Variant report

Variant	rs9651009
Chromosome Location	chr1:225834450-225834451
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	chr1:225821003..225822797-chr1:225833580..225836566,2	MCF-7	breast:

Extended variants
information (count: 26 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:24)

rs_ID	r²[population]
rs10082003	0.88[AMR][1000 genomes]
rs10915853	0.85[AMR][1000 genomes];0.83[ASN][1000 genomes]
rs12080606	0.83[AMR][1000 genomes]
rs1222434	1.00[CEU][hapmap];1.00[CHB][hapmap];0.89[JPT][hapmap]
rs1336480	0.82[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs1360958	0.84[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs1764345	0.82[EUR][1000 genomes]
rs1764347	1.00[CEU][hapmap];1.00[CHB][hapmap];0.89[JPT][hapmap];0.82[EUR][1000 genomes]
rs1771318	0.82[EUR][1000 genomes]
rs2035916	0.95[AFR][1000 genomes];0.97[AMR][1000 genomes];0.95[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs28818505	0.80[AMR][1000 genomes]
rs3904084	1.00[CEU][hapmap];1.00[JPT][hapmap];0.83[AFR][1000 genomes];0.97[AMR][1000 genomes];0.92[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs475794	0.95[AFR][1000 genomes];0.92[AMR][1000 genomes];0.93[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs481746	0.84[EUR][1000 genomes]
rs499385	1.00[CEU][hapmap];1.00[CHB][hapmap];0.84[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs516323	0.82[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs525062	0.90[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs526221	0.80[AFR][1000 genomes];0.87[AMR][1000 genomes];0.88[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs544404	1.00[CEU][hapmap];1.00[CHB][hapmap];0.89[JPT][hapmap];0.90[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs544430	1.00[CEU][hapmap];1.00[CHB][hapmap];0.89[JPT][hapmap];0.90[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs566085	0.90[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs59363938	0.90[AFR][1000 genomes];0.92[AMR][1000 genomes];0.95[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs7545317	1.00[CEU][hapmap];1.00[CHB][hapmap];0.89[JPT][hapmap];0.83[EUR][1000 genomes]
rs954534	1.00[CEU][hapmap];1.00[CHB][hapmap];0.89[JPT][hapmap];0.82[EUR][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	nsv832725	chr1:225726998-225910121	Weak transcription Enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer Strong transcription Active TSS Flanking Active TSS Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
2	nsv832736	chr1:225815717-225968619	Enhancers Weak transcription Flanking Active TSS Active TSS Genic enhancers Flanking Bivalent TSS/Enh Strong transcription Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	29 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs9651009	DNAH14,LBR,SRP9,ENAH	cis	brain	BrainEAC

Chromatin state (count:79 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:225809800-225837800	Weak transcription	Pancreatic Islets	Pancreatic Islet
2	chr1:225813600-225837600	Weak transcription	HUVEC	blood vessel
3	chr1:225813800-225838600	Weak transcription	HMEC	breast
4	chr1:225814600-225835800	Weak transcription	HSMMtube	muscle
5	chr1:225815800-225839000	Weak transcription	Fetal Intestine Large	intestine
6	chr1:225816000-225838400	Weak transcription	H9 Cell Line	embryonic stem cell
7	chr1:225816000-225838600	Weak transcription	Fetal Kidney	kidney
8	chr1:225816200-225835400	Weak transcription	Fetal Heart	heart
9	chr1:225816200-225836000	Weak transcription	Duodenum Smooth Muscle	Duodenum
10	chr1:225816200-225836600	Weak transcription	Adipose Nuclei	Adipose
11	chr1:225819600-225836400	Weak transcription	Brain Angular Gyrus	brain
12	chr1:225820000-225835800	Weak transcription	Brain Anterior Caudate	brain
13	chr1:225820800-225837200	Weak transcription	H1 Cell Line	embryonic stem cell
14	chr1:225823800-225835400	Weak transcription	Brain Hippocampus Middle	brain
15	chr1:225823800-225836600	Weak transcription	NHLF	lung
16	chr1:225825000-225837400	Weak transcription	Hela-S3	cervix
17	chr1:225825600-225839600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
18	chr1:225825800-225837200	Weak transcription	NHEK	skin
19	chr1:225826200-225838800	Weak transcription	Fetal Intestine Small	intestine
20	chr1:225826200-225839400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
21	chr1:225827800-225836000	Weak transcription	ES-I3 Cell Line	embryonic stem cell
22	chr1:225828200-225835400	Weak transcription	HepG2	liver
23	chr1:225828600-225836200	Weak transcription	Right Atrium	heart
24	chr1:225830200-225836600	Weak transcription	Stomach Smooth Muscle	stomach
25	chr1:225830200-225838800	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
26	chr1:225830400-225835800	Weak transcription	Rectal Smooth Muscle	rectum
27	chr1:225830400-225836600	Weak transcription	Brain Inferior Temporal Lobe	brain
28	chr1:225830400-225836600	Weak transcription	Right Ventricle	heart
29	chr1:225830400-225838200	Weak transcription	Pancreas	Pancrea
30	chr1:225830400-225839200	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
31	chr1:225830400-225839200	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
32	chr1:225830400-225839600	Weak transcription	Gastric	stomach
33	chr1:225830600-225835600	Weak transcription	iPS-18 Cell Line	embryonic stem cell
34	chr1:225831000-225835400	Weak transcription	HUES48 Cell Line	embryonic stem cell
35	chr1:225831000-225835400	Weak transcription	iPS-15b Cell Line	embryonic stem cell
36	chr1:225831000-225835600	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
37	chr1:225831400-225835400	Weak transcription	Fetal Brain Male	brain
38	chr1:225831400-225836200	Weak transcription	Breast Myoepithelial Primary Cells	Breast
39	chr1:225831600-225835800	Weak transcription	HSMM	muscle
40	chr1:225831600-225836600	Weak transcription	Fetal Stomach	stomach
41	chr1:225831600-225837600	Weak transcription	Fetal Muscle Leg	muscle
42	chr1:225831600-225838800	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
43	chr1:225832400-225838200	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
44	chr1:225832600-225835600	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
45	chr1:225832800-225835400	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
46	chr1:225832800-225835800	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
47	chr1:225832800-225836600	Weak transcription	NHDF-Ad	bronchial
48	chr1:225833000-225838800	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
49	chr1:225833200-225836000	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
50	chr1:225833200-225836200	Weak transcription	Brain Germinal Matrix	brain

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