Variant report

Variant	rs2539978
Chromosome Location	chr2:63195179-63195180
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 58 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:52)

rs_ID	r²[population]
rs10153716	0.81[ASN][1000 genomes]
rs1022110	0.96[CEU][hapmap];0.91[CHB][hapmap];0.95[JPT][hapmap];0.84[EUR][1000 genomes]
rs11682530	0.96[CEU][hapmap];0.81[GIH][hapmap];0.85[TSI][hapmap];0.89[EUR][1000 genomes]
rs11893131	1.00[CEU][hapmap];0.91[CHB][hapmap];0.95[JPT][hapmap];0.91[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs12713469	0.89[ASW][hapmap];0.90[LWK][hapmap]
rs12989754	0.92[CEU][hapmap];0.88[GIH][hapmap];0.89[TSI][hapmap]
rs13013218	0.92[CEU][hapmap];0.88[GIH][hapmap];0.87[TSI][hapmap]
rs13389366	0.83[CHB][hapmap]
rs13410889	0.83[CHB][hapmap];0.95[CHD][hapmap]
rs13418889	0.88[EUR][1000 genomes]
rs1420018	0.96[CEU][hapmap];0.87[EUR][1000 genomes]
rs1468748	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.97[GIH][hapmap];0.95[JPT][hapmap];0.96[TSI][hapmap];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1553832	0.96[CEU][hapmap]
rs17027429	0.96[CEU][hapmap];0.91[CHB][hapmap];0.95[CHD][hapmap];0.94[GIH][hapmap];0.95[JPT][hapmap];0.91[TSI][hapmap];0.91[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs1828398	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs1877026	0.83[CHB][hapmap];0.84[CHD][hapmap]
rs2058566	0.92[CEU][hapmap];0.88[GIH][hapmap];0.87[TSI][hapmap];0.90[EUR][1000 genomes]
rs2058567	0.92[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs2075375	0.95[CHB][hapmap];0.88[CHD][hapmap];0.85[JPT][hapmap]
rs2080227	0.84[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.87[ASN][1000 genomes]
rs2215870	1.00[CEU][hapmap];0.88[GIH][hapmap];0.89[TSI][hapmap];0.92[EUR][1000 genomes]
rs2421816	0.92[CEU][hapmap];0.91[CHB][hapmap];0.93[CHD][hapmap];0.91[GIH][hapmap];0.95[JPT][hapmap];0.83[TSI][hapmap];0.89[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs2421860	0.83[CHB][hapmap]
rs2430386	0.81[ASN][1000 genomes]
rs2430388	1.00[CEU][hapmap];0.88[GIH][hapmap];0.91[TSI][hapmap];0.90[EUR][1000 genomes]
rs2539980	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]
rs2539984	0.92[ASN][1000 genomes]
rs2539985	0.90[EUR][1000 genomes]
rs2539987	1.00[CEU][hapmap];0.88[GIH][hapmap];0.91[TSI][hapmap]
rs2539990	0.83[ASN][1000 genomes]
rs2710637	0.87[CEU][hapmap];0.95[CHB][hapmap];1.00[CHD][hapmap];0.94[GIH][hapmap];0.90[JPT][hapmap];0.89[TSI][hapmap];0.94[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2710639	0.88[CEU][hapmap];0.91[CHB][hapmap];0.95[JPT][hapmap];0.84[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2710640	0.92[EUR][1000 genomes]
rs2710642	0.92[CEU][hapmap];0.85[GIH][hapmap];0.87[TSI][hapmap];0.87[EUR][1000 genomes]
rs2710651	0.83[ASN][1000 genomes]
rs34104251	0.80[ASN][1000 genomes]
rs4461246	1.00[CEU][hapmap];0.88[GIH][hapmap];0.89[TSI][hapmap];0.85[EUR][1000 genomes]
rs4671051	0.85[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs6545971	0.95[CEU][hapmap];0.89[EUR][1000 genomes]
rs6545972	0.96[CEU][hapmap];0.91[CHB][hapmap];0.95[CHD][hapmap];0.94[GIH][hapmap];0.95[JPT][hapmap];0.91[MEX][hapmap];0.91[TSI][hapmap];0.92[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs6545973	0.92[CEU][hapmap];0.91[CHB][hapmap];0.95[CHD][hapmap];0.91[GIH][hapmap];0.95[JPT][hapmap];0.85[TSI][hapmap];0.89[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs6705798	0.88[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.91[GIH][hapmap];0.95[JPT][hapmap];0.85[TSI][hapmap];0.85[EUR][1000 genomes]
rs6714241	0.89[ASW][hapmap];0.91[CHB][hapmap];0.95[CHD][hapmap];0.95[JPT][hapmap];0.88[LWK][hapmap];0.86[YRI][hapmap];0.82[ASN][1000 genomes]
rs6739804	0.96[CEU][hapmap];0.88[GIH][hapmap];0.85[TSI][hapmap]
rs7557501	0.96[CEU][hapmap];0.91[CHB][hapmap];0.95[CHD][hapmap];0.94[GIH][hapmap];0.95[JPT][hapmap];0.91[TSI][hapmap];0.92[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs7562149	0.92[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];0.94[GIH][hapmap];0.95[JPT][hapmap];0.88[TSI][hapmap];0.81[ASN][1000 genomes]
rs7562734	0.82[EUR][1000 genomes]
rs7567923	0.96[CEU][hapmap];0.91[CHB][hapmap];0.98[CHD][hapmap];0.94[GIH][hapmap];1.00[JPT][hapmap];0.91[MEX][hapmap];0.91[TSI][hapmap];0.92[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs7571916	0.86[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs7591708	0.82[CHB][hapmap];0.88[CHD][hapmap]
rs9789661	0.81[EUR][1000 genomes]
rs9973612	0.92[CEU][hapmap];0.95[JPT][hapmap]

Variant overlapped rSNPs/rCNVs (count:6 , 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	nsv428041	chr2:63027947-63206574	Strong transcription Weak transcription ZNF genes & repeats Enhancers Flanking Active TSS Transcr. at gene 5' and 3' Active TSS Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
4	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
5	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
6	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
rs2539978	VPS54	cis	cerebellum	SCAN

Chromatin state (count:93 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:63151400-63200800	Weak transcription	Fetal Stomach	stomach
2	chr2:63151400-63208800	Weak transcription	Sigmoid Colon	Sigmoid Colon
3	chr2:63151400-63272200	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
4	chr2:63154400-63209000	Weak transcription	Rectal Mucosa Donor 31	rectum
5	chr2:63155400-63209000	Weak transcription	Psoas Muscle	Psoas
6	chr2:63157400-63207400	Weak transcription	Pancreas	Pancrea
7	chr2:63162000-63196800	Weak transcription	HUES48 Cell Line	embryonic stem cell
8	chr2:63162000-63199800	Weak transcription	ES-I3 Cell Line	embryonic stem cell
9	chr2:63165200-63209200	Weak transcription	Aorta	Aorta
10	chr2:63167400-63200800	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
11	chr2:63167400-63206400	Weak transcription	Colon Smooth Muscle	Colon
12	chr2:63167600-63206200	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
13	chr2:63167600-63256000	Weak transcription	HSMMtube	muscle
14	chr2:63167800-63225800	Weak transcription	Muscle Satellite Cultured Cells	--
15	chr2:63168200-63220200	Weak transcription	Rectal Smooth Muscle	rectum
16	chr2:63169200-63206200	Weak transcription	Fetal Muscle Trunk	muscle
17	chr2:63169200-63206600	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
18	chr2:63169400-63196400	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
19	chr2:63169600-63228800	Weak transcription	GM12878-XiMat	blood
20	chr2:63169800-63206200	Weak transcription	Brain Cingulate Gyrus	brain
21	chr2:63169800-63208600	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
22	chr2:63169800-63237000	Weak transcription	Primary T helper cells PMA-I stimulated	--
23	chr2:63170200-63208000	Weak transcription	Monocytes-CD14+_RO01746	blood
24	chr2:63170400-63206200	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
25	chr2:63170400-63255600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
26	chr2:63171400-63209800	Weak transcription	Brain Anterior Caudate	brain
27	chr2:63171800-63208600	Weak transcription	Primary B cells from peripheral blood	blood
28	chr2:63171800-63218600	Weak transcription	Brain Hippocampus Middle	brain
29	chr2:63171800-63233000	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
30	chr2:63172000-63197600	Weak transcription	iPS-18 Cell Line	embryonic stem cell
31	chr2:63172000-63207000	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
32	chr2:63173800-63225800	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
33	chr2:63174200-63206400	Weak transcription	Primary T cells fromperipheralblood	blood
34	chr2:63174200-63207400	Weak transcription	Fetal Intestine Small	intestine
35	chr2:63175000-63209000	Weak transcription	Fetal Thymus	thymus
36	chr2:63176200-63207200	Weak transcription	Fetal Muscle Leg	muscle
37	chr2:63176200-63208800	Weak transcription	NH-A	brain
38	chr2:63176200-63220200	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
39	chr2:63176400-63206200	Weak transcription	Primary T cells from cord blood	blood
40	chr2:63177800-63226800	Weak transcription	Hela-S3	cervix
41	chr2:63179600-63219800	Weak transcription	Primary hematopoietic stem cells short term culture	blood
42	chr2:63181400-63196800	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
43	chr2:63182000-63228800	Weak transcription	H9 Cell Line	embryonic stem cell
44	chr2:63182600-63215800	Strong transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
45	chr2:63183400-63206200	Weak transcription	Fetal Intestine Large	intestine
46	chr2:63183400-63218600	Weak transcription	Brain Substantia Nigra	brain
47	chr2:63183600-63206200	Weak transcription	Rectal Mucosa Donor 29	rectum
48	chr2:63183800-63198200	Weak transcription	Fetal Brain Female	brain
49	chr2:63183800-63207000	Weak transcription	Duodenum Mucosa	Duodenum
50	chr2:63184000-63208800	Weak transcription	Left Ventricle	heart

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