Variant report

Variant	rs3865442
Chromosome Location	chr19:51300819-51300820
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:79)
CpG islands
(count:0)
Chromatin interactive
region (count:15)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:79 , 50 per page) page: 1 2

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	BCL3	chr19:51296723-51300831	A549	lung:	n/a	chr19:51296878-51296891 chr19:51299623-51299631
3	POLR2A	chr19:51296363-51305119	HepG2	liver:	n/a	n/a
4	POLR2A	chr19:51296864-51303007	K562	blood:	n/a	n/a
5	CEBPB	chr19:51300694-51301077	K562	blood:	n/a	chr19:51300875-51300886
6	POLR2A	chr19:51292846-51302413	Hela-S3	cervix:	n/a	n/a
7	POLR2A	chr19:51294069-51301549	U87	brain:	n/a	n/a
8	POLR2A	chr19:51294148-51303725	Hela-S3	cervix:	n/a	n/a
9	CEBPB	chr19:51300759-51301014	A549	lung:	n/a	chr19:51300875-51300886
10	BCL3	chr19:51297840-51301578	K562	blood:	n/a	chr19:51299623-51299631
11	POLR2A	chr19:51295539-51303742	GM12891	blood:	n/a	n/a
12	POLR2A	chr19:51294090-51301585	U87	brain:	n/a	n/a
13	POLR2A	chr19:51296564-51303843	HL-60	blood:	n/a	n/a
14	POLR2A	chr19:51293982-51303950	GM12878	blood:	n/a	n/a
15	POLR2A	chr19:51296918-51304711	K562	blood:	n/a	n/a
16	POLR2A	chr19:51296661-51302056	GM12878	blood:	n/a	n/a
17	POLR2A	chr19:51292818-51303789	GM12891	blood:	n/a	n/a
18	TCF12	chr19:51296667-51300851	A549	lung:	n/a	n/a
19	POLR2A	chr19:51297423-51303234	GM12878	blood:	n/a	n/a
20	POU2F2	chr19:51296090-51300827	GM12891	blood:	n/a	chr19:51297417-51297438 chr19:51299707-51299719
21	POLR2A	chr19:51296672-51301538	HUVEC	blood vessel:	n/a	n/a
22	POLR2A	chr19:51292766-51304914	Hela-S3	cervix:	n/a	n/a
23	POLR2A	chr19:51296785-51303813	GM18951	blood:	n/a	n/a
24	POLR2A	chr19:51295423-51303985	K562	blood:	n/a	n/a
25	POLR2A	chr19:51298068-51302131	K562	blood:	n/a	n/a
26	POLR2A	chr19:51293608-51303838	GM12892	blood:	n/a	n/a
27	POLR2A	chr19:51292681-51303883	GM12891	blood:	n/a	n/a
28	POLR2A	chr19:51295184-51303796	GM12878	blood:	n/a	n/a
29	POLR2A	chr19:51297126-51301824	SK-N-MC	brain:	n/a	n/a
30	POLR2A	chr19:51296763-51303823	GM18505	blood:	n/a	n/a
31	CEBPB	chr19:51300724-51301096	Hela-S3	cervix:	n/a	chr19:51300875-51300886
32	POLR2A	chr19:51296543-51303868	K562	blood:	n/a	n/a
33	POLR2A	chr19:51296750-51303766	GM19193	blood:	n/a	n/a
34	POLR2A	chr19:51297547-51303197	A549	lung:	n/a	n/a
35	POLR2A	chr19:51296028-51303799	GM12891	blood:	n/a	n/a
36	POLR2A	chr19:51296176-51303699	GM18526	blood:	n/a	n/a
37	POLR2A	chr19:51290649-51303858	Hela-S3	cervix:	n/a	n/a
38	PML	chr19:51300749-51301796	K562	blood:	n/a	n/a
39	POLR2A	chr19:51297459-51303335	H1-hESC	embryonic stem cell:	n/a	n/a
40	POLR2A	chr19:51296650-51302255	PANC-1	pancreas:	n/a	n/a
41	CEBPB	chr19:51300715-51301056	K562	blood:	n/a	chr19:51300875-51300886
42	USF2	chr19:51296760-51302004	Hela-S3	cervix:	n/a	chr19:51299616-51299632
43	POLR2A	chr19:51292824-51303824	A549	lung:	n/a	n/a
44	POLR2A	chr19:51297537-51302234	GM10847	blood:	n/a	n/a
45	POLR2A	chr19:51296562-51302425	K562	blood:	n/a	n/a
46	CEBPB	chr19:51300739-51300966	HepG2	liver:	n/a	chr19:51300875-51300886
47	POLR2A	chr19:51296800-51301886	MCF-7	breast:	n/a	n/a
48	POLR2A	chr19:51292766-51303262	HepG2	liver:	n/a	n/a
49	POLR2A	chr19:51294029-51303861	GM12892	blood:	n/a	n/a
50	POLR2A	chr19:51296633-51303764	HL-60	blood:	n/a	n/a

No data

(count:15 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr19:51297069..51301557-chr19:51353006..51355248,4	K562	blood:
2	chr19:51296075..51301998-chr19:51356744..51362542,6	K562	blood:
3	chr19:51297209..51301271-chr19:51337976..51342137,10	K562	blood:
4	chr19:51298106..51301277-chr19:51425216..51427297,3	K562	blood:
5	chr19:51036495..51041066-chr19:51297563..51301035,4	K562	blood:
6	chr19:51159348..51161376-chr19:51298352..51301122,3	K562	blood:
7	chr19:51160675..51165510-chr19:51297124..51300859,8	K562	blood:
8	chr19:51297152..51303261-chr19:51371696..51377038,8	K562	blood:
9	chr19:51226381..51234126-chr19:51290973..51302468,19	K562	blood:
10	chr19:50834364..50836228-chr19:51297931..51300852,2	K562	blood:
11	chr19:51200009..51202961-chr19:51298275..51301166,2	MCF-7	breast:
12	chr19:51192657..51194532-chr19:51298388..51302132,3	K562	blood:
13	chr19:51300732..51302357-chr19:51358771..51360545,2	K562	blood:
14	chr19:51206207..51210755-chr19:51296263..51301273,7	K562	blood:
15	chr19:51297246..51301277-chr19:51424078..51428279,6	K562	blood:

No data

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

Extended variants
information (count: 19 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:14)

rs_ID	r²[population]
rs10401588	0.81[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs1043315	0.88[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11668685	0.81[AFR][1000 genomes];0.98[ASN][1000 genomes]
rs11668998	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12610777	0.88[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3745526	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3745528	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4801853	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4802741	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4802742	0.84[AFR][1000 genomes];0.98[ASN][1000 genomes]
rs55735528	0.86[AMR][1000 genomes]
rs55929248	0.97[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7258708	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9991	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][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
rs3865442	C19orf48	Cis_1M	lymphoblastoid	RTeQTL

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr19:51287200-51301200	Weak transcription	Primary B cells from cord blood	blood
2	chr19:51291800-51303400	Weak transcription	Fetal Kidney	kidney
3	chr19:51295600-51301000	Weak transcription	HepG2	liver
4	chr19:51296600-51304200	Weak transcription	HSMM	muscle
5	chr19:51297000-51301000	Weak transcription	HSMMtube	muscle
6	chr19:51297000-51306200	Weak transcription	Primary T killer memory cells from peripheral blood	blood
7	chr19:51297600-51301200	Weak transcription	NH-A	brain
8	chr19:51297600-51301200	Weak transcription	Osteobl	bone
9	chr19:51297600-51304200	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
10	chr19:51297800-51301000	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
11	chr19:51297800-51305600	Weak transcription	Fetal Brain Male	brain
12	chr19:51297800-51306200	Weak transcription	Primary T helper naive cells from peripheral blood	blood
13	chr19:51298000-51303000	Weak transcription	Primary hematopoietic stem cells	blood
14	chr19:51298000-51305400	Weak transcription	Fetal Heart	heart
15	chr19:51298200-51305400	Strong transcription	Fetal Intestine Small	intestine
16	chr19:51298200-51305400	Strong transcription	Fetal Stomach	stomach
17	chr19:51298200-51305800	Strong transcription	Brain Germinal Matrix	brain
18	chr19:51298200-51306000	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
19	chr19:51298200-51306800	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
20	chr19:51298400-51301000	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
21	chr19:51298400-51301200	Weak transcription	Stomach Mucosa	stomach
22	chr19:51298400-51304400	Strong transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
23	chr19:51298400-51304600	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
24	chr19:51298400-51305400	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
25	chr19:51298400-51305400	Strong transcription	Fetal Muscle Leg	muscle
26	chr19:51298400-51305800	Strong transcription	Skeletal Muscle Male	skeletal muscle
27	chr19:51298600-51301200	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
28	chr19:51298600-51301200	Strong transcription	Fetal Muscle Trunk	muscle
29	chr19:51298600-51303400	Strong transcription	Primary hematopoietic stem cells short term culture	blood
30	chr19:51298600-51304600	Strong transcription	Duodenum Mucosa	Duodenum
31	chr19:51298600-51305000	Strong transcription	Thymus	Thymus
32	chr19:51298600-51305200	Strong transcription	Rectal Mucosa Donor 29	rectum
33	chr19:51298600-51305400	Strong transcription	H9 Cell Line	embryonic stem cell
34	chr19:51298600-51305400	Strong transcription	HUES64 Cell Line	embryonic stem cell
35	chr19:51298600-51305400	Strong transcription	iPS-18 Cell Line	embryonic stem cell
36	chr19:51298600-51305400	Strong transcription	iPS-20b Cell Line	embryonic stem cell
37	chr19:51298600-51305600	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
38	chr19:51298600-51305600	Strong transcription	Fetal Brain Female	brain
39	chr19:51298800-51301000	Weak transcription	ES-I3 Cell Line	embryonic stem cell
40	chr19:51298800-51301000	Strong transcription	GM12878-XiMat	blood
41	chr19:51298800-51301400	Strong transcription	Spleen	Spleen
42	chr19:51298800-51301400	Strong transcription	A549	lung
43	chr19:51298800-51301800	Strong transcription	Breast Myoepithelial Primary Cells	Breast
44	chr19:51298800-51302200	Strong transcription	Skeletal Muscle Female	skeletal muscle
45	chr19:51298800-51302400	Strong transcription	Primary T cells from cord blood	blood
46	chr19:51298800-51303400	Strong transcription	Primary T helper naive cells fromperipheralblood	blood
47	chr19:51298800-51304600	Strong transcription	Ganglion Eminence derived primary cultured neurospheres	brain
48	chr19:51298800-51305200	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
49	chr19:51298800-51305400	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
50	chr19:51298800-51305400	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--

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