Variant report

Variant	rs2604895
Chromosome Location	chr19:41292263-41292264
allele	A/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr19:41291602..41294099-chr19:41304198..41305906,2	K562	blood:
2	chr19:41281956..41285668-chr19:41292155..41295404,3	K562	blood:
3	chr19:41283851..41288555-chr19:41290136..41292963,4	MCF-7	breast:
4	chr19:41280731..41296556-chr19:41299561..41307605,30	MCF-7	breast:

Variant related genes	Relation type
ENSG00000268797	Chromatin interaction
ENSG00000269858	Chromatin interaction
ENSG00000261857	Chromatin interaction
ENSG00000171570	Chromatin interaction
ENSG00000167578	Chromatin interaction

Extended variants
information (count: 15 )
Associated
traits (count: 1 )

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

rs_ID	r²[population]
rs2249835	0.90[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2545755	0.90[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2545774	0.84[ASN][1000 genomes]
rs2604869	0.90[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2604893	0.88[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2607414	0.90[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2607415	0.90[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2607424	0.88[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2644898	0.87[AMR][1000 genomes];0.97[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2644916	0.80[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs4803368	0.87[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7249450	0.85[AMR][1000 genomes];0.94[EUR][1000 genomes];0.92[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	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
2	esv2758500	chr19:41291627-41546068	Flanking Active TSS Enhancers Weak transcription Flanking Bivalent TSS/Enh Strong transcription Active TSS Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	36 gene(s)	inside rSNPs	diseases
3	esv2758762	chr19:41291627-41546068	Bivalent/Poised TSS Active TSS Flanking Active TSS Enhancers Weak transcription Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' Strong transcription Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	36 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs2604895	C19orf54	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:111 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr19:41285000-41292400	Weak transcription	Ovary	ovary
2	chr19:41285000-41303800	Weak transcription	Small Intestine	intestine
3	chr19:41285000-41304000	Weak transcription	Psoas Muscle	Psoas
4	chr19:41285200-41292400	Weak transcription	Brain Germinal Matrix	brain
5	chr19:41285200-41292400	Weak transcription	Left Ventricle	heart
6	chr19:41285200-41295600	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
7	chr19:41285200-41295600	Weak transcription	Duodenum Smooth Muscle	Duodenum
8	chr19:41285200-41298000	Weak transcription	Fetal Lung	lung
9	chr19:41285200-41303200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
10	chr19:41285200-41303400	Weak transcription	Pancreas	Pancrea
11	chr19:41285200-41303600	Weak transcription	Placenta Amnion	Placenta Amnion
12	chr19:41285200-41303800	Weak transcription	Muscle Satellite Cultured Cells	--
13	chr19:41285200-41304000	Weak transcription	HSMM	muscle
14	chr19:41285400-41292400	Weak transcription	Rectal Smooth Muscle	rectum
15	chr19:41285400-41292600	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
16	chr19:41285400-41292600	Weak transcription	Colonic Mucosa	Colon
17	chr19:41285400-41293400	Weak transcription	Liver	Liver
18	chr19:41285400-41295600	Weak transcription	Right Ventricle	heart
19	chr19:41285400-41296800	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
20	chr19:41285400-41297000	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
21	chr19:41285400-41297400	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
22	chr19:41285400-41297400	Weak transcription	Skeletal Muscle Female	skeletal muscle
23	chr19:41285400-41297600	Weak transcription	Stomach Mucosa	stomach
24	chr19:41285400-41297800	Weak transcription	NHDF-Ad	bronchial
25	chr19:41285400-41298000	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
26	chr19:41285400-41302400	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
27	chr19:41285400-41303400	Weak transcription	H9 Cell Line	embryonic stem cell
28	chr19:41285400-41303400	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
29	chr19:41285400-41303400	Weak transcription	Primary hematopoietic stem cells	blood
30	chr19:41285400-41303400	Weak transcription	Colon Smooth Muscle	Colon
31	chr19:41285400-41303400	Weak transcription	HMEC	breast
32	chr19:41285400-41303400	Weak transcription	Osteobl	bone
33	chr19:41285400-41303600	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
34	chr19:41285400-41303600	Weak transcription	Primary T killer memory cells from peripheral blood	blood
35	chr19:41285400-41303600	Weak transcription	NHEK	skin
36	chr19:41285400-41303800	Weak transcription	iPS-20b Cell Line	embryonic stem cell
37	chr19:41285400-41303800	Weak transcription	NH-A	brain
38	chr19:41285400-41304000	Weak transcription	HSMMtube	muscle
39	chr19:41285800-41294200	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
40	chr19:41286000-41297600	Strong transcription	Fetal Intestine Small	intestine
41	chr19:41286000-41299200	Strong transcription	Monocytes-CD14+_RO01746	blood
42	chr19:41286000-41299400	Strong transcription	Breast Myoepithelial Primary Cells	Breast
43	chr19:41286000-41300000	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
44	chr19:41286000-41303600	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
45	chr19:41286200-41292400	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
46	chr19:41286200-41294400	Strong transcription	Primary T cells from cord blood	blood
47	chr19:41286200-41303400	Weak transcription	K562	blood
48	chr19:41286200-41303800	Weak transcription	HUES6 Cell Line	embryonic stem cell
49	chr19:41286200-41304000	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
50	chr19:41286400-41295600	Weak transcription	Primary T helper cells PMA-I stimulated	--

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