Variant report

Variant	rs45613331
Chromosome Location	chr19:39880856-39880857
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	POLR2A	chr19:39880520-39882396	U87	brain:	n/a	n/a
2	BCL3	chr19:39879962-39882537	A549	lung:	n/a	n/a
3	POLR2A	chr19:39850716-39886400	PANC-1	pancreas:	n/a	n/a
4	REST	chr19:39879869-39882476	PANC-1	pancreas:	n/a	chr19:39881693-39881703 chr19:39881691-39881711 chr19:39881615-39881625 chr19:39881691-39881705 chr19:39880192-39880205 chr19:39881520-39881533
5	REST	chr19:39880549-39882700	H1-neurons	neurons:	n/a	chr19:39881693-39881703 chr19:39881691-39881711 chr19:39881615-39881625 chr19:39881691-39881705 chr19:39881520-39881533
6	ATF3	chr19:39880832-39882417	A549	lung:	n/a	chr19:39881362-39881372 chr19:39881358-39881373 chr19:39881362-39881370 chr19:39881362-39881372 chr19:39881361-39881369 chr19:39881909-39881920 chr19:39881360-39881371 chr19:39881910-39881918 chr19:39881362-39881369 chr19:39881359-39881372 chr19:39881909-39881920 chr19:39881360-39881371 chr19:39881359-39881369 chr19:39881360-39881373 chr19:39881329-39881337
7	POLR2A	chr19:39876429-39882671	HepG2	liver:	n/a	n/a
8	POLR2A	chr19:39880780-39882400	HUVEC	blood vessel:	n/a	n/a
9	FOSL2	chr19:39880711-39882508	A549	lung:	n/a	chr19:39881361-39881370
10	SIX5	chr19:39880374-39882910	A549	lung:	n/a	n/a
11	POLR2A	chr19:39879908-39881021	K562	blood:	n/a	n/a
12	SIN3AK20	chr19:39870428-39883708	PANC-1	pancreas:	n/a	n/a
13	POLR2A	chr19:39880526-39882396	U87	brain:	n/a	n/a
14	POLR2A	chr19:39879945-39880944	Hela-S3	cervix:	n/a	n/a
15	MAZ	chr19:39880771-39882394	IMR90	lung:	n/a	n/a
16	REST	chr19:39880842-39882538	A549	lung:	n/a	chr19:39881693-39881703 chr19:39881691-39881711 chr19:39881615-39881625 chr19:39881691-39881705 chr19:39881520-39881533
17	POLR2A	chr19:39880576-39880868	ECC-1	luminal epithelium:	n/a	n/a
18	POLR2A	chr19:39880229-39882430	MCF-7	breast:	n/a	n/a
19	POLR2A	chr19:39880509-39882487	H1-neurons	neurons:	n/a	n/a
20	POLR2A	chr19:39880804-39882521	SK-N-MC	brain:	n/a	n/a
21	TCF12	chr19:39879881-39882636	A549	lung:	n/a	chr19:39880201-39880211
22	BCL3	chr19:39880441-39882487	A549	lung:	n/a	n/a
23	POLR2A	chr19:39875542-39882243	K562	blood:	n/a	n/a
24	POLR2A	chr19:39880545-39880911	U87	brain:	n/a	n/a
25	POLR2A	chr19:39880493-39882483	H1-neurons	neurons:	n/a	n/a
26	POLR2A	chr19:39878621-39882617	H1-hESC	embryonic stem cell:	n/a	n/a
27	POLR2A	chr19:39879961-39882312	A549	lung:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr19:39880332..39881919-chr19:40028970..40031203,2	K562	blood:
2	chr19:39832559..39836457-chr19:39880660..39884768,5	MCF-7	breast:
3	chr19:39860348..39862519-chr19:39879962..39882388,3	K562	blood:
4	chr19:39880509..39882503-chr19:40021734..40025038,3	K562	blood:
5	chr19:39831356..39834540-chr19:39880141..39881911,4	MCF-7	breast:
6	chr19:39880299..39881893-chr19:40023517..40025617,2	K562	blood:
7	chr19:39657376..39659366-chr19:39880631..39883470,2	MCF-7	breast:
8	chr19:39859941..39863633-chr19:39878903..39882994,5	MCF-7	breast:

Variant related genes	Relation type
PAF1	TF binding region
MED29	TF binding region
ENSG00000179134	Chromatin interaction
ENSG00000176401	Chromatin interaction
ENSG00000269246	Chromatin interaction
ENSG00000269584	Chromatin interaction
ENSG00000176396	Chromatin interaction
ENSG00000130669	Chromatin interaction
ENSG00000269792	Chromatin interaction
ENSG00000130755	Chromatin interaction

Extended variants
information (count: 49 )
Associated
traits (count: 0)

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

rs_ID	r²[population]
rs11669865	1.00[AFR][1000 genomes]
rs45591338	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs61736260	1.00[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs62119672	1.00[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs62119675	1.00[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs62119676	1.00[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs62119678	1.00[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs62119679	1.00[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs62119680	1.00[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs62119682	1.00[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs62119685	1.00[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs62119686	1.00[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs62119687	1.00[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs62119688	1.00[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs62119689	1.00[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs62119690	1.00[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs62119692	1.00[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs62119693	1.00[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs62119695	1.00[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs62119697	1.00[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs62119698	1.00[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs62119699	1.00[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs62119700	1.00[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs62119702	1.00[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs62119721	1.00[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs62119722	1.00[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs62119723	1.00[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs62119730	1.00[AFR][1000 genomes]
rs62120525	1.00[AFR][1000 genomes]
rs62120527	1.00[AFR][1000 genomes]
rs62120528	1.00[AFR][1000 genomes]
rs62120529	1.00[AFR][1000 genomes]
rs62120530	1.00[AFR][1000 genomes]
rs62120531	1.00[AFR][1000 genomes]
rs62120532	1.00[AFR][1000 genomes]
rs62120669	1.00[AFR][1000 genomes]
rs62120671	1.00[AFR][1000 genomes]
rs62122887	1.00[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs62122888	1.00[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs62122889	1.00[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs62122891	1.00[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs62122892	1.00[AMR][1000 genomes];0.80[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	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
2	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
3	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
4	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
5	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
6	nsv911682	chr19:39847132-39914748	Strong transcription Active TSS Weak transcription Enhancers Genic enhancers Bivalent Enhancer Flanking Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	179 gene(s)	inside rSNPs	diseases
7	nsv911683	chr19:39847132-39924129	Strong transcription Flanking Active TSS Weak transcription Enhancers Active TSS Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	185 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	chr19:39850400-39881000	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
2	chr19:39879400-39881000	Transcr. at gene 5' and 3'	Foreskin Fibroblast Primary Cells skin02	Skin
3	chr19:39879400-39881000	Genic enhancers	Spleen	Spleen
4	chr19:39879800-39881000	Weak transcription	Aorta	Aorta
5	chr19:39880200-39881600	Transcr. at gene 5' and 3'	Dnd41	blood
6	chr19:39880400-39881000	Flanking Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
7	chr19:39880400-39881000	Enhancers	Primary B cells from cord blood	blood
8	chr19:39880400-39881000	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
9	chr19:39880400-39881000	Genic enhancers	Primary Natural Killer cells fromperipheralblood	blood
10	chr19:39880400-39881000	Flanking Active TSS	Brain Dorsolateral Prefrontal Cortex	brain
11	chr19:39880400-39881000	Flanking Active TSS	Duodenum Smooth Muscle	Duodenum
12	chr19:39880400-39881000	Transcr. at gene 5' and 3'	Fetal Intestine Small	intestine
13	chr19:39880400-39881000	Enhancers	Placenta Amnion	Placenta Amnion
14	chr19:39880400-39881000	Flanking Active TSS	GM12878-XiMat	blood
15	chr19:39880400-39881000	Flanking Active TSS	HMEC	breast
16	chr19:39880400-39881200	Flanking Active TSS	Foreskin Keratinocyte Primary Cells skin03	Skin
17	chr19:39880400-39881200	Flanking Active TSS	Foreskin Melanocyte Primary Cells skin01	Skin
18	chr19:39880400-39881400	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Female	--
19	chr19:39880400-39881400	Flanking Active TSS	Hela-S3	cervix
20	chr19:39880400-39882800	Active TSS	iPS-18 Cell Line	embryonic stem cell
21	chr19:39880400-39883000	Active TSS	HUES6 Cell Line	embryonic stem cell
22	chr19:39880400-39883400	Active TSS	HUES64 Cell Line	embryonic stem cell
23	chr19:39880600-39881000	Flanking Active TSS	H1 Cell Line	embryonic stem cell
24	chr19:39880600-39881000	Flanking Active TSS	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
25	chr19:39880600-39881000	Flanking Active TSS	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
26	chr19:39880600-39881000	Transcr. at gene 5' and 3'	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
27	chr19:39880600-39881000	Transcr. at gene 5' and 3'	iPS DF 19.11 Cell Line	embryonic stem cell
28	chr19:39880600-39881000	Flanking Active TSS	ES-UCSF4 Cell Line	embryonic stem cell
29	chr19:39880600-39881000	Flanking Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
30	chr19:39880600-39881000	Flanking Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
31	chr19:39880600-39881000	Flanking Active TSS	Breast Myoepithelial Primary Cells	Breast
32	chr19:39880600-39881000	Enhancers	Primary T cells from cord blood	blood
33	chr19:39880600-39881000	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
34	chr19:39880600-39881000	Flanking Active TSS	Foreskin Melanocyte Primary Cells skin03	Skin
35	chr19:39880600-39881000	Enhancers	Left Ventricle	heart
36	chr19:39880600-39881000	Flanking Active TSS	Pancreas	Pancrea
37	chr19:39880600-39881000	Enhancers	Sigmoid Colon	Sigmoid Colon
38	chr19:39880600-39881000	Flanking Active TSS	HSMM	muscle
39	chr19:39880600-39881200	Flanking Active TSS	H9 Derived Neuron Cultured Cells	ES cell derived
40	chr19:39880600-39881200	Flanking Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
41	chr19:39880600-39881200	Flanking Active TSS	Primary T helper 17 cells PMA-I stimulated	--
42	chr19:39880600-39881200	Flanking Active TSS	Primary T killer memory cells from peripheral blood	blood
43	chr19:39880600-39881200	Flanking Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
44	chr19:39880600-39881200	Flanking Active TSS	Muscle Satellite Cultured Cells	--
45	chr19:39880600-39881200	Flanking Active TSS	Cortex derived primary cultured neurospheres	brain
46	chr19:39880600-39881200	Flanking Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
47	chr19:39880600-39881200	Flanking Active TSS	Foreskin Keratinocyte Primary Cells skin02	Skin
48	chr19:39880600-39881200	Flanking Active TSS	Brain Angular Gyrus	brain
49	chr19:39880600-39881200	Flanking Active TSS	Brain Anterior Caudate	brain
50	chr19:39880600-39881200	Flanking Active TSS	Brain Cingulate Gyrus	brain

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