Variant report

Variant	rs6508944
Chromosome Location	chr19:41204347-41204348
allele	C/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	chr19:41195062..41198004-chr19:41203820..41206508,3	K562	blood:
3	chr19:41204060..41206882-chr19:41209146..41210846,2	MCF-7	breast:
4	chr19:41195062..41197127-chr19:41204257..41206508,3	K562	blood:

Variant related genes	Relation type
ENSG00000123815	Chromatin interaction
ENSG00000105245	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	0.85[ASN][1000 genomes]
rs2115239	0.91[ASN][1000 genomes]
rs2246095	0.97[ASN][1000 genomes]
rs2288451	0.91[ASN][1000 genomes]
rs2561535	0.94[ASN][1000 genomes]
rs2604882	0.92[ASN][1000 genomes]
rs2604885	0.82[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2604887	0.88[ASN][1000 genomes]
rs3865452	0.91[ASN][1000 genomes]
rs4802085	0.87[ASN][1000 genomes]
rs4803358	0.91[ASN][1000 genomes]
rs7257602	0.83[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
rs6508944	C19orf54	Cis_1M	lymphoblastoid	RTeQTL

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	chr19:41197800-41204600	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
22	chr19:41197800-41205400	Weak transcription	GM12878-XiMat	blood
23	chr19:41197800-41207400	Weak transcription	Primary T helper cells PMA-I stimulated	--
24	chr19:41197800-41208200	Strong transcription	Fetal Stomach	stomach
25	chr19:41197800-41211000	Weak transcription	Right Atrium	heart
26	chr19:41197800-41219000	Strong transcription	Monocytes-CD14+_RO01746	blood
27	chr19:41198000-41207800	Weak transcription	Muscle Satellite Cultured Cells	--
28	chr19:41198000-41208200	Weak transcription	ES-I3 Cell Line	embryonic stem cell
29	chr19:41198200-41205200	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
30	chr19:41198200-41205400	Strong transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
31	chr19:41198200-41205400	Weak transcription	Brain Hippocampus Middle	brain
32	chr19:41198200-41205800	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
33	chr19:41198200-41208400	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
34	chr19:41198400-41207600	Weak transcription	HSMM	muscle
35	chr19:41198400-41219800	Weak transcription	NH-A	brain
36	chr19:41198600-41207800	Weak transcription	K562	blood
37	chr19:41199000-41217600	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
38	chr19:41200200-41207800	Weak transcription	Fetal Brain Male	brain
39	chr19:41200200-41211800	Strong transcription	Ovary	ovary
40	chr19:41200400-41205600	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
41	chr19:41200400-41209400	Strong transcription	Fetal Muscle Trunk	muscle
42	chr19:41200800-41205400	Weak transcription	HMEC	breast
43	chr19:41200800-41207000	Weak transcription	iPS-15b Cell Line	embryonic stem cell
44	chr19:41201000-41204400	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
45	chr19:41201000-41205400	Weak transcription	Esophagus	oesophagus
46	chr19:41201000-41207600	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
47	chr19:41201600-41206000	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
48	chr19:41201800-41205200	Weak transcription	H9 Cell Line	embryonic stem cell
49	chr19:41201800-41205200	Weak transcription	Rectal Smooth Muscle	rectum
50	chr19:41201800-41205200	Weak transcription	Skeletal Muscle Male	skeletal muscle

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