Variant report

Variant	rs2580763
Chromosome Location	chr2:55193667-55193668
allele	C/G
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	chr2:55193161-55194898	H1-neurons	neurons:	n/a	n/a
2	POLR2A	chr2:55193058-55197604	PANC-1	pancreas:	n/a	n/a
3	POLR2A	chr2:55192057-55196307	SK-N-SH	brain:	n/a	n/a
4	POLR2A	chr2:55193400-55197464	Hela-S3	cervix:	n/a	n/a
5	POLR2A	chr2:55193200-55198888	A549	lung:	n/a	n/a
6	POLR2A	chr2:55190471-55199022	SK-N-SH	brain:	n/a	n/a
7	POLR2A	chr2:55193419-55193879	HUVEC	blood vessel:	n/a	n/a
8	POLR2A	chr2:55193167-55197152	U87	brain:	n/a	n/a
9	POLR2A	chr2:55193371-55193715	MCF-7	breast:	n/a	n/a
10	POLR2A	chr2:55190362-55199062	U87	brain:	n/a	n/a
11	POLR2A	chr2:55193660-55194241	HCT-116	colon:	n/a	n/a
12	POLR2A	chr2:55193660-55194216	GM12878	blood:	n/a	n/a
13	TFAP2C	chr2:55193220-55193688	Hela-S3	cervix:	n/a	chr2:55193469-55193484
14	POLR2A	chr2:55193545-55194166	HUVEC	blood vessel:	n/a	n/a
15	POLR2A	chr2:55193167-55197203	U87	brain:	n/a	n/a
16	POLR2A	chr2:55193277-55201440	K562	blood:	n/a	n/a
17	POLR2A	chr2:55193084-55194227	HUVEC	blood vessel:	n/a	n/a
18	POLR2A	chr2:55193505-55194349	PANC-1	pancreas:	n/a	n/a
19	POLR2A	chr2:55191336-55197109	HUVEC	blood vessel:	n/a	n/a
20	POLR2A	chr2:55193251-55193758	HUVEC	blood vessel:	n/a	n/a
21	POLR2A	chr2:55193286-55194555	SK-N-MC	brain:	n/a	n/a
22	TFAP2A	chr2:55193274-55193691	Hela-S3	cervix:	n/a	chr2:55193469-55193484
23	POLR2A	chr2:55193180-55198666	IMR90	lung:	n/a	n/a
24	POLR2A	chr2:55190362-55199105	U87	brain:	n/a	n/a
25	HDAC2	chr2:55193257-55193729	MCF-7	breast:	n/a	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr2:55192020..55193773-chr2:55201950..55203496,2	K562	blood:
2	chr2:55130491..55133378-chr2:55191719..55193881,2	MCF-7	breast:

Variant related genes	Relation type
EML6	TF binding region

Extended variants
information (count: 34 )
Associated
traits (count: 1 )

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

rs_ID	r²[population]
rs10179594	0.85[JPT][hapmap];0.85[EUR][1000 genomes]
rs10198636	0.98[ASN][1000 genomes]
rs10205017	0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11125551	0.83[AMR][1000 genomes]
rs12989576	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AMR][1000 genomes];0.93[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs13002841	1.00[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs13023202	1.00[AMR][1000 genomes];0.91[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2580766	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2588520	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2919125	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2920839	0.87[EUR][1000 genomes]
rs2920861	0.83[EUR][1000 genomes]
rs2920863	0.80[EUR][1000 genomes]
rs2920883	0.85[JPT][hapmap];0.84[EUR][1000 genomes]
rs2920884	0.85[JPT][hapmap];0.81[EUR][1000 genomes]
rs2920889	0.80[EUR][1000 genomes]
rs2920890	0.80[EUR][1000 genomes]
rs2920897	0.93[JPT][hapmap];0.85[EUR][1000 genomes]
rs2920898	0.86[CHB][hapmap];1.00[JPT][hapmap]
rs2968789	0.93[JPT][hapmap];0.85[EUR][1000 genomes]
rs2968812	0.84[JPT][hapmap]
rs2968813	0.85[JPT][hapmap]
rs2968814	0.85[JPT][hapmap]
rs2968823	0.80[EUR][1000 genomes]
rs2968824	0.80[EUR][1000 genomes]
rs2968826	0.83[EUR][1000 genomes]
rs2968831	0.86[EUR][1000 genomes]
rs2972066	0.80[EUR][1000 genomes]
rs2972069	0.80[EUR][1000 genomes]
rs2972076	0.87[EUR][1000 genomes]
rs4671998	0.83[AMR][1000 genomes]
rs7559248	0.85[EUR][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:1)

SNP	Gene	Cis/trans	Tissue	Source
rs2580763	RTN4	cis	Thyroid	GTEx

Chromatin state (count:112 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:55173200-55203400	Weak transcription	Gastric	stomach
2	chr2:55173600-55194000	Weak transcription	Stomach Smooth Muscle	stomach
3	chr2:55173600-55195000	Weak transcription	Pancreas	Pancrea
4	chr2:55174800-55194000	Weak transcription	Brain Germinal Matrix	brain
5	chr2:55175600-55194600	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
6	chr2:55175800-55193800	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
7	chr2:55177800-55193800	Weak transcription	Cortex derived primary cultured neurospheres	brain
8	chr2:55180600-55195400	Weak transcription	Monocytes-CD14+_RO01746	blood
9	chr2:55180600-55196000	Weak transcription	NH-A	brain
10	chr2:55181600-55203400	Weak transcription	Ovary	ovary
11	chr2:55183200-55206800	Weak transcription	Stomach Mucosa	stomach
12	chr2:55183400-55196600	Weak transcription	Duodenum Smooth Muscle	Duodenum
13	chr2:55184800-55195800	Weak transcription	Thymus	Thymus
14	chr2:55184800-55214800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
15	chr2:55185200-55194000	Weak transcription	H1 Cell Line	embryonic stem cell
16	chr2:55186000-55194400	Weak transcription	Primary B cells from cord blood	blood
17	chr2:55186400-55193800	Weak transcription	Brain Angular Gyrus	brain
18	chr2:55187000-55195000	Weak transcription	Dnd41	blood
19	chr2:55187600-55194200	Weak transcription	Brain Cingulate Gyrus	brain
20	chr2:55190000-55198400	Weak transcription	Colonic Mucosa	Colon
21	chr2:55190000-55203400	Weak transcription	Small Intestine	intestine
22	chr2:55190400-55194400	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
23	chr2:55190600-55198000	Genic enhancers	Fetal Muscle Leg	muscle
24	chr2:55190800-55194400	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
25	chr2:55190800-55194400	Enhancers	Primary T regulatory cells fromperipheralblood	blood
26	chr2:55190800-55196600	Weak transcription	Rectal Mucosa Donor 29	rectum
27	chr2:55191000-55193800	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
28	chr2:55191000-55194200	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
29	chr2:55191000-55194200	Enhancers	Primary T helper cells PMA-I stimulated	--
30	chr2:55191000-55194400	Enhancers	Primary T helper cells fromperipheralblood	blood
31	chr2:55191200-55194200	Enhancers	Primary T helper 17 cells PMA-I stimulated	--
32	chr2:55191200-55195400	Weak transcription	Sigmoid Colon	Sigmoid Colon
33	chr2:55191200-55198200	Strong transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
34	chr2:55191200-55199200	Weak transcription	Pancreatic Islets	Pancreatic Islet
35	chr2:55191400-55194400	Enhancers	Primary T helper naive cells from peripheral blood	blood
36	chr2:55191400-55194400	Enhancers	Primary T cells effector/memory enriched fromperipheralblood	blood
37	chr2:55191400-55195400	Weak transcription	Fetal Intestine Large	intestine
38	chr2:55191600-55194000	Enhancers	Primary T killer memory cells from peripheral blood	blood
39	chr2:55191600-55194200	Enhancers	Primary T cells fromperipheralblood	blood
40	chr2:55191600-55194400	Weak transcription	Primary neutrophils fromperipheralblood	blood
41	chr2:55191800-55194400	Enhancers	Primary T helper naive cells fromperipheralblood	blood
42	chr2:55191800-55203600	Weak transcription	Fetal Lung	lung
43	chr2:55191800-55211600	Weak transcription	Placenta Amnion	Placenta Amnion
44	chr2:55191800-55234200	Weak transcription	H9 Cell Line	embryonic stem cell
45	chr2:55192000-55193800	Enhancers	Primary T killer naive cells fromperipheralblood	blood
46	chr2:55192000-55194000	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
47	chr2:55192000-55194200	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
48	chr2:55192200-55194200	Enhancers	Esophagus	oesophagus
49	chr2:55192200-55194800	Enhancers	HUVEC	blood vessel
50	chr2:55192200-55195000	Enhancers	HUES6 Cell Line	embryonic stem cell

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