Variant report

Variant	rs1978605
Chromosome Location	chr19:51294003-51294004
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:23)
CpG islands
(count:0)
Chromatin interactive
region (count:10)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:23 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	POLR2A	chr19:51292846-51302413	Hela-S3	cervix:	n/a	n/a
2	POLR2A	chr19:51293982-51303950	GM12878	blood:	n/a	n/a
3	POLR2A	chr19:51292818-51303789	GM12891	blood:	n/a	n/a
4	NR2F2	chr19:51294003-51294803	K562	blood:	n/a	chr19:51294461-51294476
5	POLR2A	chr19:51293449-51294473	H1-hESC	embryonic stem cell:	n/a	n/a
6	POLR2A	chr19:51292766-51304914	Hela-S3	cervix:	n/a	n/a
7	POLR2A	chr19:51293608-51303838	GM12892	blood:	n/a	n/a
8	POLR2A	chr19:51292681-51303883	GM12891	blood:	n/a	n/a
9	POLR2A	chr19:51293489-51300654	MCF10A-Er-Src	breast:	n/a	n/a
10	NR2F2	chr19:51293892-51295070	MCF-7	breast:	n/a	chr19:51294461-51294476
11	POLR2A	chr19:51290649-51303858	Hela-S3	cervix:	n/a	n/a
12	POLR2A	chr19:51292824-51303824	A549	lung:	n/a	n/a
13	POLR2A	chr19:51292766-51303262	HepG2	liver:	n/a	n/a
14	POLR2A	chr19:51293721-51303283	ECC-1	luminal epithelium:	n/a	n/a
15	POLR2A	chr19:51291646-51302172	MCF10A-Er-Src	breast:	n/a	n/a
16	POLR2A	chr19:51293364-51304008	H1-hESC	embryonic stem cell:	n/a	n/a
17	POLR2A	chr19:51293339-51294356	GM12878	blood:	n/a	n/a
18	POLR2A	chr19:51291972-51304763	Hela-S3	cervix:	n/a	n/a
19	POLR2A	chr19:51293983-51294354	K562	blood:	n/a	n/a
20	POLR2A	chr19:51293286-51294399	GM12878	blood:	n/a	n/a
21	POLR2A	chr19:51293439-51303961	GM12892	blood:	n/a	n/a
22	POLR2A	chr19:51293929-51295319	GM12891	blood:	n/a	n/a
23	NR2F2	chr19:51293935-51294981	K562	blood:	n/a	chr19:51294461-51294476

No data

(count:10 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr19:51293560..51298277-chr19:51413419..51418761,7	K562	blood:
2	chr19:51288460..51291986-chr19:51292271..51294566,4	MCF-7	breast:
3	chr19:51292849..51296626-chr19:51372637..51375537,3	K562	blood:
4	chr19:51287157..51292690-chr19:51292694..51297699,7	MCF-7	breast:
5	chr19:51070614..51072810-chr19:51292938..51294549,2	K562	blood:
6	chr19:51226381..51234126-chr19:51290973..51302468,19	K562	blood:
7	chr19:51291032..51294383-chr19:51305809..51308243,6	MCF-7	breast:
8	chr19:51288587..51290873-chr19:51291890..51294916,4	K562	blood:
9	chr19:51293784..51296692-chr19:51392841..51394583,2	MCF-7	breast:
10	chr19:51226381..51234126-chr19:51290973..51298243,11	K562	blood:

No data

Variant related genes	Relation type
ENSG00000261341	TF binding region
ENSG00000167751	Chromatin interaction
ENSG00000167749	Chromatin interaction
ENSG00000167747	Chromatin interaction
ENSG00000261341	Chromatin interaction
ENSG00000131409	Chromatin interaction
ENSG00000105472	Chromatin interaction

Extended variants
information (count: 37 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:32)

rs_ID	r²[population]
rs10425724	0.86[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs1054713	0.80[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.84[ASN][1000 genomes]
rs11672844	1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[ASN][1000 genomes]
rs197589	1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[ASN][1000 genomes]
rs2247289	0.90[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.95[ASN][1000 genomes]
rs2411334	0.87[ASN][1000 genomes]
rs2434449	0.90[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.95[ASN][1000 genomes]
rs2456584	1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[ASN][1000 genomes]
rs2456585	0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2560931	0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2560933	0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2659058	0.90[CHB][hapmap];1.00[JPT][hapmap];0.81[ASN][1000 genomes]
rs2659059	0.95[ASN][1000 genomes]
rs2659099	0.89[ASN][1000 genomes]
rs2659100	0.88[ASN][1000 genomes]
rs2659101	0.80[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.85[ASN][1000 genomes]
rs2659103	0.89[CHB][hapmap];1.00[JPT][hapmap];0.82[ASN][1000 genomes]
rs2659104	0.88[CHB][hapmap];1.00[JPT][hapmap];0.82[ASN][1000 genomes]
rs266116	1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[ASN][1000 genomes]
rs266122	0.85[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs266123	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.98[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];0.92[YRI][hapmap];0.85[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs266125	0.81[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs266127	0.85[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs266128	0.81[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs5516	0.85[ASN][1000 genomes]
rs56164547	0.90[AMR][1000 genomes];0.97[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs59524380	0.90[AMR][1000 genomes];0.97[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs788886	0.92[ASN][1000 genomes]
rs788887	0.93[ASN][1000 genomes]
rs788889	0.90[CHB][hapmap];1.00[JPT][hapmap];0.95[ASN][1000 genomes]
rs788890	0.90[CHB][hapmap];1.00[JPT][hapmap];0.95[ASN][1000 genomes]
rs788891	1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[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	nsv1060760	chr19:50883425-51463712	ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer Flanking Active TSS Bivalent/Poised TSS Active TSS Enhancers Weak transcription Strong transcription Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	99 gene(s)	inside rSNPs	diseases
2	nsv1058177	chr19:50984774-51463712	Strong transcription Bivalent/Poised TSS Flanking Active TSS Active TSS Weak transcription Bivalent Enhancer Enhancers Flanking Bivalent TSS/Enh Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	84 gene(s)	inside rSNPs	diseases
3	nsv912288	chr19:51283791-51334355	Enhancers Bivalent Enhancer Bivalent/Poised TSS Strong transcription Weak transcription Genic enhancers Flanking Bivalent TSS/Enh Active TSS Flanking Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	60 gene(s)	inside rSNPs	diseases
4	nsv912289	chr19:51283791-51335943	Flanking Bivalent TSS/Enh Enhancers Weak transcription Bivalent Enhancer Active TSS Flanking Active TSS Strong transcription Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	60 gene(s)	inside rSNPs	diseases
5	nsv912290	chr19:51283791-51344483	Flanking Active TSS Active TSS Enhancers Weak transcription Strong transcription Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS Genic enhancers Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	60 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs1978605	KLK1	cis	lymphoblastoid	seeQTL
rs1978605	C19orf48	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:11 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr19:51286800-51296800	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
2	chr19:51287000-51298400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
3	chr19:51287000-51298400	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
4	chr19:51287200-51301200	Weak transcription	Primary B cells from cord blood	blood
5	chr19:51287400-51300000	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
6	chr19:51289800-51298600	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
7	chr19:51290000-51298800	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
8	chr19:51291800-51303400	Weak transcription	Fetal Kidney	kidney
9	chr19:51292600-51297200	Weak transcription	Right Atrium	heart
10	chr19:51293200-51297800	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
11	chr19:51293400-51300000	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--

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