Variant report

Variant	rs1468748
Chromosome Location	chr2:63204611-63204612
allele	C/T
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	chr2:63204209-63205304	HepG2	liver:	n/a	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr2:63183438..63186080-chr2:63202635..63205180,2	MCF-7	breast:

Variant related genes	Relation type
EHBP1	TF binding region

Extended variants
information (count: 59 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:53)

rs_ID	r²[population]
rs10153716	0.81[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs1022110	0.92[CEU][hapmap];0.91[CHB][hapmap];1.00[JPT][hapmap];0.85[EUR][1000 genomes]
rs11682530	0.93[ASW][hapmap];0.92[CEU][hapmap];0.84[GIH][hapmap];0.83[LWK][hapmap];0.89[TSI][hapmap];0.92[YRI][hapmap];0.89[EUR][1000 genomes]
rs11688816	0.93[ASW][hapmap];0.93[LWK][hapmap];0.84[YRI][hapmap]
rs11893131	0.96[CEU][hapmap];0.91[CHB][hapmap];1.00[JPT][hapmap];0.92[YRI][hapmap];0.89[AMR][1000 genomes];0.92[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs12989754	0.85[ASW][hapmap];0.96[CEU][hapmap];0.91[GIH][hapmap];0.88[LWK][hapmap];0.93[TSI][hapmap];0.88[YRI][hapmap];0.81[EUR][1000 genomes]
rs13013218	0.85[ASW][hapmap];0.96[CEU][hapmap];0.91[GIH][hapmap];0.86[LWK][hapmap];0.91[TSI][hapmap];0.80[YRI][hapmap];0.81[EUR][1000 genomes]
rs13389366	0.82[CHB][hapmap]
rs13410889	0.82[CHB][hapmap];0.95[CHD][hapmap];0.82[JPT][hapmap]
rs13418889	0.87[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs1420018	0.91[CEU][hapmap];0.88[EUR][1000 genomes]
rs1553832	0.92[CEU][hapmap]
rs17027429	0.93[ASW][hapmap];1.00[CEU][hapmap];0.91[CHB][hapmap];0.95[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];0.98[LWK][hapmap];1.00[MEX][hapmap];0.95[TSI][hapmap];0.84[YRI][hapmap];0.91[AMR][1000 genomes];0.95[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs1828398	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.84[YRI][hapmap];0.89[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs1877026	0.82[CHB][hapmap];0.83[CHD][hapmap]
rs2058566	0.96[CEU][hapmap];0.91[GIH][hapmap];0.91[TSI][hapmap];0.93[EUR][1000 genomes]
rs2058567	0.86[AMR][1000 genomes];0.96[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs2075375	0.95[CHB][hapmap];0.88[CHD][hapmap];0.91[JPT][hapmap]
rs2080227	0.80[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.84[YRI][hapmap];0.85[ASN][1000 genomes]
rs2215870	0.96[CEU][hapmap];0.91[GIH][hapmap];0.93[TSI][hapmap];0.93[EUR][1000 genomes]
rs2421816	0.96[CEU][hapmap];0.91[CHB][hapmap];0.93[CHD][hapmap];0.94[GIH][hapmap];1.00[JPT][hapmap];0.87[TSI][hapmap];0.92[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs2421860	0.82[CHB][hapmap]
rs2430386	0.91[AFR][1000 genomes];0.81[ASN][1000 genomes]
rs2430388	0.93[ASW][hapmap];0.96[CEU][hapmap];0.91[GIH][hapmap];0.84[LWK][hapmap];0.95[TSI][hapmap];0.84[YRI][hapmap];0.91[EUR][1000 genomes]
rs2539978	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]
rs2539980	1.00[CEU][hapmap];0.91[GIH][hapmap];0.87[TSI][hapmap];0.88[EUR][1000 genomes]
rs2539982	0.81[AFR][1000 genomes]
rs2539984	0.93[ASN][1000 genomes]
rs2539985	0.91[EUR][1000 genomes]
rs2539987	0.93[ASW][hapmap];0.96[CEU][hapmap];0.91[GIH][hapmap];0.84[LWK][hapmap];0.93[TSI][hapmap];0.83[YRI][hapmap]
rs2539990	0.86[AFR][1000 genomes];0.83[ASN][1000 genomes]
rs2710637	0.85[ASW][hapmap];0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.97[GIH][hapmap];0.95[JPT][hapmap];0.91[MEX][hapmap];0.93[TSI][hapmap];0.91[AMR][1000 genomes];0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2710639	0.92[CEU][hapmap];0.91[CHB][hapmap];1.00[JPT][hapmap];0.87[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2710640	0.80[AFR][1000 genomes];0.93[EUR][1000 genomes]
rs2710642	0.96[CEU][hapmap];0.88[GIH][hapmap];0.91[TSI][hapmap];0.90[EUR][1000 genomes]
rs2710651	0.86[AFR][1000 genomes];0.81[ASN][1000 genomes]
rs34104251	0.81[EUR][1000 genomes]
rs4461246	0.85[ASW][hapmap];0.96[CEU][hapmap];0.91[GIH][hapmap];0.86[LWK][hapmap];0.93[TSI][hapmap];0.86[EUR][1000 genomes]
rs4671051	0.81[AMR][1000 genomes];0.88[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs6545971	1.00[CEU][hapmap];0.91[YRI][hapmap];0.81[AFR][1000 genomes];0.92[EUR][1000 genomes]
rs6545972	0.93[ASW][hapmap];1.00[CEU][hapmap];0.91[CHB][hapmap];0.95[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];0.93[LWK][hapmap];0.95[TSI][hapmap];0.92[YRI][hapmap];0.95[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs6545973	0.96[CEU][hapmap];0.91[CHB][hapmap];0.95[CHD][hapmap];0.94[GIH][hapmap];1.00[JPT][hapmap];0.82[MEX][hapmap];0.89[TSI][hapmap];0.92[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs6705798	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.94[GIH][hapmap];1.00[JPT][hapmap];0.89[TSI][hapmap];0.87[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs6714241	0.91[CHB][hapmap];0.95[CHD][hapmap];1.00[JPT][hapmap];0.84[ASN][1000 genomes]
rs6739804	0.92[CEU][hapmap];0.84[GIH][hapmap];0.81[TSI][hapmap]
rs7557501	0.93[ASW][hapmap];1.00[CEU][hapmap];0.91[CHB][hapmap];0.95[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];0.88[LWK][hapmap];0.91[MEX][hapmap];0.95[TSI][hapmap];0.84[YRI][hapmap];0.89[AMR][1000 genomes];0.96[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs7562149	0.85[ASW][hapmap];0.96[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];0.88[LWK][hapmap];0.87[MEX][hapmap];0.91[TSI][hapmap];0.88[YRI][hapmap];0.82[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs7562734	0.85[EUR][1000 genomes]
rs7567923	0.93[ASW][hapmap];1.00[CEU][hapmap];0.91[CHB][hapmap];0.98[CHD][hapmap];0.97[GIH][hapmap];0.95[JPT][hapmap];0.93[LWK][hapmap];0.95[TSI][hapmap];0.84[YRI][hapmap];0.96[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs7571916	0.89[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs7591708	0.81[CHB][hapmap];0.89[CHD][hapmap]
rs9789661	0.84[EUR][1000 genomes]
rs9973612	0.96[CEU][hapmap];1.00[JPT][hapmap];0.88[YRI][hapmap];0.82[EUR][1000 genomes]

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
rs1468748	VPS54	cis	cerebellum	SCAN

Chromatin state (count:103 , 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	chr2:63157400-63207400	Weak transcription	Pancreas	Pancrea
6	chr2:63165200-63209200	Weak transcription	Aorta	Aorta
7	chr2:63167400-63206400	Weak transcription	Colon Smooth Muscle	Colon
8	chr2:63167600-63206200	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
9	chr2:63167600-63256000	Weak transcription	HSMMtube	muscle
10	chr2:63167800-63225800	Weak transcription	Muscle Satellite Cultured Cells	--
11	chr2:63168200-63220200	Weak transcription	Rectal Smooth Muscle	rectum
12	chr2:63169200-63206200	Weak transcription	Fetal Muscle Trunk	muscle
13	chr2:63169200-63206600	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
14	chr2:63169600-63228800	Weak transcription	GM12878-XiMat	blood
15	chr2:63169800-63206200	Weak transcription	Brain Cingulate Gyrus	brain
16	chr2:63169800-63208600	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
17	chr2:63169800-63237000	Weak transcription	Primary T helper cells PMA-I stimulated	--
18	chr2:63170200-63208000	Weak transcription	Monocytes-CD14+_RO01746	blood
19	chr2:63170400-63206200	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
20	chr2:63170400-63255600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
21	chr2:63171400-63209800	Weak transcription	Brain Anterior Caudate	brain
22	chr2:63171800-63208600	Weak transcription	Primary B cells from peripheral blood	blood
23	chr2:63171800-63218600	Weak transcription	Brain Hippocampus Middle	brain
24	chr2:63171800-63233000	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
25	chr2:63172000-63207000	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
26	chr2:63173800-63225800	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
27	chr2:63174200-63206400	Weak transcription	Primary T cells fromperipheralblood	blood
28	chr2:63174200-63207400	Weak transcription	Fetal Intestine Small	intestine
29	chr2:63175000-63209000	Weak transcription	Fetal Thymus	thymus
30	chr2:63176200-63207200	Weak transcription	Fetal Muscle Leg	muscle
31	chr2:63176200-63208800	Weak transcription	NH-A	brain
32	chr2:63176200-63220200	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
33	chr2:63176400-63206200	Weak transcription	Primary T cells from cord blood	blood
34	chr2:63177800-63226800	Weak transcription	Hela-S3	cervix
35	chr2:63179600-63219800	Weak transcription	Primary hematopoietic stem cells short term culture	blood
36	chr2:63182000-63228800	Weak transcription	H9 Cell Line	embryonic stem cell
37	chr2:63182600-63215800	Strong transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
38	chr2:63183400-63206200	Weak transcription	Fetal Intestine Large	intestine
39	chr2:63183400-63218600	Weak transcription	Brain Substantia Nigra	brain
40	chr2:63183600-63206200	Weak transcription	Rectal Mucosa Donor 29	rectum
41	chr2:63183800-63207000	Weak transcription	Duodenum Mucosa	Duodenum
42	chr2:63184000-63208800	Weak transcription	Left Ventricle	heart
43	chr2:63184200-63207200	Weak transcription	Placenta	Placenta
44	chr2:63184400-63206200	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
45	chr2:63184600-63206200	Weak transcription	Skeletal Muscle Female	skeletal muscle
46	chr2:63185600-63206200	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
47	chr2:63185800-63207000	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
48	chr2:63186600-63207200	Weak transcription	Primary hematopoietic stem cells	blood
49	chr2:63186600-63207200	Weak transcription	Dnd41	blood
50	chr2:63186600-63208200	Weak transcription	Fetal Kidney	kidney

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