Variant report

Variant	rs10483288
Chromosome Location	chr14:25333575-25333576
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 39 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:33)

rs_ID	r²[population]
rs11850146	1.00[ASN][1000 genomes]
rs12878069	1.00[CEU][hapmap];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12879323	1.00[CEU][hapmap];1.00[YRI][hapmap];0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12881201	1.00[ASN][1000 genomes]
rs12881381	1.00[CEU][hapmap];1.00[YRI][hapmap];0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12884332	0.85[AFR][1000 genomes];0.96[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs12885468	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12886050	0.93[CEU][hapmap];1.00[YRI][hapmap];0.84[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12886059	1.00[ASN][1000 genomes]
rs12886766	1.00[CEU][hapmap];1.00[GIH][hapmap];1.00[MEX][hapmap];0.95[MKK][hapmap];0.97[TSI][hapmap];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12887071	1.00[MEX][hapmap]
rs12890808	0.82[MEX][hapmap]
rs12893363	0.87[ASW][hapmap];0.83[CEU][hapmap];0.95[GIH][hapmap];0.90[MEX][hapmap];0.85[TSI][hapmap];0.86[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs12893496	1.00[CEU][hapmap];1.00[YRI][hapmap];0.88[AFR][1000 genomes];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12895258	0.88[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs12897835	1.00[ASW][hapmap];0.83[CEU][hapmap];0.91[GIH][hapmap];1.00[MEX][hapmap];0.81[MKK][hapmap];0.91[TSI][hapmap];1.00[YRI][hapmap];0.84[AFR][1000 genomes];0.92[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1461645	1.00[ASN][1000 genomes]
rs1551775	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[GIH][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.95[MKK][hapmap];0.97[TSI][hapmap];1.00[YRI][hapmap];0.90[AFR][1000 genomes];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17108566	1.00[ASN][1000 genomes]
rs17108738	1.00[ASN][1000 genomes]
rs17109209	1.00[YRI][hapmap]
rs17109263	1.00[ASN][1000 genomes]
rs17795652	1.00[ASN][1000 genomes]
rs3088325	1.00[ASN][1000 genomes]
rs34164371	0.81[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35779777	1.00[ASN][1000 genomes]
rs4097492	1.00[ASN][1000 genomes]
rs4983020	1.00[ASN][1000 genomes]
rs4983025	1.00[CEU][hapmap];1.00[GIH][hapmap];0.91[MEX][hapmap];0.94[TSI][hapmap];0.88[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs71405872	1.00[ASN][1000 genomes]
rs8018441	1.00[ASN][1000 genomes]
rs854340	0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs854342	0.89[CEU][hapmap];0.89[TSI][hapmap];0.85[EUR][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	nsv1041336	chr14:24726564-25527319	Weak transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS Enhancers Active TSS Strong transcription Flanking Active TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	107 gene(s)	inside rSNPs	diseases
2	nsv542000	chr14:24726564-25527319	Genic enhancers Enhancers Flanking Bivalent TSS/Enh Weak transcription Active TSS Strong transcription Transcr. at gene 5' and 3' Flanking Active TSS Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	107 gene(s)	inside rSNPs	diseases
3	nsv901504	chr14:25184210-25646203	Weak transcription Enhancers Flanking Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Active TSS Strong transcription Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
4	nsv901505	chr14:25237268-25360584	Weak transcription Enhancers Flanking Active TSS Genic enhancers Bivalent Enhancer Strong transcription ZNF genes & repeats Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
5	nsv901506	chr14:25295551-25377188	Enhancers Weak transcription Flanking Active TSS Strong transcription ZNF genes & repeats Active TSS Genic enhancers Bivalent Enhancer	Chromatin interactive region	n/a	inside rSNPs	diseases
6	nsv1041445	chr14:25326692-25388290	Enhancers Flanking Active TSS Weak transcription Active TSS ZNF genes & repeats	Chromatin interactive region	n/a	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs10483288	TTC5	cis	parietal	SCAN
rs10483288	CMA1	cis	parietal	SCAN

Chromatin state (count:29 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr14:25314600-25333600	Weak transcription	Lung	lung
2	chr14:25317800-25344000	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
3	chr14:25319600-25344600	Weak transcription	NHDF-Ad	bronchial
4	chr14:25321600-25333600	Weak transcription	Fetal Muscle Leg	muscle
5	chr14:25323600-25333600	Weak transcription	Sigmoid Colon	Sigmoid Colon
6	chr14:25326400-25343600	Weak transcription	Gastric	stomach
7	chr14:25329200-25340000	Weak transcription	Brain Anterior Caudate	brain
8	chr14:25329200-25341800	Weak transcription	Right Atrium	heart
9	chr14:25330400-25334600	Enhancers	Fetal Thymus	thymus
10	chr14:25330800-25344000	Weak transcription	Pancreatic Islets	Pancreatic Islet
11	chr14:25331000-25340000	Weak transcription	HepG2	liver
12	chr14:25331000-25343000	Weak transcription	Brain Angular Gyrus	brain
13	chr14:25331000-25343600	Weak transcription	Brain Hippocampus Middle	brain
14	chr14:25331000-25349800	Weak transcription	Muscle Satellite Cultured Cells	--
15	chr14:25331200-25349800	Weak transcription	HSMM	muscle
16	chr14:25331400-25337200	Weak transcription	Left Ventricle	heart
17	chr14:25332000-25333800	Enhancers	Fetal Intestine Small	intestine
18	chr14:25332600-25344400	Weak transcription	Stomach Mucosa	stomach
19	chr14:25332800-25333600	Enhancers	Monocytes-CD14+_RO01746	blood
20	chr14:25332800-25333800	Enhancers	Primary hematopoietic stem cells	blood
21	chr14:25332800-25334000	Enhancers	Primary hematopoietic stem cells short term culture	blood
22	chr14:25332800-25334200	Enhancers	Duodenum Mucosa	Duodenum
23	chr14:25332800-25334200	Enhancers	Fetal Lung	lung
24	chr14:25332800-25334200	Enhancers	Rectal Mucosa Donor 31	rectum
25	chr14:25333000-25333800	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
26	chr14:25333200-25333600	Enhancers	Primary monocytes fromperipheralblood	blood
27	chr14:25333200-25333800	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
28	chr14:25333200-25333800	Enhancers	Fetal Intestine Large	intestine
29	chr14:25333200-25333800	Enhancers	Right Ventricle	heart

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