Variant report

Variant	rs12879200
Chromosome Location	chr14:69068110-69068111
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr14:69065107..69068379-chr14:69069760..69071455,4	MCF-7	breast:
2	chr14:69067505..69070348-chr14:69070905..69074097,3	K562	blood:

Extended variants
information (count: 9 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:7)

rs_ID	r²[population]
rs2145157	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2331775	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[YRI][hapmap];0.81[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2331776	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4531674	0.86[JPT][hapmap]
rs4902606	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[YRI][hapmap];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4902608	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];0.95[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6573844	0.98[AFR][1000 genomes];0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][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	esv1795754	chr14:69017623-69079110	Enhancers Weak transcription Bivalent Enhancer Active TSS ZNF genes & repeats Flanking Active TSS Genic enhancers Strong transcription Transcr. at gene 5' and 3'	Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
2	esv1832715	chr14:69017623-69079110	Weak transcription Enhancers Flanking Active TSS Genic enhancers ZNF genes & repeats Strong transcription Transcr. at gene 5' and 3' Active TSS Bivalent Enhancer	Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs12879200	ZFYVE26	cis	parietal	SCAN
rs12879200	PLEKHG3	cis	cerebellum	SCAN

Chromatin state (count:57 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr14:69060200-69068200	Enhancers	Primary monocytes fromperipheralblood	blood
2	chr14:69061200-69078000	Weak transcription	Fetal Heart	heart
3	chr14:69061800-69070400	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
4	chr14:69062200-69073800	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
5	chr14:69064400-69070800	Enhancers	Fetal Intestine Large	intestine
6	chr14:69065200-69069000	Enhancers	Lung	lung
7	chr14:69065400-69068400	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
8	chr14:69065400-69069000	Enhancers	Pancreas	Pancrea
9	chr14:69066000-69068200	Enhancers	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
10	chr14:69066000-69070600	Weak transcription	H1 Cell Line	embryonic stem cell
11	chr14:69066000-69070600	Enhancers	Fetal Intestine Small	intestine
12	chr14:69066000-69071200	Weak transcription	Esophagus	oesophagus
13	chr14:69066000-69073800	Weak transcription	Placenta Amnion	Placenta Amnion
14	chr14:69066200-69068200	Enhancers	HepG2	liver
15	chr14:69066200-69070200	Weak transcription	HUES64 Cell Line	embryonic stem cell
16	chr14:69066200-69070400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
17	chr14:69066200-69070400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
18	chr14:69066400-69068800	Enhancers	Duodenum Mucosa	Duodenum
19	chr14:69066400-69072600	Weak transcription	Stomach Smooth Muscle	stomach
20	chr14:69066400-69073800	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
21	chr14:69066600-69070000	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
22	chr14:69066600-69070200	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
23	chr14:69066600-69070400	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
24	chr14:69066600-69070800	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
25	chr14:69066800-69070400	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
26	chr14:69066800-69072200	Weak transcription	Brain Substantia Nigra	brain
27	chr14:69066800-69072200	Weak transcription	Colon Smooth Muscle	Colon
28	chr14:69067000-69068800	Weak transcription	Gastric	stomach
29	chr14:69067000-69072800	Weak transcription	Brain Cingulate Gyrus	brain
30	chr14:69067000-69074000	Weak transcription	Spleen	Spleen
31	chr14:69067200-69068600	Enhancers	Monocytes-CD14+_RO01746	blood
32	chr14:69067200-69069800	Weak transcription	Skeletal Muscle Female	skeletal muscle
33	chr14:69067200-69070200	Weak transcription	Fetal Thymus	thymus
34	chr14:69067200-69072400	Weak transcription	Rectal Mucosa Donor 31	rectum
35	chr14:69067200-69072600	Weak transcription	Colonic Mucosa	Colon
36	chr14:69067200-69072600	Weak transcription	Left Ventricle	heart
37	chr14:69067200-69072800	Weak transcription	Duodenum Smooth Muscle	Duodenum
38	chr14:69067200-69072800	Weak transcription	Rectal Mucosa Donor 29	rectum
39	chr14:69067200-69073000	Weak transcription	Skeletal Muscle Male	skeletal muscle
40	chr14:69067200-69073400	Weak transcription	Fetal Lung	lung
41	chr14:69067200-69073400	Weak transcription	Right Ventricle	heart
42	chr14:69067200-69073400	Weak transcription	Stomach Mucosa	stomach
43	chr14:69067200-69073800	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
44	chr14:69067200-69074000	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
45	chr14:69067400-69068200	Enhancers	Brain Hippocampus Middle	brain
46	chr14:69067400-69070400	Weak transcription	Fetal Muscle Trunk	muscle
47	chr14:69067400-69073800	Weak transcription	Sigmoid Colon	Sigmoid Colon
48	chr14:69067600-69068400	Enhancers	Primary neutrophils fromperipheralblood	blood
49	chr14:69067600-69069600	Weak transcription	Fetal Muscle Leg	muscle
50	chr14:69067600-69069800	Weak transcription	Adipose Nuclei	Adipose

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