Variant report

Variant	rs2553042
Chromosome Location	chr2:63231534-63231535
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr2:63231459..63234016-chr2:63234793..63239092,4	K562	blood:
2	chr2:63231459..63234016-chr2:63236574..63239092,2	K562	blood:
3	chr2:63227377..63229760-chr2:63230122..63232451,2	K562	blood:

Extended variants
information (count: 23 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:17)

rs_ID	r²[population]
rs12617178	0.84[ASW][hapmap];1.00[CEU][hapmap];0.88[GIH][hapmap];1.00[LWK][hapmap];0.88[MKK][hapmap];0.92[TSI][hapmap];1.00[YRI][hapmap];0.81[EUR][1000 genomes]
rs12987254	0.84[CEU][hapmap];0.90[MKK][hapmap]
rs13003895	0.91[ASN][1000 genomes]
rs13398408	0.91[ASN][1000 genomes]
rs1362311	1.00[CEU][hapmap];0.88[GIH][hapmap];0.87[MKK][hapmap];0.92[TSI][hapmap];0.81[EUR][1000 genomes]
rs2539979	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.94[GIH][hapmap];0.90[JPT][hapmap];1.00[MEX][hapmap];0.95[MKK][hapmap];0.97[TSI][hapmap];0.89[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2539986	0.84[ASW][hapmap];1.00[CEU][hapmap];0.88[GIH][hapmap];1.00[LWK][hapmap];0.88[MKK][hapmap];0.92[TSI][hapmap];1.00[YRI][hapmap];0.83[EUR][1000 genomes]
rs2710635	0.81[CHD][hapmap];0.90[JPT][hapmap];0.91[ASN][1000 genomes]
rs2710636	0.92[EUR][1000 genomes]
rs2710642	0.81[MKK][hapmap]
rs2710648	0.84[ASW][hapmap];1.00[CEU][hapmap];0.90[MKK][hapmap];0.92[TSI][hapmap];1.00[YRI][hapmap];0.82[EUR][1000 genomes]
rs34503992	0.84[ASW][hapmap];1.00[CEU][hapmap];0.90[CHD][hapmap];1.00[GIH][hapmap];0.90[JPT][hapmap];1.00[LWK][hapmap];0.91[MEX][hapmap];0.92[MKK][hapmap];0.92[TSI][hapmap];1.00[YRI][hapmap]
rs36009942	0.84[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.90[CHD][hapmap];1.00[GIH][hapmap];0.90[JPT][hapmap];1.00[LWK][hapmap];0.92[MKK][hapmap];0.95[TSI][hapmap];1.00[YRI][hapmap];0.80[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs360786	0.91[ASN][1000 genomes]
rs360798	0.91[ASN][1000 genomes]
rs36193012	0.89[ASN][1000 genomes]
rs67657712	0.81[EUR][1000 genomes];0.89[ASN][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	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
6	nsv1004678	chr2:63230722-63562484	Weak transcription Bivalent Enhancer ZNF genes & repeats Strong transcription Active TSS Enhancers Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS Flanking Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	13 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs2553042	VPS54	cis	cerebellum	SCAN

Chromatin state (count:90 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:63151400-63272200	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
2	chr2:63167600-63256000	Weak transcription	HSMMtube	muscle
3	chr2:63169800-63237000	Weak transcription	Primary T helper cells PMA-I stimulated	--
4	chr2:63170400-63255600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
5	chr2:63171800-63233000	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
6	chr2:63197600-63234800	Strong transcription	HepG2	liver
7	chr2:63199800-63258200	Weak transcription	Lung	lung
8	chr2:63200800-63239400	Weak transcription	Primary T helper naive cells from peripheral blood	blood
9	chr2:63205000-63238200	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
10	chr2:63205800-63232400	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
11	chr2:63207600-63235200	Weak transcription	HUES6 Cell Line	embryonic stem cell
12	chr2:63207800-63234000	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
13	chr2:63207800-63246000	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
14	chr2:63207800-63258000	Weak transcription	Placenta	Placenta
15	chr2:63208200-63242600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
16	chr2:63209400-63260000	Weak transcription	Aorta	Aorta
17	chr2:63209600-63239800	Weak transcription	Psoas Muscle	Psoas
18	chr2:63210000-63234200	Weak transcription	Fetal Thymus	thymus
19	chr2:63210000-63235400	Weak transcription	H1 Cell Line	embryonic stem cell
20	chr2:63210200-63232200	Weak transcription	Brain Germinal Matrix	brain
21	chr2:63219200-63245600	Weak transcription	Brain Hippocampus Middle	brain
22	chr2:63219200-63269800	Weak transcription	Primary hematopoietic stem cells	blood
23	chr2:63219400-63261600	Weak transcription	Brain Angular Gyrus	brain
24	chr2:63220200-63250600	Weak transcription	Small Intestine	intestine
25	chr2:63220800-63236200	Weak transcription	Fetal Intestine Small	intestine
26	chr2:63221400-63232200	Weak transcription	NH-A	brain
27	chr2:63221600-63232200	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
28	chr2:63221600-63255600	Weak transcription	Fetal Kidney	kidney
29	chr2:63221800-63233800	Weak transcription	Primary hematopoietic stem cells short term culture	blood
30	chr2:63221800-63245800	Weak transcription	Skeletal Muscle Female	skeletal muscle
31	chr2:63221800-63255200	Weak transcription	Primary B cells from cord blood	blood
32	chr2:63224200-63242000	Weak transcription	Rectal Mucosa Donor 31	rectum
33	chr2:63224400-63232200	Weak transcription	Monocytes-CD14+_RO01746	blood
34	chr2:63224400-63233200	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
35	chr2:63224400-63234400	Weak transcription	iPS-18 Cell Line	embryonic stem cell
36	chr2:63224400-63239800	Weak transcription	Stomach Smooth Muscle	stomach
37	chr2:63224400-63240400	Weak transcription	Primary T cells from cord blood	blood
38	chr2:63224400-63240400	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
39	chr2:63224400-63240600	Weak transcription	Fetal Muscle Trunk	muscle
40	chr2:63224400-63243800	Weak transcription	Fetal Stomach	stomach
41	chr2:63224400-63248400	Weak transcription	Rectal Mucosa Donor 29	rectum
42	chr2:63224400-63251800	Weak transcription	Sigmoid Colon	Sigmoid Colon
43	chr2:63224400-63256200	Weak transcription	Duodenum Mucosa	Duodenum
44	chr2:63224600-63233200	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
45	chr2:63224600-63234000	Weak transcription	iPS-20b Cell Line	embryonic stem cell
46	chr2:63224600-63234400	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
47	chr2:63224600-63240600	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
48	chr2:63224600-63240600	Weak transcription	Left Ventricle	heart
49	chr2:63224600-63243600	Weak transcription	Fetal Intestine Large	intestine
50	chr2:63224600-63271800	Weak transcription	Esophagus	oesophagus

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