Variant report

Variant	rs17657533
Chromosome Location	chr2:63249265-63249266
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 25 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:19)

rs_ID	r²[population]
rs11125949	1.00[ASW][hapmap];0.89[GIH][hapmap];1.00[YRI][hapmap]
rs12473894	1.00[YRI][hapmap]
rs12612046	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.94[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.83[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12614162	1.00[CHB][hapmap];0.88[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.88[TSI][hapmap];0.85[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17347994	1.00[CHD][hapmap];0.88[GIH][hapmap];1.00[MEX][hapmap];0.88[TSI][hapmap];0.85[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17407696	0.87[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.95[ASN][1000 genomes]
rs17432559	1.00[CHB][hapmap];1.00[CHD][hapmap];0.94[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.88[TSI][hapmap];0.85[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17432566	1.00[CHB][hapmap];1.00[CHD][hapmap];0.88[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.88[TSI][hapmap]
rs17432580	1.00[CHB][hapmap];1.00[CHD][hapmap];0.88[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.83[TSI][hapmap];0.84[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17432615	1.00[CHB][hapmap];1.00[CHD][hapmap];0.94[GIH][hapmap];1.00[JPT][hapmap];0.88[TSI][hapmap];0.85[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17432663	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.83[AMR][1000 genomes];0.92[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs17473084	1.00[AFR][1000 genomes];0.80[EUR][1000 genomes]
rs17474666	1.00[YRI][hapmap]
rs17598689	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.90[MEX][hapmap];1.00[TSI][hapmap];0.87[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17598881	1.00[AFR][1000 genomes];0.96[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17657580	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.94[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1877027	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.94[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.94[TSI][hapmap];1.00[YRI][hapmap];0.82[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs4671458	1.00[ASW][hapmap];0.83[GIH][hapmap];1.00[YRI][hapmap]
rs4671461	1.00[YRI][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:4)

SNP	Gene	Cis/trans	Tissue	Source
rs17657533	TMEM17	cis	cerebellum	SCAN
rs17657533	OTX1	cis	Whole Blood	GTEx
rs17657533	AFTPH	cis	cerebellum	SCAN
rs17657533	PEX13	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	chr2:63220200-63250600	Weak transcription	Small Intestine	intestine
10	chr2:63221600-63255600	Weak transcription	Fetal Kidney	kidney
11	chr2:63221800-63255200	Weak transcription	Primary B cells from cord blood	blood
12	chr2:63224400-63251800	Weak transcription	Sigmoid Colon	Sigmoid Colon
13	chr2:63224400-63256200	Weak transcription	Duodenum Mucosa	Duodenum
14	chr2:63224600-63271800	Weak transcription	Esophagus	oesophagus
15	chr2:63224600-63272000	Weak transcription	NHLF	lung
16	chr2:63225600-63250000	Weak transcription	Fetal Muscle Leg	muscle
17	chr2:63225800-63250200	Weak transcription	Primary T cells fromperipheralblood	blood
18	chr2:63227400-63258400	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
19	chr2:63227400-63259200	Weak transcription	Hela-S3	cervix
20	chr2:63227600-63253000	Weak transcription	NHEK	skin
21	chr2:63227600-63256200	Weak transcription	Muscle Satellite Cultured Cells	--
22	chr2:63228000-63254400	Weak transcription	Colon Smooth Muscle	Colon
23	chr2:63228000-63267600	Weak transcription	Rectal Smooth Muscle	rectum
24	chr2:63238200-63262800	Weak transcription	Fetal Brain Male	brain
25	chr2:63238400-63267600	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
26	chr2:63239600-63256800	Strong transcription	Liver	Liver
27	chr2:63240800-63250400	Weak transcription	Right Ventricle	heart
28	chr2:63240800-63271800	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
29	chr2:63240800-63272200	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
30	chr2:63241000-63251400	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
31	chr2:63241200-63261600	Weak transcription	Brain Anterior Caudate	brain
32	chr2:63241400-63253800	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
33	chr2:63241400-63254800	Weak transcription	Left Ventricle	heart
34	chr2:63241400-63256000	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
35	chr2:63241400-63256000	Weak transcription	Fetal Lung	lung
36	chr2:63241400-63256200	Weak transcription	Fetal Muscle Trunk	muscle
37	chr2:63241400-63256800	Weak transcription	Primary T cells from cord blood	blood
38	chr2:63241400-63261600	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
39	chr2:63241400-63261600	Weak transcription	NH-A	brain
40	chr2:63241600-63254800	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
41	chr2:63241600-63258200	Weak transcription	Dnd41	blood
42	chr2:63241600-63259000	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
43	chr2:63241800-63259000	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
44	chr2:63242400-63251400	Weak transcription	Fetal Intestine Small	intestine
45	chr2:63244000-63251200	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
46	chr2:63244000-63274400	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
47	chr2:63244200-63253600	Weak transcription	A549	lung
48	chr2:63244200-63254600	Weak transcription	Ovary	ovary
49	chr2:63244200-63274600	Weak transcription	Pancreas	Pancrea
50	chr2:63244400-63252800	Weak transcription	HSMM	muscle

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