Variant report

Variant	rs12897835
Chromosome Location	chr14:25343003-25343004
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:33)

rs_ID	r²[population]
rs10483288	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]
rs11850146	1.00[ASN][1000 genomes]
rs12878069	0.82[CEU][hapmap];0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12879323	0.83[CEU][hapmap];1.00[YRI][hapmap];0.87[AFR][1000 genomes];0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12881201	1.00[ASN][1000 genomes]
rs12881381	0.83[CEU][hapmap];1.00[YRI][hapmap];0.90[AFR][1000 genomes];0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12884332	0.88[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs12885468	0.81[AFR][1000 genomes];0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12886050	1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12886059	1.00[ASN][1000 genomes]
rs12886766	0.83[CEU][hapmap];0.91[GIH][hapmap];1.00[MEX][hapmap];0.85[MKK][hapmap];0.94[TSI][hapmap];0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12887071	1.00[MEX][hapmap]
rs12890808	0.82[MEX][hapmap]
rs12893363	0.87[ASW][hapmap];0.95[GIH][hapmap];0.90[MEX][hapmap];1.00[ASN][1000 genomes]
rs12893496	0.83[CEU][hapmap];1.00[YRI][hapmap];0.84[AFR][1000 genomes];0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12895258	0.80[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs1461645	1.00[ASN][1000 genomes]
rs1551775	1.00[ASW][hapmap];0.83[CEU][hapmap];0.91[GIH][hapmap];1.00[MEX][hapmap];0.88[TSI][hapmap];1.00[YRI][hapmap];0.87[AFR][1000 genomes];0.96[AMR][1000 genomes];0.95[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	0.90[AFR][1000 genomes];0.92[AMR][1000 genomes];0.96[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	0.83[CEU][hapmap];0.91[GIH][hapmap];0.91[MEX][hapmap];0.91[TSI][hapmap];0.85[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs71405872	1.00[ASN][1000 genomes]
rs8018441	1.00[ASN][1000 genomes]
rs854340	0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs854342	0.80[TSI][hapmap];0.82[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:1)

SNP	Gene	Cis/trans	Tissue	Source
rs12897835	CMA1	cis	parietal	SCAN

Chromatin state (count:30 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr14:25317800-25344000	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
2	chr14:25319600-25344600	Weak transcription	NHDF-Ad	bronchial
3	chr14:25326400-25343600	Weak transcription	Gastric	stomach
4	chr14:25330800-25344000	Weak transcription	Pancreatic Islets	Pancreatic Islet
5	chr14:25331000-25343600	Weak transcription	Brain Hippocampus Middle	brain
6	chr14:25331000-25349800	Weak transcription	Muscle Satellite Cultured Cells	--
7	chr14:25331200-25349800	Weak transcription	HSMM	muscle
8	chr14:25332600-25344400	Weak transcription	Stomach Mucosa	stomach
9	chr14:25334200-25344000	Weak transcription	Rectal Mucosa Donor 31	rectum
10	chr14:25340600-25343600	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
11	chr14:25340600-25344400	Enhancers	Right Ventricle	heart
12	chr14:25340600-25345000	Weak transcription	Brain Inferior Temporal Lobe	brain
13	chr14:25341000-25344200	Weak transcription	Fetal Lung	lung
14	chr14:25341400-25344000	Weak transcription	Fetal Intestine Large	intestine
15	chr14:25341600-25344400	Enhancers	Left Ventricle	heart
16	chr14:25341800-25344000	Weak transcription	Fetal Intestine Small	intestine
17	chr14:25342000-25343400	Enhancers	Fetal Heart	heart
18	chr14:25342000-25343400	Weak transcription	HepG2	liver
19	chr14:25342400-25343200	Enhancers	Right Atrium	heart
20	chr14:25342400-25346800	Enhancers	Adipose Nuclei	Adipose
21	chr14:25342600-25343200	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
22	chr14:25342600-25345600	Enhancers	Brain Anterior Caudate	brain
23	chr14:25342800-25343200	Enhancers	Pancreas	Pancrea
24	chr14:25342800-25344400	Enhancers	Lung	lung
25	chr14:25342800-25351000	Enhancers	Brain Substantia Nigra	brain
26	chr14:25343000-25343200	Enhancers	Skeletal Muscle Male	skeletal muscle
27	chr14:25343000-25343200	Enhancers	Skeletal Muscle Female	skeletal muscle
28	chr14:25343000-25343400	Enhancers	Brain Angular Gyrus	brain
29	chr14:25343000-25343400	Enhancers	Brain Dorsolateral Prefrontal Cortex	brain
30	chr14:25343000-25351200	Enhancers	Brain Cingulate Gyrus	brain

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