Variant report

Variant	rs3904084
Chromosome Location	chr1:225837438-225837439
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr1:225837427..225840377-chr1:226110786..226113665,3	MCF-7	breast:
2	chr1:225811629..225814682-chr1:225837317..225840214,3	MCF-7	breast:

Variant related genes	Relation type
ENSG00000143811	Chromatin interaction

Extended variants
information (count: 24 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:22)

rs_ID	r²[population]
rs10082003	0.90[AMR][1000 genomes];0.86[ASN][1000 genomes]
rs10915853	0.87[AMR][1000 genomes];0.93[ASN][1000 genomes]
rs12080606	0.85[AMR][1000 genomes];0.88[ASN][1000 genomes]
rs1222434	1.00[CEU][hapmap];0.89[JPT][hapmap]
rs1336480	0.85[AMR][1000 genomes]
rs1360958	0.87[AMR][1000 genomes]
rs1764347	1.00[CEU][hapmap];0.89[JPT][hapmap]
rs2035916	1.00[AMR][1000 genomes];0.87[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs28818505	0.83[AMR][1000 genomes];0.81[ASN][1000 genomes]
rs475794	0.95[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs481746	0.80[AMR][1000 genomes]
rs499385	1.00[CEU][hapmap];0.87[AMR][1000 genomes]
rs516323	0.85[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs525062	0.92[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs526221	0.90[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs544404	1.00[CEU][hapmap];0.89[JPT][hapmap];0.92[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs544430	1.00[CEU][hapmap];0.89[JPT][hapmap];0.92[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs566085	0.92[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs59363938	0.95[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs7545317	1.00[CEU][hapmap];0.89[JPT][hapmap];0.80[AMR][1000 genomes]
rs954534	1.00[CEU][hapmap];0.89[JPT][hapmap]
rs9651009	0.83[AFR][1000 genomes];0.97[AMR][1000 genomes];0.92[EUR][1000 genomes];0.90[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	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

No data

Chromatin state (count:84 , 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	chr1:225815800-225839000	Weak transcription	Fetal Intestine Large	intestine
5	chr1:225816000-225838400	Weak transcription	H9 Cell Line	embryonic stem cell
6	chr1:225816000-225838600	Weak transcription	Fetal Kidney	kidney
7	chr1:225825600-225839600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
8	chr1:225826200-225838800	Weak transcription	Fetal Intestine Small	intestine
9	chr1:225826200-225839400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
10	chr1:225830200-225838800	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
11	chr1:225830400-225838200	Weak transcription	Pancreas	Pancrea
12	chr1:225830400-225839200	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
13	chr1:225830400-225839200	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
14	chr1:225830400-225839600	Weak transcription	Gastric	stomach
15	chr1:225831600-225837600	Weak transcription	Fetal Muscle Leg	muscle
16	chr1:225831600-225838800	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
17	chr1:225832400-225838200	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
18	chr1:225833000-225838800	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
19	chr1:225833200-225838200	Weak transcription	Fetal Muscle Trunk	muscle
20	chr1:225834200-225839200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
21	chr1:225834400-225838200	Weak transcription	Left Ventricle	heart
22	chr1:225834600-225837800	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
23	chr1:225834800-225837600	Flanking Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
24	chr1:225834800-225839200	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
25	chr1:225835000-225838200	Flanking Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
26	chr1:225835200-225837800	Enhancers	Cortex derived primary cultured neurospheres	brain
27	chr1:225835400-225838000	Enhancers	Brain Hippocampus Middle	brain
28	chr1:225835600-225837600	Enhancers	iPS-18 Cell Line	embryonic stem cell
29	chr1:225835600-225838400	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
30	chr1:225836000-225837800	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
31	chr1:225836200-225837600	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
32	chr1:225836200-225837600	Flanking Active TSS	Muscle Satellite Cultured Cells	--
33	chr1:225836200-225839200	Active TSS	Duodenum Smooth Muscle	Duodenum
34	chr1:225836200-225840400	Active TSS	Right Atrium	heart
35	chr1:225836200-225842000	Active TSS	Aorta	Aorta
36	chr1:225836400-225837600	Enhancers	iPS-15b Cell Line	embryonic stem cell
37	chr1:225836400-225837800	Enhancers	HSMMtube	muscle
38	chr1:225836600-225837600	Enhancers	ES-I3 Cell Line	embryonic stem cell
39	chr1:225836600-225837600	Enhancers	Adipose Nuclei	Adipose
40	chr1:225836600-225837600	Enhancers	Colon Smooth Muscle	Colon
41	chr1:225836600-225837600	Weak transcription	HSMM	muscle
42	chr1:225836600-225838200	Flanking Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
43	chr1:225836600-225841400	Active TSS	Skeletal Muscle Female	skeletal muscle
44	chr1:225836600-225842200	Active TSS	Right Ventricle	heart
45	chr1:225836600-225842200	Active TSS	Stomach Smooth Muscle	stomach
46	chr1:225836800-225837600	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
47	chr1:225836800-225837800	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
48	chr1:225836800-225837800	Weak transcription	Brain Angular Gyrus	brain
49	chr1:225836800-225838000	Enhancers	Brain Anterior Caudate	brain
50	chr1:225836800-225838200	Flanking Active TSS	HUES48 Cell Line	embryonic stem cell

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