Variant report

Variant	rs2013813
Chromosome Location	chr19:19117595-19117596
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:13)
CpG islands
(count:0)
Chromatin interactive
region (count:5)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:13 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	POLR2A	chr19:19117436-19118275	GM12878	blood:	n/a	n/a
2	POLR2A	chr19:19117381-19117740	K562	blood:	n/a	n/a
3	POLR2A	chr19:19117204-19117632	K562	blood:	n/a	n/a
4	POLR2A	chr19:19117170-19118159	PANC-1	pancreas:	n/a	n/a
5	POLR2A	chr19:19117577-19117750	Hela-S3	cervix:	n/a	n/a
6	POLR2A	chr19:19117083-19118049	SK-N-MC	brain:	n/a	n/a
7	POLR2A	chr19:19117182-19118146	K562	blood:	n/a	n/a
8	POLR2A	chr19:19117552-19117694	Hela-S3	cervix:	n/a	n/a
9	POLR2A	chr19:19117138-19118016	PFSK-1	brain:	n/a	n/a
10	POLR2A	chr19:19117402-19118440	K562	blood:	n/a	n/a
11	POLR2A	chr19:19117407-19117830	GM12892	blood:	n/a	n/a
12	POLR2A	chr19:19117497-19117888	HepG2	liver:	n/a	n/a
13	POLR2A	chr19:19117340-19118293	HL-60	blood:	n/a	n/a

No data

(count:5 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr19:19116158..19119387-chr19:19142986..19146626,3	K562	blood:
2	chr19:19117422..19119602-chr19:19143836..19146312,2	MCF-7	breast:
3	chr19:19111292..19114373-chr19:19114912..19119254,5	K562	blood:
4	chr19:19110453..19114238-chr19:19116411..19119441,3	K562	blood:
5	chr19:19108789..19110296-chr19:19117507..19119066,2	K562	blood:

No data

Variant related genes	Relation type
SUGP2	TF binding region
ENSG00000064607	Chromatin interaction
ENSG00000105676	Chromatin interaction

Extended variants
information (count: 19 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:17)

rs_ID	r²[population]
rs10403272	1.00[ASW][hapmap];0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.89[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.82[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs10410399	1.00[ASW][hapmap];0.85[CEU][hapmap];0.96[GIH][hapmap];0.94[TSI][hapmap];1.00[YRI][hapmap]
rs11085249	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.83[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs11671696	0.95[ASN][1000 genomes]
rs12978990	0.95[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs2013585	0.90[EUR][1000 genomes]
rs2269869	1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[ASN][1000 genomes]
rs2285851	0.81[CEU][hapmap];0.90[MEX][hapmap]
rs3787041	0.85[JPT][hapmap]
rs4808172	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.95[ASN][1000 genomes]
rs4808176	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4808895	0.85[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.83[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs4808900	0.95[ASN][1000 genomes]
rs4808916	0.85[JPT][hapmap]
rs4808917	0.91[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.82[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs6511019	1.00[ASW][hapmap];0.88[TSI][hapmap];1.00[YRI][hapmap]
rs7252615	0.96[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:2 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv833778	chr19:19012669-19201487	Weak transcription Flanking Active TSS Flanking Bivalent TSS/Enh Enhancers Strong transcription Genic enhancers Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	47 gene(s)	inside rSNPs	diseases
2	nsv2435	chr19:19077432-19122579	Strong transcription Bivalent Enhancer Enhancers Weak transcription Genic enhancers ZNF genes & repeats Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	14 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs2013813	TSSK6	cis	cerebellum	SCAN
rs2013813	SFRS14	Cis_1M	lymphoblastoid	RTeQTL
rs2013813	ZNF14	cis	parietal	SCAN

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr19:19100600-19122800	Strong transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
2	chr19:19101000-19125600	Strong transcription	Thymus	Thymus
3	chr19:19101000-19133000	Strong transcription	Fetal Thymus	thymus
4	chr19:19101200-19126000	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
5	chr19:19101200-19130400	Strong transcription	Duodenum Mucosa	Duodenum
6	chr19:19101200-19140200	Strong transcription	Primary neutrophils fromperipheralblood	blood
7	chr19:19101400-19130400	Strong transcription	Primary monocytes fromperipheralblood	blood
8	chr19:19101400-19142000	Strong transcription	Monocytes-CD14+_RO01746	blood
9	chr19:19101600-19130400	Strong transcription	Primary T cells from cord blood	blood
10	chr19:19101600-19130400	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
11	chr19:19102000-19130200	Strong transcription	Sigmoid Colon	Sigmoid Colon
12	chr19:19102000-19132000	Strong transcription	Dnd41	blood
13	chr19:19102600-19122600	Weak transcription	Fetal Heart	heart
14	chr19:19103200-19130200	Strong transcription	Duodenum Smooth Muscle	Duodenum
15	chr19:19103600-19123600	Strong transcription	HepG2	liver
16	chr19:19106800-19119200	Weak transcription	Stomach Mucosa	stomach
17	chr19:19106800-19143000	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
18	chr19:19107000-19119000	Weak transcription	Fetal Kidney	kidney
19	chr19:19107200-19130200	Strong transcription	Brain Germinal Matrix	brain
20	chr19:19107200-19142600	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
21	chr19:19107400-19125800	Strong transcription	Fetal Muscle Leg	muscle
22	chr19:19107600-19127200	Strong transcription	Fetal Intestine Large	intestine
23	chr19:19107600-19130200	Strong transcription	Brain Hippocampus Middle	brain
24	chr19:19107600-19142600	Strong transcription	Fetal Stomach	stomach
25	chr19:19107800-19130200	Strong transcription	Placenta	Placenta
26	chr19:19107800-19130400	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
27	chr19:19107800-19130400	Strong transcription	Fetal Brain Female	brain
28	chr19:19108000-19142000	Strong transcription	Ganglion Eminence derived primary cultured neurospheres	brain
29	chr19:19108000-19142800	Strong transcription	HUES6 Cell Line	embryonic stem cell
30	chr19:19108200-19130400	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
31	chr19:19108200-19142600	Weak transcription	Right Atrium	heart
32	chr19:19108600-19119600	Strong transcription	NHDF-Ad	bronchial
33	chr19:19108600-19130600	Strong transcription	HUES48 Cell Line	embryonic stem cell
34	chr19:19108600-19142200	Strong transcription	iPS-20b Cell Line	embryonic stem cell
35	chr19:19108600-19142800	Strong transcription	HUES64 Cell Line	embryonic stem cell
36	chr19:19108800-19123800	Strong transcription	NHEK	skin
37	chr19:19108800-19127400	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
38	chr19:19108800-19130400	Strong transcription	Primary B cells from peripheral blood	blood
39	chr19:19109000-19130400	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
40	chr19:19109000-19141800	Strong transcription	Cortex derived primary cultured neurospheres	brain
41	chr19:19109200-19121800	Strong transcription	Rectal Mucosa Donor 31	rectum
42	chr19:19109400-19130200	Strong transcription	H1 Cell Line	embryonic stem cell
43	chr19:19109400-19130200	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
44	chr19:19109400-19142400	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
45	chr19:19109800-19130200	Strong transcription	GM12878-XiMat	blood
46	chr19:19110200-19130400	Strong transcription	Stomach Smooth Muscle	stomach
47	chr19:19110400-19119600	Strong transcription	Muscle Satellite Cultured Cells	--
48	chr19:19110600-19122800	Strong transcription	Adipose Nuclei	Adipose
49	chr19:19110600-19130000	Strong transcription	Brain Cingulate Gyrus	brain
50	chr19:19110600-19142400	Strong transcription	Fetal Muscle Trunk	muscle

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