Variant report

Variant	rs40353
Chromosome Location	chr19:39879663-39879664
allele	C/T
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:1)
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	chr19:39879009-39879689	HL-60	blood:	n/a	n/a
2	POLR2A	chr19:39875493-39880799	SK-N-MC	brain:	n/a	n/a
3	POLR2A	chr19:39879250-39880035	U87	brain:	n/a	n/a
4	BCL3	chr19:39878830-39879846	A549	lung:	n/a	chr19:39879688-39879701
5	POLR2A	chr19:39879390-39879693	SK-N-SH	brain:	n/a	n/a
6	POLR2A	chr19:39850716-39886400	PANC-1	pancreas:	n/a	n/a
7	POLR2A	chr19:39879003-39880495	U87	brain:	n/a	n/a
8	POLR2A	chr19:39879380-39880471	HUVEC	blood vessel:	n/a	n/a
9	POLR2A	chr19:39876429-39882671	HepG2	liver:	n/a	n/a
10	POLR2A	chr19:39879250-39880065	U87	brain:	n/a	n/a
11	POLR2A	chr19:39879153-39879687	A549	lung:	n/a	n/a
12	POLR2A	chr19:39879596-39879694	Hela-S3	cervix:	n/a	n/a
13	POLR2A	chr19:39878769-39880629	K562	blood:	n/a	n/a
14	BCL3	chr19:39878998-39880342	A549	lung:	n/a	chr19:39879688-39879701
15	SIN3AK20	chr19:39870428-39883708	PANC-1	pancreas:	n/a	n/a
16	POLR2A	chr19:39878822-39880048	SK-N-SH	brain:	n/a	n/a
17	POLR2A	chr19:39879603-39880040	HCT-116	colon:	n/a	n/a
18	POLR2A	chr19:39878610-39880530	PFSK-1	brain:	n/a	n/a
19	POLR2A	chr19:39878997-39879755	K562	blood:	n/a	n/a
20	POLR2A	chr19:39878908-39879664	Hela-S3	cervix:	n/a	n/a
21	POLR2A	chr19:39879208-39879710	A549	lung:	n/a	n/a
22	POLR2A	chr19:39879228-39879726	GM12878	blood:	n/a	n/a
23	POLR2A	chr19:39879009-39880489	U87	brain:	n/a	n/a
24	POLR2A	chr19:39878919-39879824	MCF-7	breast:	n/a	n/a
25	POLR2A	chr19:39879168-39879706	ECC-1	luminal epithelium:	n/a	n/a
26	POLR2A	chr19:39879339-39879784	K562	blood:	n/a	n/a
27	POLR2A	chr19:39875542-39882243	K562	blood:	n/a	n/a
28	POLR2A	chr19:39878621-39882617	H1-hESC	embryonic stem cell:	n/a	n/a

No data

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

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr19:39859941..39863633-chr19:39878903..39882994,5	MCF-7	breast:

No data

Variant related genes	Relation type
MED29	TF binding region
PAF1	TF binding region
ENSG00000179134	Chromatin interaction

Extended variants
information (count: 35 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:28)

rs_ID	r²[population]
rs1375910	0.83[JPT][hapmap]
rs16973342	0.83[JPT][hapmap]
rs16973348	0.83[JPT][hapmap]
rs16973350	0.83[JPT][hapmap]
rs16973363	0.83[JPT][hapmap]
rs16973374	0.81[JPT][hapmap]
rs2067102	0.83[JPT][hapmap]
rs2074852	0.83[JPT][hapmap]
rs251906	0.83[JPT][hapmap]
rs28370340	0.84[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs30453	0.89[CHD][hapmap];0.92[JPT][hapmap]
rs30454	0.90[CHD][hapmap];0.92[JPT][hapmap]
rs30455	0.90[CHD][hapmap];0.92[JPT][hapmap]
rs30457	0.90[CHD][hapmap];0.92[JPT][hapmap]
rs36264	0.90[CHD][hapmap];0.92[JPT][hapmap]
rs36270	1.00[CHD][hapmap];1.00[JPT][hapmap]
rs3786949	0.83[JPT][hapmap]
rs3826938	0.81[JPT][hapmap]
rs3865515	0.83[JPT][hapmap]
rs40441	0.90[CHD][hapmap];0.92[JPT][hapmap];0.92[LWK][hapmap];0.85[AFR][1000 genomes]
rs45601936	0.84[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs562638	0.90[CHD][hapmap];0.92[JPT][hapmap]
rs6508860	0.82[CHB][hapmap];0.81[CHD][hapmap];0.92[JPT][hapmap];0.85[TSI][hapmap]
rs685125	1.00[CHD][hapmap];1.00[JPT][hapmap];0.83[ASN][1000 genomes]
rs7246750	0.84[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs7250420	0.84[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs8102194	0.84[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs917319	0.82[CHB][hapmap];1.00[JPT][hapmap];0.84[EUR][1000 genomes];0.85[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:7 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv911679	chr19:39735106-39924129	Active TSS Flanking Active TSS Weak transcription Enhancers Strong transcription Bivalent Enhancer Transcr. at gene 5' and 3' Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	198 gene(s)	inside rSNPs	diseases
2	nsv1058514	chr19:39744112-39902580	Flanking Active TSS Enhancers Active TSS Bivalent/Poised TSS Weak transcription Genic enhancers Strong transcription Transcr. at gene 5' and 3' Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	187 gene(s)	inside rSNPs	diseases
3	nsv911680	chr19:39792460-39924129	Enhancers Flanking Active TSS Weak transcription Strong transcription Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	194 gene(s)	inside rSNPs	diseases
4	esv10629	chr19:39811570-39886212	Flanking Active TSS Strong transcription Weak transcription Enhancers Transcr. at gene 5' and 3' Genic enhancers Active TSS Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	34 gene(s)	inside rSNPs	diseases
5	nsv870133	chr19:39822160-39938468	Weak transcription Strong transcription Flanking Active TSS Enhancers Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	233 gene(s)	inside rSNPs	diseases
6	nsv911682	chr19:39847132-39914748	Strong transcription Active TSS Weak transcription Enhancers Genic enhancers Bivalent Enhancer Flanking Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	179 gene(s)	inside rSNPs	diseases
7	nsv911683	chr19:39847132-39924129	Strong transcription Flanking Active TSS Weak transcription Enhancers Active TSS Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	185 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs40353	LGALS14	cis	lymphoblastoid	seeQTL

Chromatin state (count:126 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr19:39834800-39880000	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
2	chr19:39835800-39880200	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
3	chr19:39835800-39880200	Strong transcription	Monocytes-CD14+_RO01746	blood
4	chr19:39836200-39880400	Strong transcription	Primary T cells from cord blood	blood
5	chr19:39836600-39880400	Strong transcription	Primary monocytes fromperipheralblood	blood
6	chr19:39836600-39880400	Strong transcription	Fetal Brain Female	brain
7	chr19:39837400-39880000	Strong transcription	Primary T helper cells fromperipheralblood	blood
8	chr19:39838000-39880000	Strong transcription	Brain Germinal Matrix	brain
9	chr19:39838600-39880400	Strong transcription	HUES6 Cell Line	embryonic stem cell
10	chr19:39838800-39880200	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
11	chr19:39841600-39880000	Strong transcription	Fetal Intestine Large	intestine
12	chr19:39842000-39880000	Strong transcription	iPS-18 Cell Line	embryonic stem cell
13	chr19:39842200-39880200	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
14	chr19:39842200-39880400	Strong transcription	Primary neutrophils fromperipheralblood	blood
15	chr19:39842400-39880400	Strong transcription	Thymus	Thymus
16	chr19:39842600-39880400	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
17	chr19:39848200-39880000	Weak transcription	Fetal Heart	heart
18	chr19:39850400-39881000	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
19	chr19:39852800-39880400	Strong transcription	HUES64 Cell Line	embryonic stem cell
20	chr19:39856600-39880200	Strong transcription	Fetal Thymus	thymus
21	chr19:39857200-39880200	Strong transcription	Primary T helper 17 cells PMA-I stimulated	--
22	chr19:39857200-39880400	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
23	chr19:39859000-39880200	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
24	chr19:39860000-39880400	Strong transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
25	chr19:39864000-39880200	Strong transcription	Placenta	Placenta
26	chr19:39864000-39880400	Strong transcription	Fetal Intestine Small	intestine
27	chr19:39864200-39880400	Strong transcription	Fetal Muscle Leg	muscle
28	chr19:39864400-39879800	Strong transcription	Ganglion Eminence derived primary cultured neurospheres	brain
29	chr19:39864400-39880000	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
30	chr19:39864400-39880000	Strong transcription	Esophagus	oesophagus
31	chr19:39864400-39880000	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
32	chr19:39864400-39880200	Strong transcription	Brain Substantia Nigra	brain
33	chr19:39864400-39880200	Strong transcription	Duodenum Mucosa	Duodenum
34	chr19:39864400-39880200	Strong transcription	Fetal Stomach	stomach
35	chr19:39864400-39880400	Strong transcription	Lung	lung
36	chr19:39864400-39880400	Weak transcription	Right Atrium	heart
37	chr19:39864600-39880400	Strong transcription	Fetal Muscle Trunk	muscle
38	chr19:39864800-39880200	Strong transcription	Brain Inferior Temporal Lobe	brain
39	chr19:39864800-39880400	Strong transcription	HUES48 Cell Line	embryonic stem cell
40	chr19:39865000-39880200	Strong transcription	Placenta Amnion	Placenta Amnion
41	chr19:39865000-39880600	Strong transcription	Rectal Mucosa Donor 29	rectum
42	chr19:39865200-39880000	Strong transcription	Stomach Smooth Muscle	stomach
43	chr19:39865200-39880400	Strong transcription	Colon Smooth Muscle	Colon
44	chr19:39865200-39880400	Strong transcription	NHLF	lung
45	chr19:39865400-39880000	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
46	chr19:39865400-39880200	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
47	chr19:39865600-39880200	Strong transcription	Primary T cells fromperipheralblood	blood
48	chr19:39865600-39880200	Strong transcription	Primary T helper cells PMA-I stimulated	--
49	chr19:39865600-39880200	Strong transcription	Adipose Nuclei	Adipose
50	chr19:39865600-39880200	Strong transcription	Brain Anterior Caudate	brain

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