Variant report

Variant	rs2561535
Chromosome Location	chr19:41205165-41205166
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr19:41203041..41205301-chr19:41207131..41209748,2	K562	blood:
2	chr19:41204407..41205985-chr19:41209406..41212195,2	K562	blood:
3	chr19:41200175..41202352-chr19:41204819..41206717,3	MCF-7	breast:
4	chr19:41204648..41207445-chr19:41212507..41214384,2	K562	blood:
5	chr19:41195062..41198004-chr19:41203820..41206508,3	K562	blood:
6	chr19:41204060..41206882-chr19:41209146..41210846,2	MCF-7	breast:
7	chr19:41195062..41197127-chr19:41204257..41206508,3	K562	blood:

Variant related genes	Relation type
ENSG00000223284	Chromatin interaction
ENSG00000105245	Chromatin interaction
ENSG00000123815	Chromatin interaction

Extended variants
information (count: 16 )
Associated
traits (count: 1 )

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

rs_ID	r²[population]
rs1469427	0.86[ASN][1000 genomes]
rs2115239	0.82[AMR][1000 genomes];0.91[ASN][1000 genomes]
rs2246095	0.83[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2288451	0.91[ASN][1000 genomes]
rs2604882	0.83[AFR][1000 genomes];0.96[AMR][1000 genomes];0.85[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2604885	0.95[ASN][1000 genomes]
rs2604887	0.88[ASN][1000 genomes]
rs3865452	0.91[ASN][1000 genomes]
rs4802085	0.88[ASN][1000 genomes]
rs4803358	0.91[ASN][1000 genomes]
rs6508944	0.94[ASN][1000 genomes]
rs7257602	0.84[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv1830682	chr19:40880127-41270055	Weak transcription Strong transcription Enhancers Genic enhancers Active TSS Flanking Active TSS Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	139 gene(s)	inside rSNPs	diseases
2	nsv911728	chr19:41111069-41211056	Flanking Active TSS Weak transcription Transcr. at gene 5' and 3' Genic enhancers Enhancers Strong transcription Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	38 gene(s)	inside rSNPs	diseases
3	esv1800615	chr19:41127465-41270055	Weak transcription Active TSS Bivalent Enhancer Flanking Active TSS Enhancers Transcr. at gene 5' and 3' Genic enhancers Strong transcription ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	64 gene(s)	inside rSNPs	diseases
4	nsv1067017	chr19:41185992-41231251	Strong transcription Weak transcription Flanking Active TSS Enhancers Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region	36 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs2561535	C19orf54	cis	Nerve Tibial	GTEx

Chromatin state (count:125 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr19:41197000-41205200	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
2	chr19:41197000-41207600	Weak transcription	Fetal Kidney	kidney
3	chr19:41197000-41208000	Weak transcription	Small Intestine	intestine
4	chr19:41197200-41207400	Weak transcription	Stomach Mucosa	stomach
5	chr19:41197200-41210000	Weak transcription	Primary T helper naive cells from peripheral blood	blood
6	chr19:41197200-41210600	Weak transcription	Pancreatic Islets	Pancreatic Islet
7	chr19:41197200-41220200	Weak transcription	Fetal Heart	heart
8	chr19:41197200-41220600	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
9	chr19:41197400-41205200	Weak transcription	Colonic Mucosa	Colon
10	chr19:41197400-41205200	Weak transcription	Osteobl	bone
11	chr19:41197400-41207600	Weak transcription	NHDF-Ad	bronchial
12	chr19:41197400-41210600	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
13	chr19:41197400-41219800	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
14	chr19:41197400-41220000	Weak transcription	Primary T killer memory cells from peripheral blood	blood
15	chr19:41197400-41220000	Strong transcription	Fetal Intestine Small	intestine
16	chr19:41197400-41220200	Weak transcription	HUVEC	blood vessel
17	chr19:41197600-41207000	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
18	chr19:41197600-41208800	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
19	chr19:41197600-41216000	Strong transcription	Primary neutrophils fromperipheralblood	blood
20	chr19:41197600-41220200	Weak transcription	Psoas Muscle	Psoas
21	chr19:41197800-41205400	Weak transcription	GM12878-XiMat	blood
22	chr19:41197800-41207400	Weak transcription	Primary T helper cells PMA-I stimulated	--
23	chr19:41197800-41208200	Strong transcription	Fetal Stomach	stomach
24	chr19:41197800-41211000	Weak transcription	Right Atrium	heart
25	chr19:41197800-41219000	Strong transcription	Monocytes-CD14+_RO01746	blood
26	chr19:41198000-41207800	Weak transcription	Muscle Satellite Cultured Cells	--
27	chr19:41198000-41208200	Weak transcription	ES-I3 Cell Line	embryonic stem cell
28	chr19:41198200-41205200	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
29	chr19:41198200-41205400	Strong transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
30	chr19:41198200-41205400	Weak transcription	Brain Hippocampus Middle	brain
31	chr19:41198200-41205800	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
32	chr19:41198200-41208400	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
33	chr19:41198400-41207600	Weak transcription	HSMM	muscle
34	chr19:41198400-41219800	Weak transcription	NH-A	brain
35	chr19:41198600-41207800	Weak transcription	K562	blood
36	chr19:41199000-41217600	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
37	chr19:41200200-41207800	Weak transcription	Fetal Brain Male	brain
38	chr19:41200200-41211800	Strong transcription	Ovary	ovary
39	chr19:41200400-41205600	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
40	chr19:41200400-41209400	Strong transcription	Fetal Muscle Trunk	muscle
41	chr19:41200800-41205400	Weak transcription	HMEC	breast
42	chr19:41200800-41207000	Weak transcription	iPS-15b Cell Line	embryonic stem cell
43	chr19:41201000-41205400	Weak transcription	Esophagus	oesophagus
44	chr19:41201000-41207600	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
45	chr19:41201600-41206000	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
46	chr19:41201800-41205200	Weak transcription	H9 Cell Line	embryonic stem cell
47	chr19:41201800-41205200	Weak transcription	Rectal Smooth Muscle	rectum
48	chr19:41201800-41205200	Weak transcription	Skeletal Muscle Male	skeletal muscle
49	chr19:41201800-41205400	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
50	chr19:41201800-41205600	Weak transcription	NHLF	lung

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