Variant report

Variant	rs2710648
Chromosome Location	chr2:63250825-63250826
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr2:62683910..62684824-chr2:63250347..63250984,2	MCF-7	breast:
2	chr2:63250385..63253233-chr2:63253782..63256369,2	K562	blood:
3	chr2:63014501..63015430-chr2:63250276..63251247,4	MCF-7	breast:
4	chr2:63014409..63015384-chr2:63250444..63251251,4	MCF-7	breast:
5	chr2:63250422..63251063-chr2:63415754..63416314,2	MCF-7	breast:

Extended variants
information (count: 18 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:12)

rs_ID	r²[population]
rs12617178	1.00[ASW][hapmap];1.00[CEU][hapmap];0.85[CHB][hapmap];0.88[CHD][hapmap];0.88[MKK][hapmap];0.95[TSI][hapmap];1.00[YRI][hapmap];0.87[EUR][1000 genomes]
rs12987254	0.84[CEU][hapmap];0.90[MKK][hapmap]
rs1362311	1.00[CEU][hapmap];0.83[CHB][hapmap];0.88[CHD][hapmap];1.00[MEX][hapmap];0.87[MKK][hapmap];0.94[TSI][hapmap];0.87[EUR][1000 genomes]
rs2058566	0.82[MKK][hapmap]
rs2539979	0.84[ASW][hapmap];1.00[CEU][hapmap];0.85[MKK][hapmap];0.95[TSI][hapmap];0.83[EUR][1000 genomes]
rs2539986	1.00[ASW][hapmap];1.00[CEU][hapmap];0.85[CHB][hapmap];0.88[CHD][hapmap];0.88[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.90[EUR][1000 genomes]
rs2553042	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]
rs2710636	0.87[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs2710642	0.81[MKK][hapmap]
rs35801289	0.81[EUR][1000 genomes]
rs6545973	0.86[MKK][hapmap]
rs6705798	0.85[MKK][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	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
rs2710648	VPS54	cis	cerebellum	SCAN

Chromatin state (count:71 , 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	chr2:63170400-63255600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
4	chr2:63199800-63258200	Weak transcription	Lung	lung
5	chr2:63207800-63258000	Weak transcription	Placenta	Placenta
6	chr2:63209400-63260000	Weak transcription	Aorta	Aorta
7	chr2:63219200-63269800	Weak transcription	Primary hematopoietic stem cells	blood
8	chr2:63219400-63261600	Weak transcription	Brain Angular Gyrus	brain
9	chr2:63221600-63255600	Weak transcription	Fetal Kidney	kidney
10	chr2:63221800-63255200	Weak transcription	Primary B cells from cord blood	blood
11	chr2:63224400-63251800	Weak transcription	Sigmoid Colon	Sigmoid Colon
12	chr2:63224400-63256200	Weak transcription	Duodenum Mucosa	Duodenum
13	chr2:63224600-63271800	Weak transcription	Esophagus	oesophagus
14	chr2:63224600-63272000	Weak transcription	NHLF	lung
15	chr2:63227400-63258400	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
16	chr2:63227400-63259200	Weak transcription	Hela-S3	cervix
17	chr2:63227600-63253000	Weak transcription	NHEK	skin
18	chr2:63227600-63256200	Weak transcription	Muscle Satellite Cultured Cells	--
19	chr2:63228000-63254400	Weak transcription	Colon Smooth Muscle	Colon
20	chr2:63228000-63267600	Weak transcription	Rectal Smooth Muscle	rectum
21	chr2:63238200-63262800	Weak transcription	Fetal Brain Male	brain
22	chr2:63238400-63267600	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
23	chr2:63239600-63256800	Strong transcription	Liver	Liver
24	chr2:63240800-63271800	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
25	chr2:63240800-63272200	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
26	chr2:63241000-63251400	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
27	chr2:63241200-63261600	Weak transcription	Brain Anterior Caudate	brain
28	chr2:63241400-63253800	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
29	chr2:63241400-63254800	Weak transcription	Left Ventricle	heart
30	chr2:63241400-63256000	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
31	chr2:63241400-63256000	Weak transcription	Fetal Lung	lung
32	chr2:63241400-63256200	Weak transcription	Fetal Muscle Trunk	muscle
33	chr2:63241400-63256800	Weak transcription	Primary T cells from cord blood	blood
34	chr2:63241400-63261600	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
35	chr2:63241400-63261600	Weak transcription	NH-A	brain
36	chr2:63241600-63254800	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
37	chr2:63241600-63258200	Weak transcription	Dnd41	blood
38	chr2:63241600-63259000	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
39	chr2:63241800-63259000	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
40	chr2:63242400-63251400	Weak transcription	Fetal Intestine Small	intestine
41	chr2:63244000-63251200	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
42	chr2:63244000-63274400	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
43	chr2:63244200-63253600	Weak transcription	A549	lung
44	chr2:63244200-63254600	Weak transcription	Ovary	ovary
45	chr2:63244200-63274600	Weak transcription	Pancreas	Pancrea
46	chr2:63244400-63252800	Weak transcription	HSMM	muscle
47	chr2:63244400-63260200	Weak transcription	Cortex derived primary cultured neurospheres	brain
48	chr2:63244600-63253200	Weak transcription	HMEC	breast
49	chr2:63244600-63255400	Weak transcription	Fetal Intestine Large	intestine
50	chr2:63244600-63256600	Weak transcription	Osteobl	bone

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