Variant report

Variant	rs2539980
Chromosome Location	chr2:63208460-63208461
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr2:63168550..63170983-chr2:63208224..63209824,2	K562	blood:

Variant related genes	Relation type
ENSG00000115504	Chromatin interaction

Extended variants
information (count: 52 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:47)

rs_ID	r²[population]
rs10173115	0.81[CHB][hapmap]
rs1022110	0.92[CEU][hapmap]
rs11682530	0.92[CEU][hapmap];1.00[CHB][hapmap];0.94[CHD][hapmap];0.87[GIH][hapmap];0.93[JPT][hapmap];0.84[TSI][hapmap];0.88[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs11688816	0.95[CHB][hapmap];0.91[CHD][hapmap];0.92[JPT][hapmap];0.84[ASN][1000 genomes]
rs11890276	0.81[CHB][hapmap]
rs11893131	0.96[CEU][hapmap];0.85[EUR][1000 genomes]
rs12713467	0.81[ASN][1000 genomes]
rs12713468	0.83[ASN][1000 genomes]
rs12713469	0.84[ASW][hapmap];0.85[CHB][hapmap];0.91[CHD][hapmap];0.90[LWK][hapmap]
rs12989754	0.96[CEU][hapmap];1.00[CHB][hapmap];0.94[CHD][hapmap];0.94[GIH][hapmap];0.93[JPT][hapmap];0.85[MEX][hapmap];0.85[TSI][hapmap];0.84[ASN][1000 genomes]
rs12994674	0.84[ASN][1000 genomes]
rs13013218	0.96[CEU][hapmap];1.00[CHB][hapmap];0.84[CHD][hapmap];0.94[GIH][hapmap];0.85[JPT][hapmap];0.90[MEX][hapmap];0.87[TSI][hapmap];0.84[ASN][1000 genomes]
rs13418889	0.81[EUR][1000 genomes]
rs1420018	0.91[CEU][hapmap];1.00[CHB][hapmap];0.93[JPT][hapmap];0.86[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs1468748	1.00[CEU][hapmap];0.91[GIH][hapmap];0.87[TSI][hapmap];0.88[EUR][1000 genomes]
rs1553832	0.92[CEU][hapmap];1.00[CHB][hapmap];0.93[JPT][hapmap];0.84[ASN][1000 genomes]
rs17027429	1.00[CEU][hapmap];0.87[GIH][hapmap];0.87[TSI][hapmap];0.85[EUR][1000 genomes]
rs1828398	1.00[CEU][hapmap];0.80[EUR][1000 genomes]
rs2058566	0.96[CEU][hapmap];1.00[CHB][hapmap];0.91[CHD][hapmap];0.94[GIH][hapmap];0.93[JPT][hapmap];0.86[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2058567	0.85[EUR][1000 genomes]
rs2080227	0.80[CEU][hapmap]
rs2215870	0.96[CEU][hapmap];1.00[CHB][hapmap];0.94[CHD][hapmap];0.94[GIH][hapmap];0.92[JPT][hapmap];0.85[MEX][hapmap];0.89[TSI][hapmap];0.90[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2421816	0.96[CEU][hapmap];0.84[GIH][hapmap];0.82[TSI][hapmap];0.82[EUR][1000 genomes]
rs2430388	0.96[CEU][hapmap];0.90[CHB][hapmap];0.91[CHD][hapmap];0.94[GIH][hapmap];0.93[JPT][hapmap];0.90[MEX][hapmap];0.87[TSI][hapmap];0.88[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs2539978	0.94[ASW][hapmap];0.96[CEU][hapmap];0.94[GIH][hapmap];1.00[LWK][hapmap];0.89[MKK][hapmap];0.91[TSI][hapmap];1.00[YRI][hapmap];0.91[AFR][1000 genomes];0.86[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs2539985	0.87[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2539987	0.96[CEU][hapmap];0.94[CHB][hapmap];0.88[CHD][hapmap];0.94[GIH][hapmap];0.81[MEX][hapmap];0.86[TSI][hapmap]
rs2710637	0.92[CEU][hapmap];0.87[GIH][hapmap];0.85[EUR][1000 genomes]
rs2710638	0.94[CHB][hapmap];0.90[CHD][hapmap];0.93[JPT][hapmap];0.84[ASN][1000 genomes]
rs2710639	0.92[CEU][hapmap]
rs2710640	0.89[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2710642	0.96[CEU][hapmap];1.00[CHB][hapmap];0.94[CHD][hapmap];0.91[GIH][hapmap];0.93[JPT][hapmap];0.84[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2710644	0.81[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs2710647	0.90[CHB][hapmap];0.97[CHD][hapmap];0.85[MKK][hapmap]
rs3927201	0.84[ASN][1000 genomes]
rs4461246	0.96[CEU][hapmap];1.00[CHB][hapmap];0.94[CHD][hapmap];0.94[GIH][hapmap];0.93[JPT][hapmap];0.90[MEX][hapmap];0.89[TSI][hapmap];0.83[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs6545971	1.00[CEU][hapmap];0.89[CHB][hapmap];0.92[JPT][hapmap];0.88[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs6545972	1.00[CEU][hapmap];0.87[GIH][hapmap];0.87[TSI][hapmap];0.85[EUR][1000 genomes]
rs6545973	0.96[CEU][hapmap];0.84[GIH][hapmap];0.80[TSI][hapmap];0.82[EUR][1000 genomes]
rs6705798	0.92[CEU][hapmap];0.84[GIH][hapmap]
rs6714241	0.84[ASW][hapmap];0.88[LWK][hapmap];0.86[YRI][hapmap]
rs6739804	0.92[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];0.94[GIH][hapmap];0.85[JPT][hapmap];0.90[MEX][hapmap];0.87[MKK][hapmap];0.85[TSI][hapmap];0.83[EUR][1000 genomes]
rs7557501	1.00[CEU][hapmap];0.87[GIH][hapmap];0.87[TSI][hapmap];0.85[EUR][1000 genomes]
rs7567923	1.00[CEU][hapmap];0.87[GIH][hapmap];0.86[TSI][hapmap];0.85[EUR][1000 genomes]
rs7573756	0.84[ASN][1000 genomes]
rs9678329	0.81[ASN][1000 genomes]
rs9973612	0.96[CEU][hapmap]

Variant overlapped rSNPs/rCNVs (count:5 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv535767	chr2:62461582-63413596	Bivalent Enhancer Strong transcription Weak transcription Enhancers Active TSS Flanking Bivalent TSS/Enh Flanking Active TSS Bivalent/Poised TSS ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	50 gene(s)	inside rSNPs	diseases
2	esv3417336	chr2:62957866-63749654	Strong transcription Enhancers Weak transcription Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh Flanking Active TSS Genic enhancers Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	18 gene(s)	inside rSNPs	diseases
3	nsv1006848	chr2:63061816-63631407	Weak transcription Strong transcription Bivalent Enhancer Genic enhancers ZNF genes & repeats Enhancers Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Flanking Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	15 gene(s)	inside rSNPs	diseases
4	esv2756598	chr2:63085848-63491438	Strong transcription Bivalent/Poised TSS Weak transcription Enhancers Flanking Bivalent TSS/Enh Flanking Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer Active TSS ZNF genes & repeats Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	15 gene(s)	inside rSNPs	diseases
5	esv3340700	chr2:63127412-63534998	Bivalent Enhancer Enhancers Weak transcription Active TSS Flanking Active TSS Strong transcription Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	14 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs2539980	VPS54	cis	cerebellum	SCAN

Chromatin state (count:114 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:63151400-63208800	Weak transcription	Sigmoid Colon	Sigmoid Colon
2	chr2:63151400-63272200	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
3	chr2:63154400-63209000	Weak transcription	Rectal Mucosa Donor 31	rectum
4	chr2:63155400-63209000	Weak transcription	Psoas Muscle	Psoas
5	chr2:63165200-63209200	Weak transcription	Aorta	Aorta
6	chr2:63167600-63256000	Weak transcription	HSMMtube	muscle
7	chr2:63167800-63225800	Weak transcription	Muscle Satellite Cultured Cells	--
8	chr2:63168200-63220200	Weak transcription	Rectal Smooth Muscle	rectum
9	chr2:63169600-63228800	Weak transcription	GM12878-XiMat	blood
10	chr2:63169800-63208600	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
11	chr2:63169800-63237000	Weak transcription	Primary T helper cells PMA-I stimulated	--
12	chr2:63170400-63255600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
13	chr2:63171400-63209800	Weak transcription	Brain Anterior Caudate	brain
14	chr2:63171800-63208600	Weak transcription	Primary B cells from peripheral blood	blood
15	chr2:63171800-63218600	Weak transcription	Brain Hippocampus Middle	brain
16	chr2:63171800-63233000	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
17	chr2:63173800-63225800	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
18	chr2:63175000-63209000	Weak transcription	Fetal Thymus	thymus
19	chr2:63176200-63208800	Weak transcription	NH-A	brain
20	chr2:63176200-63220200	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
21	chr2:63177800-63226800	Weak transcription	Hela-S3	cervix
22	chr2:63179600-63219800	Weak transcription	Primary hematopoietic stem cells short term culture	blood
23	chr2:63182000-63228800	Weak transcription	H9 Cell Line	embryonic stem cell
24	chr2:63182600-63215800	Strong transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
25	chr2:63183400-63218600	Weak transcription	Brain Substantia Nigra	brain
26	chr2:63184000-63208800	Weak transcription	Left Ventricle	heart
27	chr2:63190400-63228800	Weak transcription	Gastric	stomach
28	chr2:63194600-63216000	Weak transcription	Fetal Brain Male	brain
29	chr2:63194600-63223600	Weak transcription	K562	blood
30	chr2:63194600-63223800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
31	chr2:63197200-63208600	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
32	chr2:63197200-63225400	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
33	chr2:63197600-63234800	Strong transcription	HepG2	liver
34	chr2:63197800-63227800	Strong transcription	Liver	Liver
35	chr2:63198000-63211600	Weak transcription	Fetal Heart	heart
36	chr2:63198800-63218800	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
37	chr2:63199800-63258200	Weak transcription	Lung	lung
38	chr2:63200800-63239400	Weak transcription	Primary T helper naive cells from peripheral blood	blood
39	chr2:63201400-63223800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
40	chr2:63203600-63225800	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
41	chr2:63203800-63210800	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
42	chr2:63204400-63210600	Strong transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
43	chr2:63204600-63208600	Weak transcription	iPS-18 Cell Line	embryonic stem cell
44	chr2:63204600-63217800	Weak transcription	Primary T killer memory cells from peripheral blood	blood
45	chr2:63204800-63209000	Weak transcription	Brain Inferior Temporal Lobe	brain
46	chr2:63204800-63225200	Weak transcription	Spleen	Spleen
47	chr2:63204800-63229800	Weak transcription	Thymus	Thymus
48	chr2:63205000-63223800	Weak transcription	Placenta Amnion	Placenta Amnion
49	chr2:63205000-63238200	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
50	chr2:63205600-63208800	Weak transcription	Colonic Mucosa	Colon

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