Variant report

Variant	rs2588510
Chromosome Location	chr2:55199248-55199249
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr2:55190781..55193657-chr2:55198367..55200199,2	K562	blood:
2	chr2:55198243..55200430-chr2:55275521..55278393,2	MCF-7	breast:
3	chr2:55198988..55201900-chr2:55213351..55214997,2	MCF-7	breast:
4	chr2:55195869..55197384-chr2:55197903..55200472,2	K562	blood:

Variant related genes	Relation type
ENSG00000214595	Chromatin interaction
ENSG00000115310	Chromatin interaction

Extended variants
information (count: 43 )
Associated
traits (count: 9 )

rSNPs within LD-proxies of this variant (count:41)

rs_ID	r²[population]
rs10174838	0.86[AMR][1000 genomes];0.83[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs10210840	0.95[CHB][hapmap];1.00[JPT][hapmap];0.81[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs12713284	0.95[CHB][hapmap];1.00[JPT][hapmap];0.89[AMR][1000 genomes];0.84[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs13387751	0.95[CHB][hapmap];0.95[JPT][hapmap];0.90[AMR][1000 genomes];0.83[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2015919	0.89[AMR][1000 genomes];0.81[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs2044291	0.87[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs2255112	0.91[ASW][hapmap];0.96[CEU][hapmap];0.86[CHB][hapmap];0.85[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];0.88[LWK][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.90[AFR][1000 genomes];0.99[AMR][1000 genomes];0.97[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2255393	0.90[JPT][hapmap];0.82[ASN][1000 genomes]
rs2580764	0.94[ASN][1000 genomes]
rs2580765	0.91[ASW][hapmap];0.96[CEU][hapmap];0.91[CHB][hapmap];0.90[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];0.96[MEX][hapmap];1.00[TSI][hapmap];0.94[AMR][1000 genomes];0.94[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2580772	1.00[ASW][hapmap];0.95[CHB][hapmap];0.83[CHD][hapmap];0.93[GIH][hapmap];1.00[JPT][hapmap];0.94[LWK][hapmap];0.91[MEX][hapmap];0.97[MKK][hapmap];0.95[TSI][hapmap];0.92[AMR][1000 genomes];0.86[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2580773	0.90[AMR][1000 genomes]
rs2580776	0.88[AMR][1000 genomes];0.84[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2588514	0.84[AFR][1000 genomes];0.88[AMR][1000 genomes];0.84[ASN][1000 genomes]
rs2588517	0.95[CHB][hapmap];0.82[ASN][1000 genomes]
rs2588518	0.82[CHB][hapmap];0.88[CHD][hapmap];0.95[JPT][hapmap];0.84[ASN][1000 genomes]
rs2588519	0.86[JPT][hapmap]
rs2588521	0.96[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.98[AMR][1000 genomes];0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2860453	0.83[CHB][hapmap];1.00[JPT][hapmap];0.84[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs2919129	0.91[ASW][hapmap];0.87[CHB][hapmap];0.92[CHD][hapmap];0.90[GIH][hapmap];0.95[JPT][hapmap];0.96[MEX][hapmap];0.95[TSI][hapmap];0.93[AMR][1000 genomes];0.86[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2920893	0.84[AMR][1000 genomes]
rs2968786	0.91[CHB][hapmap];1.00[JPT][hapmap];0.80[EUR][1000 genomes]
rs2968787	0.83[CHB][hapmap];1.00[JPT][hapmap]
rs2968794	0.82[TSI][hapmap]
rs2968804	0.86[JPT][hapmap]
rs2972072	0.82[TSI][hapmap]
rs2972090	0.91[CHB][hapmap];0.82[JPT][hapmap]
rs2972097	0.83[CHB][hapmap];1.00[JPT][hapmap]
rs35631428	0.82[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs35826668	0.84[ASN][1000 genomes]
rs3806570	0.82[ASN][1000 genomes]
rs4672005	0.84[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs6545466	0.87[CHB][hapmap];1.00[JPT][hapmap];0.88[AMR][1000 genomes];0.84[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs6726158	0.83[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs6755468	0.83[ASW][hapmap];0.95[CHB][hapmap];0.85[CHD][hapmap];0.87[GIH][hapmap];0.95[JPT][hapmap];0.83[LWK][hapmap];0.91[MEX][hapmap];0.95[TSI][hapmap];0.86[AMR][1000 genomes];0.83[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs6760429	0.87[CHB][hapmap];1.00[JPT][hapmap];0.88[AMR][1000 genomes];0.84[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs7340476	0.95[CHB][hapmap];0.95[JPT][hapmap];0.90[AMR][1000 genomes];0.83[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs7562292	0.87[CHB][hapmap];1.00[JPT][hapmap];0.88[AMR][1000 genomes];0.83[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs7570629	0.91[CHB][hapmap];1.00[JPT][hapmap]
rs7584430	0.81[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs968998	0.95[CHB][hapmap]

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:9)

SNP	Gene	Cis/trans	Tissue	Source
rs2588510	TSPYL6	cis	cerebellum	SCAN
rs2588510	RTN4	cis	Artery Aorta	GTEx
rs2588510	RTN4	cis	Artery Tibial	GTEx
rs2588510	RTN4	cis	Whole Blood	GTEx
rs2588510	RTN4	cis	Nerve Tibial	GTEx
rs2588510	RTN4	cis	Thyroid	GTEx
rs2588510	RTN4	cis	Adipose Subcutaneous	GTEx
rs2588510	RTN4	cis	Esophagus Mucosa	GTEx
rs2588510	RTN4	cis	Skin Sun Exposed Lower leg	GTEx

Chromatin state (count:124 , 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	chr2:55190000-55203400	Weak transcription	Small Intestine	intestine
6	chr2:55191800-55203600	Weak transcription	Fetal Lung	lung
7	chr2:55191800-55211600	Weak transcription	Placenta Amnion	Placenta Amnion
8	chr2:55191800-55234200	Weak transcription	H9 Cell Line	embryonic stem cell
9	chr2:55193400-55201800	Strong transcription	Muscle Satellite Cultured Cells	--
10	chr2:55193400-55214800	Strong transcription	HepG2	liver
11	chr2:55193600-55200800	Strong transcription	A549	lung
12	chr2:55193600-55201800	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
13	chr2:55193600-55214600	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
14	chr2:55193800-55202400	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
15	chr2:55193800-55211800	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
16	chr2:55194000-55211800	Weak transcription	Primary T killer memory cells from peripheral blood	blood
17	chr2:55194200-55204400	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
18	chr2:55194400-55200200	Strong transcription	Primary neutrophils fromperipheralblood	blood
19	chr2:55194400-55200200	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
20	chr2:55194400-55201400	Strong transcription	Primary B cells from cord blood	blood
21	chr2:55194600-55202200	Strong transcription	NHDF-Ad	bronchial
22	chr2:55194600-55204400	Strong transcription	Primary T cells from cord blood	blood
23	chr2:55194800-55201200	Strong transcription	Primary B cells from peripheral blood	blood
24	chr2:55194800-55202400	Strong transcription	NHLF	lung
25	chr2:55195000-55199600	Strong transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
26	chr2:55195000-55203200	Strong transcription	Primary hematopoietic stem cells short term culture	blood
27	chr2:55195000-55215200	Strong transcription	Dnd41	blood
28	chr2:55195200-55201200	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
29	chr2:55195200-55201600	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
30	chr2:55195200-55202000	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
31	chr2:55195200-55202600	Strong transcription	Osteobl	bone
32	chr2:55195200-55205600	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
33	chr2:55195200-55205800	Strong transcription	HMEC	breast
34	chr2:55195400-55199400	Strong transcription	Fetal Intestine Large	intestine
35	chr2:55195400-55202200	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
36	chr2:55195400-55205200	Strong transcription	Monocytes-CD14+_RO01746	blood
37	chr2:55195600-55210800	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
38	chr2:55195800-55199600	Enhancers	Fetal Heart	heart
39	chr2:55195800-55216200	Weak transcription	iPS-15b Cell Line	embryonic stem cell
40	chr2:55196000-55202200	Strong transcription	NH-A	brain
41	chr2:55196000-55203400	Weak transcription	Pancreas	Pancrea
42	chr2:55196000-55205800	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
43	chr2:55196200-55199400	Strong transcription	Foreskin Fibroblast Primary Cells skin01	Skin
44	chr2:55196200-55200800	Weak transcription	Brain Anterior Caudate	brain
45	chr2:55196200-55202600	Strong transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
46	chr2:55196200-55202600	Enhancers	Skeletal Muscle Male	skeletal muscle
47	chr2:55196200-55203400	Weak transcription	Right Atrium	heart
48	chr2:55196200-55214600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
49	chr2:55196200-55226400	Weak transcription	Thymus	Thymus
50	chr2:55196400-55199400	Strong transcription	Rectal Mucosa Donor 31	rectum

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