Variant report

Variant	rs55735528
Chromosome Location	chr19:51297826-51297827
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:368)
CpG islands
(count:0)
Chromatin interactive
region (count:34)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:368 , 50 per page) page: 1 2 3 4 5 6 7 8

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	POLR2A	chr19:51294162-51303858	H1-hESC	embryonic stem cell:	n/a	n/a
2	RAD21	chr19:51297615-51297848	GM12878	blood:	n/a	n/a
3	BCL3	chr19:51296723-51300831	A549	lung:	n/a	chr19:51296878-51296891 chr19:51299623-51299631
4	POLR2A	chr19:51296363-51305119	HepG2	liver:	n/a	n/a
5	ATF2	chr19:51297404-51300281	GM12878	blood:	n/a	n/a
6	ATF2	chr19:51297146-51300313	GM12878	blood:	n/a	n/a
7	CTCF	chr19:51297632-51297904	GM19239	blood:	n/a	n/a
8	CHD2	chr19:51296875-51300537	K562	blood:	n/a	n/a
9	POLR2A	chr19:51296864-51303007	K562	blood:	n/a	n/a
10	MAFK	chr19:51297150-51298738	Hela-S3	cervix:	n/a	n/a
11	NFIC	chr19:51297069-51299908	GM12878	blood:	n/a	n/a
12	CEBPD	chr19:51297516-51298541	HepG2	liver:	n/a	n/a
13	POLR2A	chr19:51292846-51302413	Hela-S3	cervix:	n/a	n/a
14	NFIC	chr19:51297575-51298938	ECC-1	luminal epithelium:	n/a	n/a
15	CTCF	chr19:51297700-51297850	GM12873	blood:	n/a	n/a
16	POLR2A	chr19:51296691-51300705	GM19099	blood:	n/a	n/a
17	POLR2A	chr19:51294069-51301549	U87	brain:	n/a	n/a
18	PAX5	chr19:51297465-51298090	GM12878	blood:	n/a	n/a
19	YY1	chr19:51297551-51299215	GM12878	blood:	n/a	n/a
20	MXI1	chr19:51297742-51298175	H1-hESC	embryonic stem cell:	n/a	chr19:51297918-51297927
21	RELA	chr19:51297542-51298741	GM19193	blood:	n/a	n/a
22	POLR2A	chr19:51294148-51303725	Hela-S3	cervix:	n/a	n/a
23	POLR2A	chr19:51296692-51299975	U87	brain:	n/a	n/a
24	YY1	chr19:51297572-51298002	GM12891	blood:	n/a	n/a
25	RAD21	chr19:51297633-51297880	A549	lung:	n/a	n/a
26	CTCF	chr19:51297646-51297838	Pancreas_OC	pancreas:	n/a	n/a
27	CTCF	chr19:51297629-51297829	GM10266	blood:	n/a	n/a
28	CTCF	chr19:51297546-51297949	GM12878	blood:	n/a	n/a
29	CCNT2	chr19:51297579-51300481	K562	blood:	n/a	n/a
30	ELF1	chr19:51297557-51297954	K562	blood:	n/a	n/a
31	POLR2A	chr19:51297601-51298842	MCF-7	breast:	n/a	n/a
32	POLR2A	chr19:51295539-51303742	GM12891	blood:	n/a	n/a
33	PBX3	chr19:51297668-51297983	GM12878	blood:	n/a	n/a
34	SMC3	chr19:51297561-51297960	GM12878	blood:	n/a	n/a
35	ZNF263	chr19:51296948-51300470	HEK293-T-REx	kidney:	n/a	chr19:51298009-51298018
36	POLR2A	chr19:51294090-51301585	U87	brain:	n/a	n/a
37	POLR2A	chr19:51296564-51303843	HL-60	blood:	n/a	n/a
38	SRF	chr19:51297641-51298606	ECC-1	luminal epithelium:	n/a	n/a
39	POLR2A	chr19:51293982-51303950	GM12878	blood:	n/a	n/a
40	YY1	chr19:51297585-51298319	GM12891	blood:	n/a	n/a
41	CTCF	chr19:51297613-51297907	GM12891	blood:	n/a	n/a
42	TBL1XR1	chr19:51297530-51298208	K562	blood:	n/a	n/a
43	POLR2A	chr19:51296918-51304711	K562	blood:	n/a	n/a
44	E2F6	chr19:51297617-51298121	K562	blood:	n/a	n/a
45	SP1	chr19:51297419-51299459	A549	lung:	n/a	n/a
46	POLR2A	chr19:51296661-51302056	GM12878	blood:	n/a	n/a
47	ZEB1	chr19:51297668-51297978	GM12878	blood:	n/a	n/a
48	NFIC	chr19:51297823-51298738	HepG2	liver:	n/a	n/a
49	POLR2A	chr19:51292818-51303789	GM12891	blood:	n/a	n/a
50	EBF1	chr19:51297641-51298027	GM12878	blood:	n/a	n/a

No data

(count:34 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr19:51172710..51173605-chr19:51297366..51298079,2	MCF-7	breast:
2	chr19:51295777..51298371-chr5:133339070..133341774,2	MCF-7	breast:
3	chr19:51297069..51301557-chr19:51353006..51355248,4	K562	blood:
4	chr19:51293560..51298277-chr19:51413419..51418761,7	K562	blood:
5	chr19:51297217..51300572-chr19:51389305..51392408,3	MCF-7	breast:
6	chr19:51296429..51299323-chr19:51371370..51374659,5	K562	blood:
7	chr19:51297754..51299382-chr19:51396945..51399003,2	K562	blood:
8	chr19:51296075..51301998-chr19:51356744..51362542,6	K562	blood:
9	chr19:51105210..51106764-chr19:51296992..51298664,2	K562	blood:
10	chr19:51297209..51301271-chr19:51337976..51342137,10	K562	blood:
11	chr15:26110612..26111613-chr19:51297440..51297999,3	MCF-7	breast:
12	chr19:51207455..51209701-chr19:51296263..51298998,3	K562	blood:
13	chr19:51036495..51041066-chr19:51297563..51301035,4	K562	blood:
14	chr19:51289647..51292228-chr19:51297726..51299404,2	MCF-7	breast:
15	chr19:51210355..51211982-chr19:51296996..51299615,2	K562	blood:
16	chr19:51160675..51165510-chr19:51297124..51300859,8	K562	blood:
17	chr19:51297152..51303261-chr19:51371696..51377038,8	K562	blood:
18	chr19:51226381..51234126-chr19:51290973..51302468,19	K562	blood:
19	chr19:51297446..51299225-chr19:51366827..51368327,2	K562	blood:
20	chr19:51297173..51300001-chr19:51396139..51397785,2	MCF-7	breast:
21	chr19:51297115..51298679-chr19:51410981..51413037,2	K562	blood:
22	chr19:51297529..51298368-chr19:51409144..51409704,2	K562	blood:
23	chr19:51295821..51300740-chr19:51378160..51386074,8	K562	blood:
24	chr19:51279277..51281371-chr19:51297725..51300722,2	K562	blood:
25	chr19:51297794..51299902-chr19:51431890..51433458,2	K562	blood:
26	chr19:51297375..51300335-chr19:51393395..51395432,2	MCF-7	breast:
27	chr19:51295821..51300740-chr19:51378160..51386074,7	K562	blood:
28	chr19:51191963..51194196-chr19:51295538..51298347,2	K562	blood:
29	chr19:51206207..51210755-chr19:51296263..51301273,7	K562	blood:
30	chr19:51226381..51234126-chr19:51290973..51298243,11	K562	blood:
31	chr19:51297092..51299196-chr19:51400128..51402648,2	K562	blood:
32	chr19:51297246..51301277-chr19:51424078..51428279,6	K562	blood:
33	chr19:51225708..51229784-chr19:51294422..51298363,4	MCF-7	breast:
34	chr19:51297554..51299254-chr19:51396945..51399764,2	K562	blood:

No data

Variant related genes	Relation type
ENSG00000268375	TF binding region
ENSG00000167749	Chromatin interaction
ENSG00000167751	Chromatin interaction
ENSG00000235034	Chromatin interaction
ENSG00000142515	Chromatin interaction
ENSG00000213585	Chromatin interaction
ENSG00000174562	Chromatin interaction
ENSG00000197588	Chromatin interaction
ENSG00000271737	Chromatin interaction
ENSG00000161681	Chromatin interaction
ENSG00000105472	Chromatin interaction

Extended variants
information (count: 17 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:12)

rs_ID	r²[population]
rs10401588	0.86[AMR][1000 genomes]
rs1043315	0.86[AMR][1000 genomes]
rs11668998	0.86[AMR][1000 genomes]
rs12610777	0.86[AMR][1000 genomes]
rs3745526	0.86[AMR][1000 genomes]
rs3745528	0.86[AMR][1000 genomes]
rs3865442	0.86[AMR][1000 genomes]
rs4801853	0.86[AMR][1000 genomes]
rs4802741	0.86[AMR][1000 genomes]
rs55929248	0.84[AMR][1000 genomes]
rs7258708	0.86[AMR][1000 genomes]
rs9991	0.86[AMR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:5 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1060760	chr19:50883425-51463712	ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer Flanking Active TSS Bivalent/Poised TSS Active TSS Enhancers Weak transcription Strong transcription Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	99 gene(s)	inside rSNPs	diseases
2	nsv1058177	chr19:50984774-51463712	Strong transcription Bivalent/Poised TSS Flanking Active TSS Active TSS Weak transcription Bivalent Enhancer Enhancers Flanking Bivalent TSS/Enh Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	84 gene(s)	inside rSNPs	diseases
3	nsv912288	chr19:51283791-51334355	Enhancers Bivalent Enhancer Bivalent/Poised TSS Strong transcription Weak transcription Genic enhancers Flanking Bivalent TSS/Enh Active TSS Flanking Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	60 gene(s)	inside rSNPs	diseases
4	nsv912289	chr19:51283791-51335943	Flanking Bivalent TSS/Enh Enhancers Weak transcription Bivalent Enhancer Active TSS Flanking Active TSS Strong transcription Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	60 gene(s)	inside rSNPs	diseases
5	nsv912290	chr19:51283791-51344483	Flanking Active TSS Active TSS Enhancers Weak transcription Strong transcription Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS Genic enhancers Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	60 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs55735528	C19orf48	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:94 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr19:51287000-51298400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
2	chr19:51287000-51298400	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
3	chr19:51287200-51301200	Weak transcription	Primary B cells from cord blood	blood
4	chr19:51287400-51300000	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
5	chr19:51289800-51298600	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
6	chr19:51290000-51298800	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
7	chr19:51291800-51303400	Weak transcription	Fetal Kidney	kidney
8	chr19:51293400-51300000	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
9	chr19:51295600-51301000	Weak transcription	HepG2	liver
10	chr19:51295800-51299200	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
11	chr19:51296000-51299000	Weak transcription	Dnd41	blood
12	chr19:51296000-51300200	Weak transcription	Placenta Amnion	Placenta Amnion
13	chr19:51296000-51300400	Weak transcription	Fetal Lung	lung
14	chr19:51296200-51298600	Weak transcription	iPS-20b Cell Line	embryonic stem cell
15	chr19:51296400-51298200	Weak transcription	Brain Germinal Matrix	brain
16	chr19:51296400-51298400	Weak transcription	Brain Cingulate Gyrus	brain
17	chr19:51296400-51300600	Weak transcription	Brain Angular Gyrus	brain
18	chr19:51296600-51298600	Weak transcription	HUES64 Cell Line	embryonic stem cell
19	chr19:51296600-51298600	Weak transcription	iPS-18 Cell Line	embryonic stem cell
20	chr19:51296600-51304200	Weak transcription	HSMM	muscle
21	chr19:51296800-51298000	Enhancers	Fetal Intestine Small	intestine
22	chr19:51296800-51298200	Enhancers	H1 Cell Line	embryonic stem cell
23	chr19:51296800-51299800	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
24	chr19:51297000-51298400	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
25	chr19:51297000-51298600	Enhancers	Spleen	Spleen
26	chr19:51297000-51300000	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
27	chr19:51297000-51301000	Weak transcription	HSMMtube	muscle
28	chr19:51297000-51306200	Weak transcription	Primary T killer memory cells from peripheral blood	blood
29	chr19:51297200-51298000	Enhancers	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
30	chr19:51297200-51298000	Enhancers	iPS DF 19.11 Cell Line	embryonic stem cell
31	chr19:51297200-51298200	Enhancers	ES-I3 Cell Line	embryonic stem cell
32	chr19:51297200-51298400	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
33	chr19:51297200-51298400	Weak transcription	Skeletal Muscle Male	skeletal muscle
34	chr19:51297200-51298600	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
35	chr19:51297200-51299000	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
36	chr19:51297200-51299000	Weak transcription	Liver	Liver
37	chr19:51297200-51299600	Weak transcription	Lung	lung
38	chr19:51297200-51299800	Weak transcription	Brain Inferior Temporal Lobe	brain
39	chr19:51297200-51300000	Strong transcription	Right Atrium	heart
40	chr19:51297200-51300400	Weak transcription	Brain Anterior Caudate	brain
41	chr19:51297400-51298000	Enhancers	Primary mononuclear cells fromperipheralblood	Blood
42	chr19:51297400-51298200	Enhancers	Fetal Intestine Large	intestine
43	chr19:51297400-51298200	Bivalent Enhancer	Fetal Stomach	stomach
44	chr19:51297400-51298600	Enhancers	Breast Myoepithelial Primary Cells	Breast
45	chr19:51297400-51298600	Weak transcription	Duodenum Mucosa	Duodenum
46	chr19:51297400-51298800	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
47	chr19:51297400-51298800	Weak transcription	Skeletal Muscle Female	skeletal muscle
48	chr19:51297400-51299600	Weak transcription	Primary T helper cells fromperipheralblood	blood
49	chr19:51297400-51299600	Weak transcription	NHEK	skin
50	chr19:51297400-51300200	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived

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