Variant report

Variant	rs17726258
Chromosome Location	chr19:41287605-41287606
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:3)
CpG islands
(count:0)
Chromatin interactive
region (count:8)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:3 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	POLR2A	chr19:41285848-41288309	K562	blood:	n/a	n/a
2	SPI1	chr19:41287237-41287636	HL-60	blood:	n/a	n/a
3	CEBPB	chr19:41287406-41287627	HepG2	liver:	n/a	chr19:41287490-41287501 chr19:41287519-41287532

No data

(count:8 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr19:41280553..41283413-chr19:41284684..41288209,4	MCF-7	breast:
2	chr19:41280731..41296556-chr19:41299561..41307605,30	MCF-7	breast:
3	chr19:41267351..41269618-chr19:41286663..41289461,3	K562	blood:
4	chr19:41255216..41257049-chr19:41286171..41288357,2	MCF-7	breast:
5	chr19:41286626..41288208-chr19:41304060..41306609,2	K562	blood:
6	chr19:41286626..41290245-chr19:41304017..41305752,4	K562	blood:
7	chr19:41267351..41269459-chr19:41286783..41289461,2	K562	blood:
8	chr19:41283851..41288555-chr19:41290136..41292963,4	MCF-7	breast:

No data

Variant related genes	Relation type
RAB4B	TF binding region
ENSG00000261857	Chromatin interaction
ENSG00000269858	Chromatin interaction
ENSG00000188493	Chromatin interaction
ENSG00000167578	Chromatin interaction
ENSG00000077312	Chromatin interaction
ENSG00000268797	Chromatin interaction

Extended variants
information (count: 49 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:48)

rs_ID	r²[population]
rs10420651	1.00[CEU][hapmap];0.84[CHB][hapmap]
rs10420685	1.00[CEU][hapmap];0.84[CHB][hapmap];0.85[GIH][hapmap]
rs13108	0.92[CHB][hapmap];0.83[CHD][hapmap];0.87[JPT][hapmap];0.83[TSI][hapmap];0.87[ASN][1000 genomes]
rs1455434	1.00[CEU][hapmap];0.92[CHB][hapmap];1.00[GIH][hapmap];0.87[MKK][hapmap];0.83[TSI][hapmap];0.82[YRI][hapmap];0.85[EUR][1000 genomes]
rs1869710	1.00[CEU][hapmap];0.92[CHB][hapmap];0.85[GIH][hapmap];0.83[TSI][hapmap];0.85[EUR][1000 genomes]
rs2230694	0.85[ASN][1000 genomes]
rs2233153	0.88[AMR][1000 genomes];0.94[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2233154	0.92[CHB][hapmap];0.83[CHD][hapmap];0.87[JPT][hapmap];0.83[TSI][hapmap];0.88[ASN][1000 genomes]
rs2233156	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.88[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2233159	0.92[CHB][hapmap];0.87[JPT][hapmap];0.88[ASN][1000 genomes]
rs2249854	0.92[CHB][hapmap];0.83[CHD][hapmap];0.87[JPT][hapmap];0.83[TSI][hapmap];0.85[ASN][1000 genomes]
rs2254326	1.00[CEU][hapmap];0.84[CHB][hapmap];0.85[GIH][hapmap];1.00[TSI][hapmap]
rs2279699	1.00[CEU][hapmap];0.88[ASN][1000 genomes]
rs2303723	1.00[CEU][hapmap];0.84[CHB][hapmap];0.85[GIH][hapmap]
rs2545760	1.00[AMR][1000 genomes];0.80[ASN][1000 genomes]
rs2545761	0.83[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs2545763	0.85[GIH][hapmap];0.83[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs2545766	1.00[AMR][1000 genomes]
rs2545771	1.00[GIH][hapmap];1.00[MEX][hapmap]
rs2545777	0.91[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2545778	0.91[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2561531	0.92[CHB][hapmap];0.85[GIH][hapmap]
rs2604866	1.00[GIH][hapmap];1.00[MEX][hapmap];1.00[AMR][1000 genomes]
rs2604868	1.00[AMR][1000 genomes]
rs2604876	0.91[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2604877	0.86[ASN][1000 genomes]
rs2604909	0.83[ASN][1000 genomes]
rs2604910	0.92[JPT][hapmap];0.83[ASN][1000 genomes]
rs2604911	0.83[ASN][1000 genomes]
rs2607411	0.91[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs2607412	0.85[ASN][1000 genomes]
rs2607413	0.91[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs2607416	1.00[CHB][hapmap];0.88[CHD][hapmap];1.00[JPT][hapmap];0.94[ASN][1000 genomes]
rs2607418	1.00[CEU][hapmap];0.84[CHB][hapmap];1.00[GIH][hapmap];0.83[TSI][hapmap]
rs2607419	0.87[ASN][1000 genomes]
rs2607421	0.87[ASN][1000 genomes]
rs2607422	0.87[ASN][1000 genomes]
rs2607423	0.87[ASN][1000 genomes]
rs2607425	0.92[CHB][hapmap];0.87[JPT][hapmap];0.83[TSI][hapmap];0.87[ASN][1000 genomes]
rs2607426	0.92[CHB][hapmap];0.83[CHD][hapmap];0.87[JPT][hapmap];0.83[TSI][hapmap];0.87[ASN][1000 genomes]
rs2644888	1.00[AMR][1000 genomes]
rs2644915	0.93[AMR][1000 genomes]
rs2644917	0.91[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs34842744	0.83[ASN][1000 genomes]
rs56891752	0.83[AMR][1000 genomes];0.91[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs60533951	1.00[AMR][1000 genomes];0.88[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs8107978	0.92[CHB][hapmap];0.87[JPT][hapmap];0.88[ASN][1000 genomes]
rs8109099	0.91[EUR][1000 genomes];0.88[ASN][1000 genomes]

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

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv833832	chr19:41260363-41334597	Strong transcription Genic enhancers Weak transcription Enhancers Transcr. at gene 5' and 3' Active TSS Flanking Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	29 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs17726258	C19orf54	cis	lymphoblastoid	seeQTL

Chromatin state (count:109 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr19:41285000-41287800	Weak transcription	Aorta	Aorta
2	chr19:41285000-41292400	Weak transcription	Ovary	ovary
3	chr19:41285000-41303800	Weak transcription	Small Intestine	intestine
4	chr19:41285000-41304000	Weak transcription	Psoas Muscle	Psoas
5	chr19:41285200-41288000	Weak transcription	Brain Hippocampus Middle	brain
6	chr19:41285200-41289800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
7	chr19:41285200-41289800	Weak transcription	Adipose Nuclei	Adipose
8	chr19:41285200-41289800	Weak transcription	Brain Angular Gyrus	brain
9	chr19:41285200-41289800	Weak transcription	Brain Substantia Nigra	brain
10	chr19:41285200-41289800	Weak transcription	Fetal Muscle Leg	muscle
11	chr19:41285200-41290200	Weak transcription	Fetal Muscle Trunk	muscle
12	chr19:41285200-41291600	Weak transcription	Esophagus	oesophagus
13	chr19:41285200-41292200	Weak transcription	Rectal Mucosa Donor 31	rectum
14	chr19:41285200-41292400	Weak transcription	Brain Germinal Matrix	brain
15	chr19:41285200-41292400	Weak transcription	Left Ventricle	heart
16	chr19:41285200-41295600	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
17	chr19:41285200-41295600	Weak transcription	Duodenum Smooth Muscle	Duodenum
18	chr19:41285200-41298000	Weak transcription	Fetal Lung	lung
19	chr19:41285200-41303200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
20	chr19:41285200-41303400	Weak transcription	Pancreas	Pancrea
21	chr19:41285200-41303600	Weak transcription	Placenta Amnion	Placenta Amnion
22	chr19:41285200-41303800	Weak transcription	Muscle Satellite Cultured Cells	--
23	chr19:41285200-41304000	Weak transcription	HSMM	muscle
24	chr19:41285400-41288000	Weak transcription	Primary monocytes fromperipheralblood	blood
25	chr19:41285400-41288000	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
26	chr19:41285400-41288000	Weak transcription	Skeletal Muscle Male	skeletal muscle
27	chr19:41285400-41289400	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
28	chr19:41285400-41289600	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
29	chr19:41285400-41289800	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
30	chr19:41285400-41289800	Weak transcription	Fetal Intestine Large	intestine
31	chr19:41285400-41290200	Weak transcription	Duodenum Mucosa	Duodenum
32	chr19:41285400-41291000	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
33	chr19:41285400-41291400	Weak transcription	A549	lung
34	chr19:41285400-41291600	Weak transcription	Fetal Brain Female	brain
35	chr19:41285400-41292200	Weak transcription	Cortex derived primary cultured neurospheres	brain
36	chr19:41285400-41292200	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
37	chr19:41285400-41292200	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
38	chr19:41285400-41292400	Weak transcription	Rectal Smooth Muscle	rectum
39	chr19:41285400-41292600	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
40	chr19:41285400-41292600	Weak transcription	Colonic Mucosa	Colon
41	chr19:41285400-41293400	Weak transcription	Liver	Liver
42	chr19:41285400-41295600	Weak transcription	Right Ventricle	heart
43	chr19:41285400-41296800	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
44	chr19:41285400-41297000	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
45	chr19:41285400-41297400	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
46	chr19:41285400-41297400	Weak transcription	Skeletal Muscle Female	skeletal muscle
47	chr19:41285400-41297600	Weak transcription	Stomach Mucosa	stomach
48	chr19:41285400-41297800	Weak transcription	NHDF-Ad	bronchial
49	chr19:41285400-41298000	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
50	chr19:41285400-41302400	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin

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