Variant report

Variant	rs2233154
Chromosome Location	chr19:41281346-41281347
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:1)
CpG islands
(count:0)
Chromatin interactive
region (count:5)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

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

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	RUNX3	chr19:41280813-41281390	GM12878	blood:	n/a	n/a

No data

(count:5 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr19:41254259..41260312-chr19:41280225..41287427,15	K562	blood:
2	chr19:41280553..41283413-chr19:41284684..41288209,4	MCF-7	breast:
3	chr19:41280805..41286068-chr19:41308324..41316733,13	K562	blood:
4	chr19:41280731..41296556-chr19:41299561..41307605,30	MCF-7	breast:
5	chr19:41274845..41278396-chr19:41279079..41284996,6	K562	blood:

No data

Variant related genes	Relation type
MIA	TF binding region
RAB4B-EGLN2	TF binding region
RAB4B	TF binding region
ENSG00000171570	Chromatin interaction
ENSG00000188493	Chromatin interaction
ENSG00000167578	Chromatin interaction
ENSG00000077312	Chromatin interaction
ENSG00000268797	Chromatin interaction
ENSG00000269858	Chromatin interaction
ENSG00000261857	Chromatin interaction

Extended variants
information (count: 46 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:43)

rs_ID	r²[population]
rs10420651	0.92[CHB][hapmap]
rs10420685	0.92[CHB][hapmap];0.83[CHD][hapmap]
rs13108	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[TSI][hapmap];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1455434	0.85[CHB][hapmap]
rs17726258	0.92[CHB][hapmap];0.83[CHD][hapmap];0.87[JPT][hapmap];0.83[TSI][hapmap];0.88[ASN][1000 genomes]
rs1869710	0.85[CHB][hapmap]
rs2230694	1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2233153	0.89[ASN][1000 genomes]
rs2233156	0.92[CHB][hapmap];0.83[CHD][hapmap];0.87[JPT][hapmap];0.85[TSI][hapmap];0.89[ASN][1000 genomes]
rs2233159	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2249854	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[TSI][hapmap];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2254326	0.92[CHB][hapmap];0.80[CHD][hapmap];0.85[TSI][hapmap]
rs2279699	0.97[AFR][1000 genomes];0.96[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2303723	0.92[CHB][hapmap];0.83[CHD][hapmap]
rs2545760	0.92[ASN][1000 genomes]
rs2545763	0.87[JPT][hapmap]
rs2545772	0.81[JPT][hapmap]
rs2545777	1.00[ASN][1000 genomes]
rs2545778	1.00[ASN][1000 genomes]
rs2561531	0.85[CHB][hapmap]
rs2604866	0.87[JPT][hapmap]
rs2604876	0.99[ASN][1000 genomes]
rs2604877	0.86[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2604909	0.95[ASN][1000 genomes]
rs2604910	1.00[JPT][hapmap];0.95[ASN][1000 genomes]
rs2604911	0.95[ASN][1000 genomes]
rs2607411	0.89[AFR][1000 genomes];0.97[ASN][1000 genomes]
rs2607412	1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2607413	0.92[AFR][1000 genomes];0.97[ASN][1000 genomes]
rs2607416	1.00[CEU][hapmap];0.92[CHB][hapmap];1.00[GIH][hapmap];0.87[JPT][hapmap];0.87[TSI][hapmap];0.88[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs2607418	0.92[CHB][hapmap];0.80[CHD][hapmap]
rs2607419	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2607421	0.90[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2607422	0.86[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2607423	0.83[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2607425	1.00[CEU][hapmap];1.00[CHB][hapmap];0.93[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[TSI][hapmap];0.86[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2607426	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[TSI][hapmap];0.86[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2644917	0.88[AFR][1000 genomes];0.98[ASN][1000 genomes]
rs34842744	0.95[ASN][1000 genomes]
rs56891752	1.00[ASN][1000 genomes]
rs60533951	0.96[ASN][1000 genomes]
rs8107978	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs8109099	0.97[AFR][1000 genomes];1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv1802033	chr19:41256131-41284240	Active TSS Flanking Active TSS Weak transcription Strong transcription Enhancers Transcr. at gene 5' and 3' Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region	40 gene(s)	inside rSNPs	diseases
2	esv1801805	chr19:41256581-41284363	Strong transcription Genic enhancers Weak transcription Active TSS Flanking Active TSS Enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region	37 gene(s)	inside rSNPs	diseases
3	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:2)

SNP	Gene	Cis/trans	Tissue	Source
rs2233154	C19orf54	cis	Lymphoblastoid	GTEx
rs2233154	C19orf54	cis	lymphoblastoid	seeQTL

Chromatin state (count:122 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr19:41258000-41283000	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
2	chr19:41260800-41283200	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
3	chr19:41261800-41282800	Weak transcription	Right Atrium	heart
4	chr19:41270400-41282600	Weak transcription	Fetal Brain Male	brain
5	chr19:41271800-41282600	Weak transcription	Fetal Kidney	kidney
6	chr19:41271800-41282600	Weak transcription	HSMM	muscle
7	chr19:41271800-41283000	Weak transcription	Pancreatic Islets	Pancreatic Islet
8	chr19:41272000-41282600	Weak transcription	iPS-15b Cell Line	embryonic stem cell
9	chr19:41272000-41282600	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
10	chr19:41272000-41282600	Weak transcription	Brain Angular Gyrus	brain
11	chr19:41272000-41282600	Weak transcription	HUVEC	blood vessel
12	chr19:41272000-41282800	Weak transcription	H9 Cell Line	embryonic stem cell
13	chr19:41272000-41282800	Weak transcription	Psoas Muscle	Psoas
14	chr19:41272000-41282800	Weak transcription	Small Intestine	intestine
15	chr19:41272000-41282800	Weak transcription	NHDF-Ad	bronchial
16	chr19:41272200-41282600	Weak transcription	Fetal Lung	lung
17	chr19:41272200-41282600	Weak transcription	Stomach Smooth Muscle	stomach
18	chr19:41272200-41282600	Weak transcription	Dnd41	blood
19	chr19:41272200-41282600	Weak transcription	HSMMtube	muscle
20	chr19:41272200-41282600	Weak transcription	NHLF	lung
21	chr19:41272200-41282800	Weak transcription	HUES48 Cell Line	embryonic stem cell
22	chr19:41272200-41282800	Weak transcription	iPS-18 Cell Line	embryonic stem cell
23	chr19:41272200-41282800	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
24	chr19:41272200-41282800	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
25	chr19:41272200-41282800	Weak transcription	Muscle Satellite Cultured Cells	--
26	chr19:41272200-41282800	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
27	chr19:41272200-41282800	Weak transcription	Aorta	Aorta
28	chr19:41272200-41282800	Weak transcription	Brain Inferior Temporal Lobe	brain
29	chr19:41272200-41282800	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
30	chr19:41272200-41282800	Weak transcription	Brain Substantia Nigra	brain
31	chr19:41272200-41282800	Weak transcription	Esophagus	oesophagus
32	chr19:41272200-41282800	Weak transcription	Gastric	stomach
33	chr19:41272200-41282800	Weak transcription	Left Ventricle	heart
34	chr19:41272200-41282800	Weak transcription	Rectal Smooth Muscle	rectum
35	chr19:41272200-41282800	Weak transcription	Skeletal Muscle Female	skeletal muscle
36	chr19:41272200-41282800	Weak transcription	Hela-S3	cervix
37	chr19:41272200-41283000	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
38	chr19:41272400-41282600	Weak transcription	iPS-20b Cell Line	embryonic stem cell
39	chr19:41272400-41282600	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
40	chr19:41272400-41282800	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
41	chr19:41272400-41282800	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
42	chr19:41272400-41282800	Weak transcription	Brain Anterior Caudate	brain
43	chr19:41272400-41282800	Weak transcription	Brain Cingulate Gyrus	brain
44	chr19:41272400-41282800	Weak transcription	Pancreas	Pancrea
45	chr19:41272400-41282800	Weak transcription	Skeletal Muscle Male	skeletal muscle
46	chr19:41272600-41281600	Weak transcription	Cortex derived primary cultured neurospheres	brain
47	chr19:41272600-41282600	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
48	chr19:41272600-41282600	Weak transcription	Adipose Nuclei	Adipose
49	chr19:41272600-41282800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
50	chr19:41272600-41282800	Weak transcription	Brain Hippocampus Middle	brain

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