Variant report

Variant	rs1255953
Chromosome Location	chr14:64551688-64551689
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 39 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:35)

rs_ID	r²[population]
rs10132638	0.84[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs10136783	0.84[MEX][hapmap]
rs10138253	0.86[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs1255949	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs1255954	0.85[CEU][hapmap];0.89[GIH][hapmap];0.93[MEX][hapmap];0.93[TSI][hapmap];0.87[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs1255957	0.87[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs1255959	0.85[CEU][hapmap];0.84[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs1255962	0.81[AMR][1000 genomes]
rs1255963	0.89[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs1255965	0.90[TSI][hapmap]
rs1255966	0.85[CEU][hapmap];0.90[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs1255967	0.85[CEU][hapmap];1.00[MEX][hapmap];0.93[TSI][hapmap];0.84[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs1255969	0.89[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs1255970	0.84[AMR][1000 genomes]
rs1255971	0.89[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs1255972	0.84[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs1255974	0.87[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs1255975	0.83[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs1262240	0.85[CEU][hapmap];0.89[TSI][hapmap];0.83[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs1266925	0.84[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs17101637	0.84[MEX][hapmap]
rs17101640	0.84[MEX][hapmap]
rs17101651	0.84[MEX][hapmap]
rs1954051	0.87[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs2185453	0.83[EUR][1000 genomes]
rs2357345	0.80[EUR][1000 genomes]
rs3829767	0.85[CEU][hapmap];0.93[MEX][hapmap];0.93[TSI][hapmap];0.80[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs4027402	0.93[MEX][hapmap];0.82[TSI][hapmap]
rs4027404	1.00[MEX][hapmap];0.82[TSI][hapmap]
rs4902264	0.83[TSI][hapmap]
rs7158401	0.85[CEU][hapmap];0.89[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs8010699	0.85[CEU][hapmap];1.00[MEX][hapmap];0.93[TSI][hapmap];0.87[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs8010911	0.85[CEU][hapmap];0.86[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs8022428	0.82[AMR][1000 genomes]
rs963289	0.85[CEU][hapmap];1.00[YRI][hapmap];0.99[AFR][1000 genomes];0.92[AMR][1000 genomes];0.85[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv915909	chr14:63620440-64560369	Active TSS Genic enhancers Weak transcription Enhancers Flanking Active TSS Strong transcription ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	67 gene(s)	inside rSNPs	diseases
2	nsv902019	chr14:64395569-64882380	Enhancers Strong transcription Flanking Active TSS Weak transcription Flanking Bivalent TSS/Enh Genic enhancers ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3' Active TSS Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	48 gene(s)	inside rSNPs	diseases
3	nsv456326	chr14:64420413-64754361	Strong transcription Weak transcription Enhancers Genic enhancers Transcr. at gene 5' and 3' Flanking Active TSS Active TSS ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	6 gene(s)	inside rSNPs	diseases
4	nsv564905	chr14:64420413-64754361	Enhancers Strong transcription Weak transcription ZNF genes & repeats Genic enhancers Flanking Active TSS Transcr. at gene 5' and 3' Active TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	6 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs1255953	ITK	trans	parietal	SCAN

Chromatin state (count:100 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr14:64466600-64593200	Weak transcription	Colon Smooth Muscle	Colon
2	chr14:64481400-64574000	Weak transcription	Stomach Mucosa	stomach
3	chr14:64489400-64568600	Weak transcription	Small Intestine	intestine
4	chr14:64491200-64565200	Weak transcription	Rectal Smooth Muscle	rectum
5	chr14:64519400-64592000	Weak transcription	Fetal Brain Male	brain
6	chr14:64525400-64566600	Strong transcription	Primary T helper cells fromperipheralblood	blood
7	chr14:64526000-64552200	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
8	chr14:64526800-64577000	Weak transcription	Pancreatic Islets	Pancreatic Islet
9	chr14:64527600-64551800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
10	chr14:64527800-64552000	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
11	chr14:64527800-64556600	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
12	chr14:64528000-64557000	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
13	chr14:64528000-64567400	Weak transcription	Fetal Heart	heart
14	chr14:64529000-64553200	Strong transcription	Dnd41	blood
15	chr14:64529400-64566800	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
16	chr14:64536800-64552200	Strong transcription	Placenta	Placenta
17	chr14:64539600-64552400	Weak transcription	Brain Anterior Caudate	brain
18	chr14:64542200-64557800	Weak transcription	HMEC	breast
19	chr14:64542600-64552000	Strong transcription	HUES64 Cell Line	embryonic stem cell
20	chr14:64542800-64556200	Weak transcription	iPS-15b Cell Line	embryonic stem cell
21	chr14:64542800-64574000	Weak transcription	HUVEC	blood vessel
22	chr14:64542800-64575400	Weak transcription	Hela-S3	cervix
23	chr14:64543000-64576400	Weak transcription	NHDF-Ad	bronchial
24	chr14:64544000-64616200	Strong transcription	Primary T cells fromperipheralblood	blood
25	chr14:64544200-64552400	Strong transcription	Primary neutrophils fromperipheralblood	blood
26	chr14:64544600-64551800	Strong transcription	Breast Myoepithelial Primary Cells	Breast
27	chr14:64545200-64552000	Strong transcription	Primary T cells from cord blood	blood
28	chr14:64545200-64552000	Strong transcription	Fetal Intestine Large	intestine
29	chr14:64545400-64552000	Strong transcription	Fetal Stomach	stomach
30	chr14:64545800-64551800	Strong transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
31	chr14:64546400-64551800	Strong transcription	Brain Germinal Matrix	brain
32	chr14:64546600-64551800	Strong transcription	Primary T helper 17 cells PMA-I stimulated	--
33	chr14:64546800-64551800	Strong transcription	HUES6 Cell Line	embryonic stem cell
34	chr14:64547000-64573800	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
35	chr14:64547200-64551800	Strong transcription	iPS-20b Cell Line	embryonic stem cell
36	chr14:64548000-64556600	Weak transcription	Gastric	stomach
37	chr14:64548200-64554200	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
38	chr14:64548400-64551800	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
39	chr14:64548400-64556600	Weak transcription	ES-I3 Cell Line	embryonic stem cell
40	chr14:64548400-64556600	Weak transcription	H9 Cell Line	embryonic stem cell
41	chr14:64548400-64556600	Weak transcription	NHEK	skin
42	chr14:64548400-64590800	Weak transcription	Stomach Smooth Muscle	stomach
43	chr14:64548600-64564800	Weak transcription	Duodenum Smooth Muscle	Duodenum
44	chr14:64548800-64562400	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
45	chr14:64549400-64554400	Weak transcription	GM12878-XiMat	blood
46	chr14:64549600-64556600	Weak transcription	H1 Cell Line	embryonic stem cell
47	chr14:64549600-64564000	Weak transcription	Right Ventricle	heart
48	chr14:64549600-64564200	Weak transcription	Colonic Mucosa	Colon
49	chr14:64549800-64552600	Weak transcription	Right Atrium	heart
50	chr14:64549800-64554800	Weak transcription	Liver	Liver

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