Variant report

Variant	rs2525525
Chromosome Location	chr14:69008575-69008576
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr14:69006886..69009005-chr14:69017187..69019247,2	MCF-7	breast:
2	chr14:69007812..69009771-chr14:69024457..69026624,2	MCF-7	breast:

Extended variants
information (count: 31 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:28)

rs_ID	r²[population]
rs10134446	0.94[JPT][hapmap]
rs1023529	0.86[CHB][hapmap];0.97[CHD][hapmap];1.00[JPT][hapmap];0.82[MEX][hapmap];0.91[ASN][1000 genomes]
rs11158749	0.88[JPT][hapmap]
rs1476586	1.00[CEU][hapmap];1.00[CHB][hapmap];0.94[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1859302	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2040782	0.85[AMR][1000 genomes]
rs2079211	0.92[CHB][hapmap];0.87[AMR][1000 genomes];0.80[ASN][1000 genomes]
rs2107341	0.88[CEU][hapmap];0.90[AMR][1000 genomes]
rs2158358	1.00[ASW][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];0.91[MEX][hapmap];0.97[MKK][hapmap];0.92[AMR][1000 genomes];0.82[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2189517	0.88[JPT][hapmap]
rs2244814	0.90[CHB][hapmap];0.93[GIH][hapmap];0.82[MEX][hapmap]
rs2247048	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2525521	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2525522	0.98[AMR][1000 genomes];0.94[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2525523	0.93[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2525524	0.94[CEU][hapmap];0.92[CHB][hapmap];1.00[JPT][hapmap];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2525526	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2525527	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.94[JPT][hapmap];0.95[MEX][hapmap];0.93[MKK][hapmap];1.00[TSI][hapmap];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2842325	0.92[CHB][hapmap];0.85[AMR][1000 genomes]
rs2842329	1.00[ASW][hapmap];1.00[CHB][hapmap];0.94[CHD][hapmap];0.86[GIH][hapmap];0.94[JPT][hapmap];0.91[MEX][hapmap];1.00[MKK][hapmap];1.00[YRI][hapmap];0.87[AMR][1000 genomes];0.90[ASN][1000 genomes]
rs2842331	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[MEX][hapmap];0.97[MKK][hapmap];1.00[TSI][hapmap];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2842338	0.96[AMR][1000 genomes];0.88[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7140266	0.94[JPT][hapmap]
rs757370	0.91[CHB][hapmap];0.87[AMR][1000 genomes];0.80[ASN][1000 genomes]
rs916962	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.91[CHD][hapmap];0.98[GIH][hapmap];0.94[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs929285	0.92[CHB][hapmap];0.84[AMR][1000 genomes];0.80[ASN][1000 genomes]
rs9323513	0.87[JPT][hapmap]
rs9323514	0.87[JPT][hapmap]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv869154	chr14:68366754-69041768	Enhancers Flanking Active TSS Weak transcription Active TSS ZNF genes & repeats Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Strong transcription Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	19 gene(s)	inside rSNPs	diseases
2	nsv832822	chr14:68874640-69060272	Enhancers Weak transcription Flanking Active TSS ZNF genes & repeats Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
3	nsv1048064	chr14:68991041-69012766	Enhancers Weak transcription Flanking Active TSS ZNF genes & repeats Genic enhancers Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs2525525	FAM71D	cis	parietal	SCAN
rs2525525	ATP6V1D	cis	cerebellum	SCAN
rs2525525	PLEKHG3	cis	cerebellum	SCAN

Chromatin state (count:63 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr14:69002400-69016600	Weak transcription	Gastric	stomach
2	chr14:69003000-69009000	Weak transcription	Muscle Satellite Cultured Cells	--
3	chr14:69003200-69009000	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
4	chr14:69003600-69009000	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
5	chr14:69003600-69009000	Weak transcription	NHEK	skin
6	chr14:69004400-69008600	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
7	chr14:69004600-69009800	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
8	chr14:69004600-69010600	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
9	chr14:69004800-69008600	Enhancers	Fetal Muscle Leg	muscle
10	chr14:69005000-69008800	Enhancers	Colon Smooth Muscle	Colon
11	chr14:69005000-69008800	Enhancers	Fetal Stomach	stomach
12	chr14:69005000-69010400	Weak transcription	Pancreas	Pancrea
13	chr14:69005000-69013400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
14	chr14:69005000-69015000	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
15	chr14:69006000-69014600	Enhancers	NHDF-Ad	bronchial
16	chr14:69006200-69010400	Weak transcription	Aorta	Aorta
17	chr14:69006200-69012000	Weak transcription	Lung	lung
18	chr14:69006400-69013200	Weak transcription	Placenta Amnion	Placenta Amnion
19	chr14:69006400-69013800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
20	chr14:69006800-69009200	Weak transcription	Fetal Brain Male	brain
21	chr14:69006800-69010200	Weak transcription	Fetal Lung	lung
22	chr14:69006800-69010400	Weak transcription	HSMMtube	muscle
23	chr14:69006800-69011200	Weak transcription	Placenta	Placenta
24	chr14:69006800-69011600	Weak transcription	Brain Cingulate Gyrus	brain
25	chr14:69006800-69012800	Weak transcription	Esophagus	oesophagus
26	chr14:69006800-69013800	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
27	chr14:69006800-69014200	Weak transcription	Brain Substantia Nigra	brain
28	chr14:69006800-69014400	Weak transcription	Brain Hippocampus Middle	brain
29	chr14:69006800-69014600	Weak transcription	Brain Angular Gyrus	brain
30	chr14:69007000-69011000	Weak transcription	Left Ventricle	heart
31	chr14:69007000-69011400	Enhancers	Duodenum Smooth Muscle	Duodenum
32	chr14:69007200-69013400	Weak transcription	Right Ventricle	heart
33	chr14:69007400-69013600	Weak transcription	Fetal Heart	heart
34	chr14:69007800-69008600	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
35	chr14:69007800-69010000	Enhancers	Hela-S3	cervix
36	chr14:69007800-69013800	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
37	chr14:69007800-69014000	Weak transcription	Brain Anterior Caudate	brain
38	chr14:69008000-69008800	Enhancers	Foreskin Fibroblast Primary Cells skin02	Skin
39	chr14:69008000-69010400	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
40	chr14:69008000-69013800	Enhancers	HMEC	breast
41	chr14:69008000-69013800	Enhancers	HSMM	muscle
42	chr14:69008200-69008600	Enhancers	NHLF	lung
43	chr14:69008200-69009200	Weak transcription	Skeletal Muscle Female	skeletal muscle
44	chr14:69008200-69010200	Weak transcription	Fetal Muscle Trunk	muscle
45	chr14:69008200-69013400	Weak transcription	Ovary	ovary
46	chr14:69008400-69008600	Enhancers	Rectal Smooth Muscle	rectum
47	chr14:69008400-69009400	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
48	chr14:69008400-69009600	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
49	chr14:69008400-69009600	Weak transcription	Breast Myoepithelial Primary Cells	Breast
50	chr14:69008400-69009800	Weak transcription	Psoas Muscle	Psoas

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