Variant report

Variant	rs12887071
Chromosome Location	chr14:25317301-25317302
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 21 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:16)

rs_ID	r²[population]
rs10483288	1.00[MEX][hapmap]
rs11550670	0.96[GIH][hapmap]
rs12878320	0.85[CEU][hapmap]
rs12880667	0.90[CEU][hapmap];0.88[EUR][1000 genomes]
rs12886766	1.00[MEX][hapmap]
rs12888023	0.89[EUR][1000 genomes]
rs12889497	0.95[CEU][hapmap];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs12890808	0.82[MEX][hapmap]
rs12893363	0.90[MEX][hapmap]
rs12893848	0.98[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs12894282	1.00[CHD][hapmap];0.96[GIH][hapmap]
rs12897835	1.00[MEX][hapmap]
rs1551775	1.00[MEX][hapmap]
rs2297061	0.95[CEU][hapmap];0.85[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4983025	0.91[MEX][hapmap]
rs854325	1.00[CHD][hapmap]

Variant overlapped rSNPs/rCNVs (count:5 , 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

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs12887071	CMA1	cis	parietal	SCAN
rs12887071	SLC7A8	cis	cerebellum	SCAN
rs12887071	TTC5	cis	parietal	SCAN
rs12887071	DHRS2	cis	parietal	SCAN

Chromatin state (count:46 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr14:25288600-25322800	Weak transcription	Placenta	Placenta
2	chr14:25288800-25317400	Weak transcription	Placenta Amnion	Placenta Amnion
3	chr14:25306600-25321200	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
4	chr14:25307200-25319400	Weak transcription	Fetal Muscle Leg	muscle
5	chr14:25309000-25328000	Weak transcription	Duodenum Smooth Muscle	Duodenum
6	chr14:25309800-25323000	Weak transcription	Pancreas	Pancrea
7	chr14:25309800-25324400	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
8	chr14:25310000-25321000	Weak transcription	ES-I3 Cell Line	embryonic stem cell
9	chr14:25310200-25320800	Weak transcription	iPS-20b Cell Line	embryonic stem cell
10	chr14:25313200-25319200	Weak transcription	HUES64 Cell Line	embryonic stem cell
11	chr14:25313600-25317400	Weak transcription	Right Ventricle	heart
12	chr14:25313800-25320800	Weak transcription	Left Ventricle	heart
13	chr14:25313800-25323400	Weak transcription	Small Intestine	intestine
14	chr14:25314000-25317400	Weak transcription	Fetal Heart	heart
15	chr14:25314600-25333600	Weak transcription	Lung	lung
16	chr14:25315000-25317400	Enhancers	HSMMtube	muscle
17	chr14:25315000-25317600	Enhancers	Muscle Satellite Cultured Cells	--
18	chr14:25315000-25319600	Enhancers	Brain Anterior Caudate	brain
19	chr14:25315400-25317400	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
20	chr14:25315400-25319200	Weak transcription	iPS-18 Cell Line	embryonic stem cell
21	chr14:25315400-25319400	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
22	chr14:25315400-25320800	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
23	chr14:25315600-25317400	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
24	chr14:25315600-25320800	Weak transcription	Rectal Mucosa Donor 29	rectum
25	chr14:25315600-25321000	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
26	chr14:25315600-25321400	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
27	chr14:25315600-25330400	Weak transcription	Brain Angular Gyrus	brain
28	chr14:25315800-25318000	Weak transcription	Brain Inferior Temporal Lobe	brain
29	chr14:25315800-25320200	Weak transcription	Fetal Intestine Large	intestine
30	chr14:25315800-25320800	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
31	chr14:25315800-25320800	Weak transcription	HepG2	liver
32	chr14:25315800-25324200	Weak transcription	Brain Cingulate Gyrus	brain
33	chr14:25316000-25320800	Weak transcription	Rectal Mucosa Donor 31	rectum
34	chr14:25316000-25330400	Weak transcription	Brain Hippocampus Middle	brain
35	chr14:25316400-25319200	Enhancers	HSMM	muscle
36	chr14:25316600-25317800	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
37	chr14:25316600-25320800	Weak transcription	Fetal Intestine Small	intestine
38	chr14:25316800-25317600	Enhancers	Fetal Kidney	kidney
39	chr14:25316800-25317800	Enhancers	Fetal Brain Male	brain
40	chr14:25316800-25319200	Enhancers	Fetal Lung	lung
41	chr14:25316800-25320200	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
42	chr14:25317000-25317400	Weak transcription	NH-A	brain
43	chr14:25317000-25317800	Enhancers	Sigmoid Colon	Sigmoid Colon
44	chr14:25317000-25318200	Enhancers	Pancreatic Islets	Pancreatic Islet
45	chr14:25317000-25318200	Enhancers	Hela-S3	cervix
46	chr14:25317000-25320000	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin

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