS	Foreskin Keratinocyte Primary Cells skin03	Skin
39	chr19:39832000-39833800	Active TSS	Brain Angular Gyrus	brain
40	chr19:39832000-39833800	Active TSS	Brain Inferior Temporal Lobe	brain
41	chr19:39832000-39833800	Active TSS	Duodenum Mucosa	Duodenum
42	chr19:39832000-39833800	Active TSS	Fetal Brain Female	brain
43	chr19:39832000-39833800	Active TSS	Fetal Intestine Small	intestine
44	chr19:39832000-39833800	Active TSS	Left Ventricle	heart
45	chr19:39832000-39833800	Active TSS	Rectal Smooth Muscle	rectum
46	chr19:39832000-39833800	Active TSS	A549	lung
47	chr19:39832000-39834000	Active TSS	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
48	chr19:39832000-39834000	Active TSS	iPS-18 Cell Line	embryonic stem cell
49	chr19:39832000-39834000	Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
50	chr19:39832000-39834000	Active TSS	Esophagus	oesophagus

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