Variant report

Variant	rs2604866
Chromosome Location	chr19:41318757-41318758
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	POLR2A	chr19:41318705-41318951	K562	blood:	n/a	n/a
2	NR3C1	chr19:41318640-41319423	A549	lung:	n/a	chr19:41319226-41319247 chr19:41319229-41319243 chr19:41319262-41319275 chr19:41319229-41319243
3	NR3C1	chr19:41318621-41319426	A549	lung:	n/a	chr19:41319226-41319247 chr19:41319229-41319243 chr19:41319262-41319275 chr19:41319229-41319243
4	POLR2A	chr19:41318656-41319149	MCF10A-Er-Src	breast:	n/a	n/a
5	POLR2A	chr19:41318486-41318824	HepG2	liver:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr19:41312625..41314191-chr19:41317244..41319686,2	MCF-7	breast:
2	chr19:41307688..41310230-chr19:41318329..41321323,2	MCF-7	breast:
3	chr19:41304267..41305951-chr19:41317494..41319797,2	MCF-7	breast:

Variant related genes	Relation type
CYP2T2P	TF binding region
ENSG00000269858	Chromatin interaction

Extended variants
information (count: 36 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:31)

rs_ID	r²[population]
rs10420685	0.85[GIH][hapmap]
rs13108	0.87[JPT][hapmap]
rs1455434	1.00[GIH][hapmap]
rs17726258	1.00[GIH][hapmap];1.00[MEX][hapmap];1.00[AMR][1000 genomes]
rs1869710	0.85[GIH][hapmap]
rs2233153	0.88[AMR][1000 genomes]
rs2233154	0.87[JPT][hapmap]
rs2233156	1.00[GIH][hapmap];1.00[MEX][hapmap];0.83[TSI][hapmap];0.88[AMR][1000 genomes]
rs2233159	0.87[JPT][hapmap]
rs2249854	0.87[JPT][hapmap]
rs2254326	0.85[GIH][hapmap];0.83[TSI][hapmap]
rs2303723	0.85[GIH][hapmap]
rs2545760	1.00[AMR][1000 genomes]
rs2545761	0.83[AMR][1000 genomes];0.87[ASN][1000 genomes]
rs2545763	1.00[CEU][hapmap];0.85[CHB][hapmap];0.86[CHD][hapmap];0.85[GIH][hapmap];1.00[JPT][hapmap];0.86[LWK][hapmap];0.90[MKK][hapmap];0.83[YRI][hapmap];0.83[AMR][1000 genomes];0.92[ASN][1000 genomes]
rs2545766	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2545771	0.87[ASW][hapmap];1.00[CEU][hapmap];0.84[CHB][hapmap];0.89[CHD][hapmap];1.00[GIH][hapmap];0.88[LWK][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.94[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2545772	1.00[CEU][hapmap];0.94[JPT][hapmap];1.00[YRI][hapmap];0.94[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2561531	0.85[GIH][hapmap]
rs2604864	0.83[ASN][1000 genomes]
rs2604868	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.94[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2604910	0.92[JPT][hapmap]
rs2607418	1.00[GIH][hapmap]
rs2607425	0.87[JPT][hapmap]
rs2607426	0.87[JPT][hapmap]
rs2644888	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2644915	1.00[AFR][1000 genomes];0.93[AMR][1000 genomes];0.84[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34950672	0.85[ASN][1000 genomes]
rs56891752	0.83[AMR][1000 genomes]
rs60533951	1.00[AMR][1000 genomes]
rs8107978	0.87[JPT][hapmap]

Variant overlapped rSNPs/rCNVs (count:5 , 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
4	nsv1066637	chr19:41309211-41597896	Weak transcription Enhancers Genic enhancers Active TSS Bivalent Enhancer Flanking Active TSS Bivalent/Poised TSS 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	29 gene(s)	inside rSNPs	diseases
5	nsv521459	chr19:41313202-41333284	Enhancers Weak transcription Genic enhancers Active TSS Flanking Active TSS Bivalent Enhancer ZNF genes & repeats Strong transcription Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region miRNA target site	12 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs2604866	C19orf54	cis	lymphoblastoid	seeQTL

Chromatin state (count:96 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr19:41315000-41324400	Weak transcription	HepG2	liver
2	chr19:41315000-41332600	Weak transcription	Aorta	Aorta
3	chr19:41316000-41319400	Enhancers	Spleen	Spleen
4	chr19:41316000-41319800	Enhancers	Fetal Heart	heart
5	chr19:41316200-41324400	Weak transcription	Gastric	stomach
6	chr19:41316400-41318800	Weak transcription	HSMMtube	muscle
7	chr19:41316400-41325400	Weak transcription	Dnd41	blood
8	chr19:41317000-41318800	Weak transcription	HSMM	muscle
9	chr19:41317200-41319200	Enhancers	Lung	lung
10	chr19:41317200-41320800	Enhancers	Cortex derived primary cultured neurospheres	brain
11	chr19:41317400-41318800	Weak transcription	NHLF	lung
12	chr19:41317400-41319800	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
13	chr19:41317400-41320200	Enhancers	Placenta	Placenta
14	chr19:41317400-41320400	Enhancers	Breast Myoepithelial Primary Cells	Breast
15	chr19:41317600-41318800	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
16	chr19:41317600-41318800	Weak transcription	Muscle Satellite Cultured Cells	--
17	chr19:41317600-41318800	Weak transcription	HMEC	breast
18	chr19:41317600-41320400	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
19	chr19:41317600-41324000	Weak transcription	Hela-S3	cervix
20	chr19:41317600-41324400	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
21	chr19:41317800-41318800	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
22	chr19:41317800-41319200	Enhancers	Adipose Nuclei	Adipose
23	chr19:41317800-41319400	Enhancers	Colonic Mucosa	Colon
24	chr19:41317800-41320000	Enhancers	Brain Substantia Nigra	brain
25	chr19:41317800-41324200	Weak transcription	Skeletal Muscle Female	skeletal muscle
26	chr19:41317800-41324400	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
27	chr19:41317800-41324400	Weak transcription	Rectal Mucosa Donor 29	rectum
28	chr19:41318000-41319000	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
29	chr19:41318000-41319000	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
30	chr19:41318000-41319000	Weak transcription	Left Ventricle	heart
31	chr19:41318000-41319000	Weak transcription	Right Ventricle	heart
32	chr19:41318000-41319200	Enhancers	Duodenum Mucosa	Duodenum
33	chr19:41318000-41319400	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
34	chr19:41318000-41324400	Weak transcription	Pancreas	Pancrea
35	chr19:41318000-41324400	Weak transcription	Rectal Mucosa Donor 31	rectum
36	chr19:41318000-41324400	Weak transcription	Right Atrium	heart
37	chr19:41318200-41318800	Bivalent Enhancer	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
38	chr19:41318200-41318800	Enhancers	Primary B cells from peripheral blood	blood
39	chr19:41318200-41318800	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
40	chr19:41318200-41318800	Enhancers	Foreskin Melanocyte Primary Cells skin01	Skin
41	chr19:41318200-41318800	Enhancers	Fetal Intestine Large	intestine
42	chr19:41318200-41318800	Bivalent Enhancer	Fetal Thymus	thymus
43	chr19:41318200-41318800	Bivalent Enhancer	Skeletal Muscle Male	skeletal muscle
44	chr19:41318200-41319000	Bivalent/Poised TSS	Brain Germinal Matrix	brain
45	chr19:41318200-41319200	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
46	chr19:41318200-41319200	Enhancers	Primary hematopoietic stem cells short term culture	blood
47	chr19:41318200-41319200	Enhancers	Brain Anterior Caudate	brain
48	chr19:41318200-41319400	Enhancers	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
49	chr19:41318200-41319400	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
50	chr19:41318200-41319800	Enhancers	Colon Smooth Muscle	Colon

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