Variant report

Variant	rs2607415
Chromosome Location	chr19:41262687-41262688
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:28)
CpG islands
(count:0)
Chromatin interactive
region (count:9)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:28 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	POLR2A	chr19:41262465-41263927	SK-N-MC	brain:	n/a	n/a
2	POLR2A	chr19:41262388-41263160	HepG2	liver:	n/a	n/a
3	POLR2A	chr19:41261233-41263651	H1-hESC	embryonic stem cell:	n/a	n/a
4	POLR2A	chr19:41262417-41263187	PANC-1	pancreas:	n/a	n/a
5	POLR2A	chr19:41262655-41263014	GM12891	blood:	n/a	n/a
6	POLR2A	chr19:41262559-41263181	HepG2	liver:	n/a	n/a
7	RUNX3	chr19:41262544-41262910	GM12878	blood:	n/a	n/a
8	POLR2A	chr19:41262417-41263066	Hela-S3	cervix:	n/a	n/a
9	POLR2A	chr19:41262426-41263098	H1-hESC	embryonic stem cell:	n/a	n/a
10	POLR2A	chr19:41262523-41263094	H1-hESC	embryonic stem cell:	n/a	n/a
11	POLR2A	chr19:41262557-41262749	Hela-S3	cervix:	n/a	n/a
12	POLR2A	chr19:41262517-41263136	K562	blood:	n/a	n/a
13	STAT3	chr19:41262649-41262928	MCF10A-Er-Src	breast:	n/a	n/a
14	POLR2A	chr19:41262524-41263164	H1-hESC	embryonic stem cell:	n/a	n/a
15	EBF1	chr19:41262594-41262846	GM12878	blood:	n/a	chr19:41262749-41262760
16	POLR2A	chr19:41262539-41263070	GM12878	blood:	n/a	n/a
17	POLR2A	chr19:41262684-41263445	K562	blood:	n/a	n/a
18	POLR2A	chr19:41262506-41263747	PFSK-1	brain:	n/a	n/a
19	POLR2A	chr19:41262376-41263123	GM12892	blood:	n/a	n/a
20	POLR2A	chr19:41262524-41263147	GM12891	blood:	n/a	n/a
21	WRNIP1	chr19:41262546-41262860	GM12878	blood:	n/a	n/a
22	POLR2A	chr19:41262638-41263763	K562	blood:	n/a	n/a
23	POLR2A	chr19:41262558-41263153	A549	lung:	n/a	n/a
24	POLR2A	chr19:41262536-41262957	GM12892	blood:	n/a	n/a
25	POLR2A	chr19:41262588-41263113	GM12892	blood:	n/a	n/a
26	POLR2A	chr19:41261290-41263606	H1-hESC	embryonic stem cell:	n/a	n/a
27	STAT3	chr19:41262631-41262975	MCF10A-Er-Src	breast:	n/a	n/a
28	POLR2A	chr19:41262549-41263049	Hela-S3	cervix:	n/a	n/a

No data

(count:9 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr19:41260700..41263624-chr19:41281746..41284711,4	K562	blood:
2	chr19:41261509..41264476-chr19:41312368..41314936,2	K562	blood:
3	chr19:41260139..41263549-chr19:41263654..41270764,10	MCF-7	breast:
4	chr19:41195613..41198968-chr19:41260956..41263433,3	MCF-7	breast:
5	chr19:41260895..41264688-chr19:41281653..41284501,3	MCF-7	breast:
6	chr19:41261125..41262805-chr19:41283211..41284852,2	K562	blood:
7	chr19:41253887..41263110-chr19:41303366..41316425,33	K562	blood:
8	chr19:41221165..41222932-chr19:41261508..41263224,2	MCF-7	breast:
9	chr19:41206422..41208384-chr19:41260383..41263313,2	K562	blood:

No data

Variant related genes	Relation type
SNRPA	TF binding region
ENSG00000077312	Chromatin interaction
ENSG00000261857	Chromatin interaction
ENSG00000269858	Chromatin interaction
ENSG00000167578	Chromatin interaction
ENSG00000171570	Chromatin interaction
ENSG00000123815	Chromatin interaction
ENSG00000105245	Chromatin interaction
ENSG00000268797	Chromatin interaction

Extended variants
information (count: 17 )
Associated
traits (count: 2 )

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

rs_ID	r²[population]
rs2249835	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2545755	0.97[AMR][1000 genomes];0.94[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2545774	0.81[EUR][1000 genomes]
rs2604869	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[YRI][hapmap];0.81[AFR][1000 genomes];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2604893	0.91[CEU][hapmap];0.90[CHB][hapmap];1.00[JPT][hapmap];0.95[AMR][1000 genomes];0.94[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2604895	0.90[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2607414	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2607424	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[YRI][hapmap];0.82[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2644898	0.91[CEU][hapmap];0.90[CHB][hapmap];1.00[JPT][hapmap];0.94[AMR][1000 genomes];0.94[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2644916	0.86[CEU][hapmap];0.90[CHB][hapmap];1.00[JPT][hapmap];0.81[ASN][1000 genomes]
rs4803368	0.91[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.94[AMR][1000 genomes];0.94[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs7249450	0.93[AMR][1000 genomes];0.91[EUR][1000 genomes];0.88[ASN][1000 genomes]

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	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	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
3	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
4	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
5	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
rs2607415	C19orf54	cis	Lymphoblastoid	GTEx
rs2607415	C19orf54	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:127 , 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	chr19:41258400-41265200	Weak transcription	Brain Cingulate Gyrus	brain
3	chr19:41258800-41268400	Weak transcription	Psoas Muscle	Psoas
4	chr19:41259000-41275200	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
5	chr19:41259200-41264200	Weak transcription	Fetal Brain Male	brain
6	chr19:41259200-41272800	Strong transcription	H1 Cell Line	embryonic stem cell
7	chr19:41259800-41263200	Genic enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
8	chr19:41260000-41263000	Genic enhancers	Lung	lung
9	chr19:41260000-41263000	Genic enhancers	Sigmoid Colon	Sigmoid Colon
10	chr19:41260000-41263200	Genic enhancers	Fetal Muscle Leg	muscle
11	chr19:41260200-41262800	Genic enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
12	chr19:41260200-41262800	Genic enhancers	Colon Smooth Muscle	Colon
13	chr19:41260200-41263000	Genic enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
14	chr19:41260200-41263400	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
15	chr19:41260200-41263400	Genic enhancers	HMEC	breast
16	chr19:41260200-41263800	Genic enhancers	Fetal Adrenal Gland	Adrenal Gland
17	chr19:41260200-41266800	Genic enhancers	Spleen	Spleen
18	chr19:41260200-41272000	Strong transcription	H9 Cell Line	embryonic stem cell
19	chr19:41260400-41263200	Genic enhancers	Primary B cells from cord blood	blood
20	chr19:41260400-41263200	Transcr. at gene 5' and 3'	GM12878-XiMat	blood
21	chr19:41260400-41263400	Genic enhancers	Breast Myoepithelial Primary Cells	Breast
22	chr19:41260400-41263400	Genic enhancers	Primary Natural Killer cells fromperipheralblood	blood
23	chr19:41260400-41266600	Strong transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
24	chr19:41260400-41271800	Strong transcription	ES-I3 Cell Line	embryonic stem cell
25	chr19:41260600-41263200	Genic enhancers	Gastric	stomach
26	chr19:41260600-41272400	Strong transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
27	chr19:41260600-41272600	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
28	chr19:41260600-41277200	Strong transcription	Fetal Brain Female	brain
29	chr19:41260800-41262800	Weak transcription	Brain Inferior Temporal Lobe	brain
30	chr19:41260800-41263000	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
31	chr19:41260800-41263200	Genic enhancers	Primary B cells from peripheral blood	blood
32	chr19:41260800-41264200	Weak transcription	Brain Substantia Nigra	brain
33	chr19:41260800-41264200	Weak transcription	Pancreatic Islets	Pancreatic Islet
34	chr19:41260800-41264400	Genic enhancers	Placenta	Placenta
35	chr19:41260800-41272200	Strong transcription	HUES6 Cell Line	embryonic stem cell
36	chr19:41260800-41272200	Strong transcription	iPS-18 Cell Line	embryonic stem cell
37	chr19:41260800-41272400	Strong transcription	iPS-20b Cell Line	embryonic stem cell
38	chr19:41260800-41272400	Strong transcription	Brain Anterior Caudate	brain
39	chr19:41260800-41283200	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
40	chr19:41261000-41262800	Enhancers	Primary T killer naive cells fromperipheralblood	blood
41	chr19:41261000-41263000	Genic enhancers	Foreskin Fibroblast Primary Cells skin02	Skin
42	chr19:41261000-41263000	Genic enhancers	Adipose Nuclei	Adipose
43	chr19:41261000-41263000	Genic enhancers	A549	lung
44	chr19:41261000-41263200	Genic enhancers	Primary T helper naive cells fromperipheralblood	blood
45	chr19:41261000-41263400	Genic enhancers	Primary T helper cells fromperipheralblood	blood
46	chr19:41261000-41263400	Genic enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
47	chr19:41261000-41263400	Genic enhancers	HepG2	liver
48	chr19:41261000-41263600	Genic enhancers	Pancreas	Pancrea
49	chr19:41261000-41271800	Strong transcription	HSMM	muscle
50	chr19:41261000-41272200	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived

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