Variant report

Variant	rs2588517
Chromosome Location	chr2:55220960-55220961
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr2:55214294..55216592-chr2:55220369..55222757,2	K562	blood:
2	chr2:55220380..55222677-chr2:55274921..55277767,2	MCF-7	breast:
3	chr2:55219389..55222736-chr2:55233484..55237490,3	MCF-7	breast:

Variant related genes	Relation type
ENSG00000115310	Chromatin interaction

Extended variants
information (count: 44 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:42)

rs_ID	r²[population]
rs10174838	0.92[ASN][1000 genomes]
rs10210840	1.00[CHB][hapmap];0.91[ASN][1000 genomes]
rs10496037	0.83[MKK][hapmap];0.83[YRI][hapmap]
rs12464070	0.82[ASN][1000 genomes]
rs12477711	0.84[ASN][1000 genomes]
rs12713284	1.00[CHB][hapmap];0.89[ASN][1000 genomes]
rs13387751	1.00[CHB][hapmap];0.82[JPT][hapmap];0.92[ASN][1000 genomes]
rs2015919	0.87[ASN][1000 genomes]
rs2044291	0.84[ASN][1000 genomes]
rs2255112	0.82[CHB][hapmap];0.82[CHD][hapmap];0.84[ASN][1000 genomes]
rs2580765	0.86[CHB][hapmap];0.82[CHD][hapmap];0.84[ASN][1000 genomes]
rs2580772	1.00[CHB][hapmap];0.81[CHD][hapmap];0.92[ASN][1000 genomes]
rs2580776	0.93[ASN][1000 genomes]
rs2588510	0.95[CHB][hapmap];0.82[ASN][1000 genomes]
rs2588514	0.81[ASN][1000 genomes]
rs2588518	0.86[CHB][hapmap];0.85[CHD][hapmap];0.82[JPT][hapmap];0.80[LWK][hapmap];0.90[ASN][1000 genomes]
rs2588519	0.94[ASW][hapmap];0.87[CHD][hapmap];0.98[GIH][hapmap];0.80[JPT][hapmap];0.84[LWK][hapmap];0.91[MEX][hapmap];0.98[MKK][hapmap];0.93[TSI][hapmap];0.89[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs2588521	1.00[CHB][hapmap];0.87[ASN][1000 genomes]
rs2860453	0.87[CHB][hapmap]
rs2902649	0.84[ASN][1000 genomes]
rs2919129	0.91[CHB][hapmap];0.85[CHD][hapmap];0.82[JPT][hapmap];0.88[ASN][1000 genomes]
rs2968786	0.95[CHB][hapmap];0.83[ASN][1000 genomes]
rs2968787	0.87[CHB][hapmap];0.80[ASN][1000 genomes]
rs2968791	0.83[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs2968804	0.80[JPT][hapmap];0.89[AMR][1000 genomes];0.88[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs2972090	1.00[CEU][hapmap];0.95[CHB][hapmap];0.95[JPT][hapmap];0.87[YRI][hapmap];0.83[AFR][1000 genomes];0.93[AMR][1000 genomes];0.92[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2972097	0.87[CHB][hapmap]
rs35631428	0.87[ASN][1000 genomes]
rs35826668	0.87[ASN][1000 genomes]
rs3806570	0.88[ASN][1000 genomes]
rs4358163	0.81[LWK][hapmap]
rs4672005	0.84[ASN][1000 genomes]
rs6545466	0.91[CHB][hapmap];0.88[ASN][1000 genomes]
rs6713935	0.95[LWK][hapmap];0.96[YRI][hapmap];0.88[AFR][1000 genomes]
rs6726158	0.91[ASN][1000 genomes]
rs6755468	1.00[CHB][hapmap];0.82[CHD][hapmap];0.82[JPT][hapmap];0.88[ASN][1000 genomes]
rs6760429	0.91[CHB][hapmap];0.88[ASN][1000 genomes]
rs7340476	1.00[CHB][hapmap];0.82[JPT][hapmap];0.92[ASN][1000 genomes]
rs7562292	0.91[CHB][hapmap];0.88[ASN][1000 genomes]
rs7570629	0.95[CHB][hapmap]
rs7584430	0.82[ASN][1000 genomes]
rs968998	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[AFR][1000 genomes];0.94[AMR][1000 genomes];0.91[EUR][1000 genomes];0.97[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	nsv874155	chr2:55205262-55307646	Weak transcription Enhancers Flanking Active TSS Active TSS Strong transcription Transcr. at gene 5' and 3' ZNF genes & repeats Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	37 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs2588517	RTN4	cis	Artery Tibial	GTEx
rs2588517	CCDC88A	cis	cerebellum	SCAN
rs2588517	RTN4	cis	Thyroid	GTEx

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:55191800-55234200	Weak transcription	H9 Cell Line	embryonic stem cell
2	chr2:55196200-55226400	Weak transcription	Thymus	Thymus
3	chr2:55198200-55237200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
4	chr2:55203800-55222600	Weak transcription	Spleen	Spleen
5	chr2:55203800-55223800	Weak transcription	Pancreas	Pancrea
6	chr2:55203800-55258400	Weak transcription	Esophagus	oesophagus
7	chr2:55205200-55223800	Weak transcription	Left Ventricle	heart
8	chr2:55210000-55228200	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
9	chr2:55211200-55232000	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
10	chr2:55212600-55226400	Weak transcription	Fetal Stomach	stomach
11	chr2:55213800-55226400	Weak transcription	Ovary	ovary
12	chr2:55214200-55224600	Weak transcription	Primary T cells from cord blood	blood
13	chr2:55214200-55225000	Weak transcription	Sigmoid Colon	Sigmoid Colon
14	chr2:55214200-55234400	Weak transcription	Fetal Muscle Trunk	muscle
15	chr2:55214400-55222800	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
16	chr2:55214400-55232800	Weak transcription	Fetal Brain Female	brain
17	chr2:55214600-55225600	Weak transcription	NH-A	brain
18	chr2:55214600-55226000	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
19	chr2:55214800-55221600	Weak transcription	HSMMtube	muscle
20	chr2:55214800-55221800	Weak transcription	Primary B cells from peripheral blood	blood
21	chr2:55214800-55222000	Weak transcription	GM12878-XiMat	blood
22	chr2:55214800-55223600	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
23	chr2:55214800-55223800	Weak transcription	Gastric	stomach
24	chr2:55214800-55224400	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
25	chr2:55214800-55224400	Weak transcription	Rectal Mucosa Donor 31	rectum
26	chr2:55214800-55224600	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
27	chr2:55214800-55225000	Weak transcription	Primary monocytes fromperipheralblood	blood
28	chr2:55214800-55225000	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
29	chr2:55214800-55225200	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
30	chr2:55214800-55225200	Weak transcription	Fetal Brain Male	brain
31	chr2:55214800-55225600	Weak transcription	Primary neutrophils fromperipheralblood	blood
32	chr2:55214800-55225600	Weak transcription	Brain Germinal Matrix	brain
33	chr2:55214800-55226000	Weak transcription	HUVEC	blood vessel
34	chr2:55214800-55226400	Weak transcription	Fetal Muscle Leg	muscle
35	chr2:55214800-55226400	Weak transcription	Fetal Thymus	thymus
36	chr2:55214800-55227200	Weak transcription	ES-I3 Cell Line	embryonic stem cell
37	chr2:55214800-55227200	Weak transcription	HepG2	liver
38	chr2:55214800-55228800	Weak transcription	Fetal Intestine Large	intestine
39	chr2:55214800-55230600	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
40	chr2:55214800-55231600	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
41	chr2:55214800-55234200	Weak transcription	HUES6 Cell Line	embryonic stem cell
42	chr2:55214800-55236800	Weak transcription	Primary T cells fromperipheralblood	blood
43	chr2:55215000-55222600	Weak transcription	Primary T helper cells fromperipheralblood	blood
44	chr2:55215000-55225200	Weak transcription	Liver	Liver
45	chr2:55215000-55225800	Weak transcription	Primary B cells from cord blood	blood
46	chr2:55215000-55225800	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
47	chr2:55215000-55225800	Weak transcription	Hela-S3	cervix
48	chr2:55215200-55225000	Weak transcription	Monocytes-CD14+_RO01746	blood
49	chr2:55215200-55225400	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
50	chr2:55215200-55227200	Weak transcription	iPS-20b Cell Line	embryonic stem cell

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