Variant report

Variant	rs4547459
Chromosome Location	chr19:36129789-36129790
allele	C/T
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	chr19:36129731-36130244	HUVEC	blood vessel:	n/a	n/a
2	POLR2A	chr19:36129033-36131166	SK-N-MC	brain:	n/a	n/a
3	POLR2A	chr19:36129751-36130503	SK-N-SH	brain:	n/a	n/a
4	POLR2A	chr19:36129719-36130833	PANC-1	pancreas:	n/a	n/a
5	BCL3	chr19:36129715-36131188	A549	lung:	n/a	chr19:36130151-36130160
6	POLR2A	chr19:36129787-36130553	GM12891	blood:	n/a	n/a
7	POLR2A	chr19:36129714-36130024	K562	blood:	n/a	n/a
8	POLR2A	chr19:36129700-36130538	K562	blood:	n/a	n/a
9	ZNF384	chr19:36129552-36130269	K562	blood:	n/a	n/a
10	POLR2A	chr19:36129590-36130413	PFSK-1	brain:	n/a	n/a
11	POLR2A	chr19:36129663-36130681	H1-hESC	embryonic stem cell:	n/a	n/a
12	POLR2A	chr19:36129774-36130627	GM12892	blood:	n/a	n/a
13	POLR2A	chr19:36129367-36130964	HepG2	liver:	n/a	n/a
14	POLR2A	chr19:36129732-36130213	GM12892	blood:	n/a	n/a
15	POLR2A	chr19:36128128-36131051	K562	blood:	n/a	n/a
16	POLR2A	chr19:36129677-36130516	H1-hESC	embryonic stem cell:	n/a	n/a
17	POLR2A	chr19:36129644-36130568	K562	blood:	n/a	n/a
18	POLR2A	chr19:36129571-36131186	MCF10A-Er-Src	breast:	n/a	n/a
19	POLR2A	chr19:36129774-36130539	GM12892	blood:	n/a	n/a
20	POLR2A	chr19:36128559-36130881	GM12878	blood:	n/a	n/a
21	POLR2A	chr19:36128703-36131061	PANC-1	pancreas:	n/a	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr19:36118444..36125285-chr19:36125367..36133017,11	MCF-7	breast:
2	chr19:36118572..36120760-chr19:36128325..36130152,2	MCF-7	breast:

Variant related genes	Relation type
ETV2	TF binding region
ENSG00000126254	Chromatin interaction

Extended variants
information (count: 14 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:10)

rs_ID	r²[population]
rs2239914	0.80[AMR][1000 genomes];0.96[ASN][1000 genomes]
rs2285414	0.95[ASN][1000 genomes]
rs2285415	0.93[ASN][1000 genomes]
rs4806180	0.93[ASN][1000 genomes]
rs4806181	0.91[ASN][1000 genomes]
rs4806183	0.91[ASN][1000 genomes]
rs756783	0.84[ASN][1000 genomes]
rs756784	0.96[ASN][1000 genomes]
rs8110747	0.82[AMR][1000 genomes];0.80[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs916659	0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv432045	chr19:35556260-36520760	Flanking Active TSS Enhancers Active TSS Weak transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer Strong transcription Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	191 gene(s)	inside rSNPs	diseases
2	nsv1060100	chr19:35658505-36170042	Weak transcription Bivalent Enhancer Enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Strong transcription Genic enhancers Active TSS Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	107 gene(s)	inside rSNPs	diseases
3	nsv543993	chr19:35658505-36170042	Enhancers Strong transcription Active TSS Weak transcription Bivalent Enhancer Flanking Active TSS Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	107 gene(s)	inside rSNPs	diseases
4	nsv911629	chr19:36122886-36136449	Flanking Active TSS Strong transcription Weak transcription Bivalent Enhancer Enhancers Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Genic enhancers Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region	16 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs4547459	AC002398.13	cis	Thyroid	GTEx

Chromatin state (count:125 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr19:36120600-36129800	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
2	chr19:36120800-36132400	Weak transcription	Fetal Heart	heart
3	chr19:36120800-36134000	Weak transcription	Pancreatic Islets	Pancreatic Islet
4	chr19:36121800-36130600	Strong transcription	Fetal Brain Female	brain
5	chr19:36122200-36132800	Weak transcription	Stomach Mucosa	stomach
6	chr19:36123000-36134000	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
7	chr19:36123400-36133600	Weak transcription	Fetal Brain Male	brain
8	chr19:36123600-36132200	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
9	chr19:36123800-36130000	Weak transcription	ES-I3 Cell Line	embryonic stem cell
10	chr19:36124000-36132200	Weak transcription	Primary T helper naive cells from peripheral blood	blood
11	chr19:36124200-36134000	Weak transcription	Psoas Muscle	Psoas
12	chr19:36128000-36134000	Weak transcription	HSMM	muscle
13	chr19:36128000-36134400	Weak transcription	Fetal Kidney	kidney
14	chr19:36128200-36132000	Weak transcription	Primary hematopoietic stem cells	blood
15	chr19:36128400-36129800	Strong transcription	Foreskin Fibroblast Primary Cells skin02	Skin
16	chr19:36128400-36132200	Weak transcription	Primary B cells from cord blood	blood
17	chr19:36128400-36132200	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
18	chr19:36128400-36132400	Weak transcription	NH-A	brain
19	chr19:36128800-36132200	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
20	chr19:36128800-36132200	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
21	chr19:36129000-36129800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
22	chr19:36129000-36129800	Weak transcription	HUES48 Cell Line	embryonic stem cell
23	chr19:36129000-36129800	Weak transcription	Adipose Nuclei	Adipose
24	chr19:36129000-36130200	Weak transcription	H9 Cell Line	embryonic stem cell
25	chr19:36129000-36132200	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
26	chr19:36129000-36132200	Weak transcription	Primary T killer memory cells from peripheral blood	blood
27	chr19:36129000-36132200	Weak transcription	Small Intestine	intestine
28	chr19:36129000-36132200	Weak transcription	HMEC	breast
29	chr19:36129000-36132200	Weak transcription	NHDF-Ad	bronchial
30	chr19:36129000-36132400	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
31	chr19:36129000-36132400	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
32	chr19:36129000-36132400	Weak transcription	Cortex derived primary cultured neurospheres	brain
33	chr19:36129000-36132400	Weak transcription	Sigmoid Colon	Sigmoid Colon
34	chr19:36129000-36132800	Weak transcription	Colonic Mucosa	Colon
35	chr19:36129000-36133200	Weak transcription	Duodenum Mucosa	Duodenum
36	chr19:36129000-36133400	Weak transcription	Esophagus	oesophagus
37	chr19:36129000-36133600	Weak transcription	Colon Smooth Muscle	Colon
38	chr19:36129000-36133800	Weak transcription	Rectal Smooth Muscle	rectum
39	chr19:36129000-36133800	Weak transcription	Hela-S3	cervix
40	chr19:36129000-36134000	Weak transcription	Aorta	Aorta
41	chr19:36129000-36134000	Weak transcription	Brain Cingulate Gyrus	brain
42	chr19:36129000-36134000	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
43	chr19:36129000-36134000	Weak transcription	Brain Substantia Nigra	brain
44	chr19:36129000-36134000	Weak transcription	Rectal Mucosa Donor 31	rectum
45	chr19:36129000-36134200	Weak transcription	Brain Angular Gyrus	brain
46	chr19:36129000-36134200	Weak transcription	HSMMtube	muscle
47	chr19:36129200-36129800	Weak transcription	iPS-15b Cell Line	embryonic stem cell
48	chr19:36129200-36129800	Weak transcription	K562	blood
49	chr19:36129200-36130000	Weak transcription	iPS-18 Cell Line	embryonic stem cell
50	chr19:36129200-36130200	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived

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