Variant report

Variant	rs17762499
Chromosome Location	chr14:56645265-56645266
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr14:56643693..56645416-chr14:56800419..56803265,2	K562	blood:
2	chr14:56643728..56646285-chr14:56664453..56666938,2	K562	blood:
3	chr14:56643621..56646971-chr14:56684832..56688465,3	K562	blood:

Extended variants
information (count: 25 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:23)

rs_ID	r²[population]
rs10144612	0.81[CEU][hapmap];1.00[CHD][hapmap];0.81[GIH][hapmap];0.89[MEX][hapmap];0.86[TSI][hapmap];0.85[EUR][1000 genomes]
rs10483656	0.81[CEU][hapmap];0.85[EUR][1000 genomes]
rs12147737	0.80[EUR][1000 genomes]
rs1427556	0.81[CEU][hapmap];1.00[CHD][hapmap];0.81[GIH][hapmap];0.89[MEX][hapmap];0.80[TSI][hapmap];0.80[EUR][1000 genomes]
rs17688725	0.90[CEU][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.90[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs17688801	1.00[CEU][hapmap];1.00[CHD][hapmap];0.90[GIH][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.90[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs17689278	1.00[CEU][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs17761563	1.00[CHD][hapmap];0.81[GIH][hapmap]
rs17762733	0.90[CEU][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.84[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs17769788	0.80[EUR][1000 genomes]
rs17832675	0.90[CEU][hapmap];0.90[GIH][hapmap];1.00[MEX][hapmap];0.96[TSI][hapmap];0.88[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs1951955	0.89[CEU][hapmap];0.88[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs2035283	1.00[ASW][hapmap];0.81[CEU][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.91[LWK][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.91[AFR][1000 genomes];0.95[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs2343376	0.82[ASW][hapmap];1.00[CEU][hapmap];1.00[CHD][hapmap];0.90[GIH][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.93[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs2343604	0.80[EUR][1000 genomes]
rs28712711	0.85[EUR][1000 genomes]
rs2880615	1.00[CEU][hapmap];1.00[CHD][hapmap];0.90[GIH][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.95[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs3850298	1.00[CEU][hapmap];1.00[YRI][hapmap];0.89[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs3912203	0.90[CEU][hapmap];0.95[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs4127813	0.90[CEU][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.89[MEX][hapmap];1.00[TSI][hapmap];0.88[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs58502917	0.80[EUR][1000 genomes]
rs8020301	0.81[CEU][hapmap];0.80[EUR][1000 genomes]
rs959459	0.80[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:2 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv533129	chr14:56568535-56819234	Enhancers Weak transcription Strong transcription Flanking Active TSS Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
2	esv1844788	chr14:56594420-56771207	Weak transcription Enhancers Strong transcription ZNF genes & repeats Flanking Active TSS Genic enhancers Bivalent Enhancer Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs17762499	GCH1	cis	cerebellum	SCAN
rs17762499	CGRRF1	cis	cerebellum	SCAN

Chromatin state (count:69 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr14:56635000-56654600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
2	chr14:56635600-56647200	Weak transcription	Ovary	ovary
3	chr14:56639200-56647200	Weak transcription	Left Ventricle	heart
4	chr14:56639200-56662000	Weak transcription	Right Ventricle	heart
5	chr14:56639400-56652800	Weak transcription	Cortex derived primary cultured neurospheres	brain
6	chr14:56639400-56659200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
7	chr14:56639800-56647400	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
8	chr14:56639800-56647400	Weak transcription	Breast Myoepithelial Primary Cells	Breast
9	chr14:56639800-56647400	Weak transcription	Aorta	Aorta
10	chr14:56640000-56646800	Weak transcription	Adipose Nuclei	Adipose
11	chr14:56640000-56647600	Weak transcription	K562	blood
12	chr14:56640000-56648800	Weak transcription	Duodenum Mucosa	Duodenum
13	chr14:56640000-56652400	Weak transcription	Brain Substantia Nigra	brain
14	chr14:56640000-56652600	Weak transcription	Brain Anterior Caudate	brain
15	chr14:56640000-56652800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
16	chr14:56640000-56659800	Weak transcription	Fetal Intestine Large	intestine
17	chr14:56640000-56661800	Weak transcription	iPS-18 Cell Line	embryonic stem cell
18	chr14:56640200-56647600	Weak transcription	Muscle Satellite Cultured Cells	--
19	chr14:56640200-56648000	Weak transcription	Sigmoid Colon	Sigmoid Colon
20	chr14:56640400-56649600	Weak transcription	Skeletal Muscle Male	skeletal muscle
21	chr14:56640400-56661000	Weak transcription	Primary T killer memory cells from peripheral blood	blood
22	chr14:56640600-56646600	Weak transcription	HUVEC	blood vessel
23	chr14:56640600-56655800	Weak transcription	NHLF	lung
24	chr14:56640800-56647600	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
25	chr14:56640800-56648200	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
26	chr14:56640800-56653000	Weak transcription	Primary T cells from cord blood	blood
27	chr14:56641000-56660800	Weak transcription	Primary T helper cells fromperipheralblood	blood
28	chr14:56643400-56647200	Weak transcription	Gastric	stomach
29	chr14:56643400-56662000	Weak transcription	Spleen	Spleen
30	chr14:56643600-56647800	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
31	chr14:56643600-56648200	Weak transcription	Rectal Mucosa Donor 31	rectum
32	chr14:56643600-56652800	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
33	chr14:56643600-56655800	Weak transcription	Duodenum Smooth Muscle	Duodenum
34	chr14:56643600-56662000	Weak transcription	Fetal Kidney	kidney
35	chr14:56643800-56645400	Enhancers	Brain Germinal Matrix	brain
36	chr14:56644000-56647200	Weak transcription	Psoas Muscle	Psoas
37	chr14:56644000-56647600	Weak transcription	Pancreatic Islets	Pancreatic Islet
38	chr14:56644000-56652200	Weak transcription	Brain Cingulate Gyrus	brain
39	chr14:56644000-56662000	Weak transcription	Rectal Smooth Muscle	rectum
40	chr14:56644200-56652200	Weak transcription	Brain Hippocampus Middle	brain
41	chr14:56644200-56660600	Weak transcription	Primary hematopoietic stem cells	blood
42	chr14:56644400-56647400	Weak transcription	Colon Smooth Muscle	Colon
43	chr14:56644600-56645600	Genic enhancers	Dnd41	blood
44	chr14:56644600-56646400	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
45	chr14:56644800-56645400	Enhancers	Fetal Brain Male	brain
46	chr14:56644800-56661000	Weak transcription	Fetal Brain Female	brain
47	chr14:56645000-56645400	Enhancers	ES-I3 Cell Line	embryonic stem cell
48	chr14:56645000-56645400	Enhancers	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
49	chr14:56645000-56645400	ZNF genes & repeats	Lung	lung
50	chr14:56645000-56645600	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung

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