Variant report

Variant	rs2580764
Chromosome Location	chr2:55196956-55196957
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:26)
CpG islands
(count:0)
Chromatin interactive
region (count:1)
LncRNA
region (count:1)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:26 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	POLR2A	chr2:55193058-55197604	PANC-1	pancreas:	n/a	n/a
2	POLR2A	chr2:55196687-55197055	Hela-S3	cervix:	n/a	n/a
3	POLR2A	chr2:55196822-55197256	HCT-116	colon:	n/a	n/a
4	POLR2A	chr2:55195673-55197556	K562	blood:	n/a	n/a
5	POLR2A	chr2:55193400-55197464	Hela-S3	cervix:	n/a	n/a
6	POLR2A	chr2:55196379-55197561	HL-60	blood:	n/a	n/a
7	CCNT2	chr2:55196054-55197980	K562	blood:	n/a	n/a
8	POLR2A	chr2:55193200-55198888	A549	lung:	n/a	n/a
9	POLR2A	chr2:55196555-55196962	GM12878	blood:	n/a	n/a
10	POLR2A	chr2:55196938-55197652	SK-N-SH	brain:	n/a	n/a
11	POLR2A	chr2:55190471-55199022	SK-N-SH	brain:	n/a	n/a
12	POLR2A	chr2:55193167-55197152	U87	brain:	n/a	n/a
13	POLR2A	chr2:55196395-55197269	H1-neurons	neurons:	n/a	n/a
14	POLR2A	chr2:55190362-55199062	U87	brain:	n/a	n/a
15	PML	chr2:55196942-55197714	K562	blood:	n/a	n/a
16	POLR2A	chr2:55195607-55197627	H1-hESC	embryonic stem cell:	n/a	n/a
17	POLR2A	chr2:55194821-55197414	GM12891	blood:	n/a	n/a
18	POLR2A	chr2:55196658-55197510	GM12892	blood:	n/a	n/a
19	POLR2A	chr2:55193167-55197203	U87	brain:	n/a	n/a
20	POLR2A	chr2:55193277-55201440	K562	blood:	n/a	n/a
21	POLR2A	chr2:55196333-55197514	K562	blood:	n/a	n/a
22	POLR2A	chr2:55191336-55197109	HUVEC	blood vessel:	n/a	n/a
23	POLR2A	chr2:55194497-55197512	K562	blood:	n/a	n/a
24	POLR2A	chr2:55196518-55197561	HepG2	liver:	n/a	n/a
25	POLR2A	chr2:55193180-55198666	IMR90	lung:	n/a	n/a
26	POLR2A	chr2:55190362-55199105	U87	brain:	n/a	n/a

No data

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

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr2:55195869..55197384-chr2:55197903..55200472,2	K562	blood:

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

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-RTN4-1	chr2:55196736-55198803	ENSG00000248316

No data

Variant related genes	Relation type
EML6	TF binding region

Extended variants
information (count: 22 )
Associated
traits (count: 6 )

rSNPs within LD-proxies of this variant (count:20)

rs_ID	r²[population]
rs10174838	0.82[ASN][1000 genomes]
rs10210840	0.83[ASN][1000 genomes]
rs12713284	0.83[ASN][1000 genomes]
rs13387751	0.85[ASN][1000 genomes]
rs2015919	0.84[ASN][1000 genomes]
rs2255112	0.86[ASN][1000 genomes]
rs2580765	0.88[ASN][1000 genomes]
rs2580772	0.86[ASN][1000 genomes]
rs2580776	0.85[ASN][1000 genomes]
rs2588510	0.94[ASN][1000 genomes]
rs2588514	0.82[ASN][1000 genomes]
rs2588518	0.81[ASN][1000 genomes]
rs2588521	0.91[ASN][1000 genomes]
rs2919129	0.85[ASN][1000 genomes]
rs35826668	0.81[ASN][1000 genomes]
rs6545466	0.82[ASN][1000 genomes]
rs6726158	0.82[ASN][1000 genomes]
rs6760429	0.82[ASN][1000 genomes]
rs7340476	0.85[ASN][1000 genomes]
rs7562292	0.82[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	nsv834069	chr2:55096597-55251680	Weak transcription Enhancers Flanking Active TSS Genic enhancers Strong transcription Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	7 gene(s)	inside rSNPs	diseases
2	nsv582029	chr2:55159043-55204498	Enhancers Weak transcription Flanking Active TSS Strong transcription Genic enhancers Bivalent Enhancer Active TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	4 gene(s)	inside rSNPs	diseases

mRNA abundance (count:6)

SNP	Gene	Cis/trans	Tissue	Source
rs2580764	RTN4	cis	Thyroid	GTEx
rs2580764	RTN4	cis	Skin Sun Exposed Lower leg	GTEx
rs2580764	RTN4	cis	Artery Tibial	GTEx
rs2580764	RTN4	cis	Esophagus Mucosa	GTEx
rs2580764	RTN4	cis	Nerve Tibial	GTEx
rs2580764	RTN4	cis	Whole Blood	GTEx

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:55173200-55203400	Weak transcription	Gastric	stomach
2	chr2:55181600-55203400	Weak transcription	Ovary	ovary
3	chr2:55183200-55206800	Weak transcription	Stomach Mucosa	stomach
4	chr2:55184800-55214800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
5	chr2:55190000-55198400	Weak transcription	Colonic Mucosa	Colon
6	chr2:55190000-55203400	Weak transcription	Small Intestine	intestine
7	chr2:55190600-55198000	Genic enhancers	Fetal Muscle Leg	muscle
8	chr2:55191200-55198200	Strong transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
9	chr2:55191200-55199200	Weak transcription	Pancreatic Islets	Pancreatic Islet
10	chr2:55191800-55203600	Weak transcription	Fetal Lung	lung
11	chr2:55191800-55211600	Weak transcription	Placenta Amnion	Placenta Amnion
12	chr2:55191800-55234200	Weak transcription	H9 Cell Line	embryonic stem cell
13	chr2:55192200-55198600	Strong transcription	Fetal Stomach	stomach
14	chr2:55192600-55198600	Strong transcription	Fetal Intestine Small	intestine
15	chr2:55193400-55197400	Genic enhancers	Breast Myoepithelial Primary Cells	Breast
16	chr2:55193400-55199000	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
17	chr2:55193400-55201800	Strong transcription	Muscle Satellite Cultured Cells	--
18	chr2:55193400-55214800	Strong transcription	HepG2	liver
19	chr2:55193600-55197000	Weak transcription	Primary hematopoietic stem cells	blood
20	chr2:55193600-55197400	Genic enhancers	Fetal Muscle Trunk	muscle
21	chr2:55193600-55200800	Strong transcription	A549	lung
22	chr2:55193600-55201800	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
23	chr2:55193600-55214600	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
24	chr2:55193800-55197400	Enhancers	Psoas Muscle	Psoas
25	chr2:55193800-55198200	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
26	chr2:55193800-55198600	Genic enhancers	Lung	lung
27	chr2:55193800-55202400	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
28	chr2:55193800-55211800	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
29	chr2:55194000-55198600	Strong transcription	Brain Germinal Matrix	brain
30	chr2:55194000-55199000	Strong transcription	Stomach Smooth Muscle	stomach
31	chr2:55194000-55211800	Weak transcription	Primary T killer memory cells from peripheral blood	blood
32	chr2:55194200-55197000	Weak transcription	Hela-S3	cervix
33	chr2:55194200-55197200	Weak transcription	HUES64 Cell Line	embryonic stem cell
34	chr2:55194200-55197200	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
35	chr2:55194200-55197200	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
36	chr2:55194200-55197200	Weak transcription	K562	blood
37	chr2:55194200-55197400	Genic enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
38	chr2:55194200-55198600	Weak transcription	Primary T helper cells PMA-I stimulated	--
39	chr2:55194200-55204400	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
40	chr2:55194400-55197000	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
41	chr2:55194400-55197200	Weak transcription	Primary T helper naive cells from peripheral blood	blood
42	chr2:55194400-55197200	Weak transcription	Liver	Liver
43	chr2:55194400-55197400	Weak transcription	H1 Cell Line	embryonic stem cell
44	chr2:55194400-55197600	Weak transcription	Primary T helper cells fromperipheralblood	blood
45	chr2:55194400-55198200	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
46	chr2:55194400-55200200	Strong transcription	Primary neutrophils fromperipheralblood	blood
47	chr2:55194400-55200200	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
48	chr2:55194400-55201400	Strong transcription	Primary B cells from cord blood	blood
49	chr2:55194600-55202200	Strong transcription	NHDF-Ad	bronchial
50	chr2:55194600-55204400	Strong transcription	Primary T cells from cord blood	blood

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