Variant report

Variant	rs2609404
Chromosome Location	chr1:223103402-223103403
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	chr1:223102979..223104793-chr1:223106636..223108178,2	MCF-7	breast:

Extended variants
information (count: 35 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:29)

rs_ID	r²[population]
rs1890615	0.81[ASN][1000 genomes]
rs1970382	0.83[ASN][1000 genomes]
rs2254329	0.81[ASN][1000 genomes]
rs2609343	0.81[ASN][1000 genomes]
rs2609384	0.83[AMR][1000 genomes];0.81[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2609387	0.81[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2609391	0.86[AMR][1000 genomes];0.81[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2609392	0.80[ASN][1000 genomes]
rs2609393	0.80[ASN][1000 genomes]
rs2609394	0.83[AFR][1000 genomes];0.93[AMR][1000 genomes];0.84[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2609395	0.90[AFR][1000 genomes];0.97[AMR][1000 genomes];0.88[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2609396	0.80[ASN][1000 genomes]
rs2609397	0.90[AFR][1000 genomes];0.97[AMR][1000 genomes];0.88[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2609398	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];0.92[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2609401	0.98[AFR][1000 genomes];0.97[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2609402	0.98[AFR][1000 genomes];0.97[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2609408	0.98[AFR][1000 genomes];0.97[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2789960	0.80[ASN][1000 genomes]
rs2789962	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];0.92[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2789963	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];0.92[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2789964	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];0.92[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2789965	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];0.93[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2789968	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2789969	0.98[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2789970	0.98[AFR][1000 genomes];0.97[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2789971	0.95[AFR][1000 genomes];0.97[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2789973	0.83[ASN][1000 genomes]
rs2789974	0.81[AMR][1000 genomes];0.82[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs3101114	0.86[AMR][1000 genomes];0.81[EUR][1000 genomes];0.95[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:6 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv999185	chr1:222500725-223278032	Strong transcription Enhancers Weak transcription Flanking Active TSS Transcr. at gene 5' and 3' Active TSS Genic enhancers Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	45 gene(s)	inside rSNPs	diseases
2	nsv535304	chr1:222500725-223278032	Enhancers Flanking Active TSS Weak transcription Active TSS Genic enhancers Strong transcription Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	45 gene(s)	inside rSNPs	diseases
3	nsv1012537	chr1:222755091-223512243	Weak transcription Strong transcription Enhancers Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Active TSS Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	48 gene(s)	inside rSNPs	diseases
4	nsv873206	chr1:222985197-223124916	Active TSS Enhancers Flanking Active TSS Weak transcription Strong transcription ZNF genes & repeats Genic enhancers Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
5	nsv1014896	chr1:223070446-223327185	Active TSS Enhancers Flanking Active TSS ZNF genes & repeats Weak transcription Flanking Bivalent TSS/Enh Strong transcription Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
6	nsv873207	chr1:223078802-223292632	Genic enhancers Enhancers Weak transcription Active TSS Bivalent Enhancer Strong transcription Transcr. at gene 5' and 3' Flanking Active TSS ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:45 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:223092400-223116200	Weak transcription	Primary B cells from cord blood	blood
2	chr1:223100200-223116200	Weak transcription	Fetal Intestine Small	intestine
3	chr1:223100400-223104400	Weak transcription	HSMMtube	muscle
4	chr1:223101800-223104200	Active TSS	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
5	chr1:223101800-223104600	Weak transcription	HSMM	muscle
6	chr1:223101800-223105400	Active TSS	Right Atrium	heart
7	chr1:223102000-223104200	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
8	chr1:223102000-223104200	Weak transcription	Muscle Satellite Cultured Cells	--
9	chr1:223102000-223104200	Weak transcription	Osteobl	bone
10	chr1:223102000-223113600	Weak transcription	Left Ventricle	heart
11	chr1:223102000-223116200	Weak transcription	Brain Substantia Nigra	brain
12	chr1:223102200-223104200	Weak transcription	ES-I3 Cell Line	embryonic stem cell
13	chr1:223102200-223104200	Weak transcription	iPS-15b Cell Line	embryonic stem cell
14	chr1:223102200-223104600	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
15	chr1:223102200-223104800	Weak transcription	Stomach Mucosa	stomach
16	chr1:223102200-223106800	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
17	chr1:223102200-223116000	Weak transcription	Placenta	Placenta
18	chr1:223102200-223116200	Weak transcription	Fetal Stomach	stomach
19	chr1:223102200-223116200	Weak transcription	Skeletal Muscle Female	skeletal muscle
20	chr1:223102200-223119400	Weak transcription	NHLF	lung
21	chr1:223102200-223128000	Weak transcription	Fetal Muscle Trunk	muscle
22	chr1:223102200-223130800	Weak transcription	Fetal Brain Male	brain
23	chr1:223102400-223104200	Weak transcription	iPS-18 Cell Line	embryonic stem cell
24	chr1:223102400-223104600	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
25	chr1:223102400-223106200	Weak transcription	NHEK	skin
26	chr1:223102400-223121600	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
27	chr1:223102600-223103600	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
28	chr1:223102600-223103600	Weak transcription	Colon Smooth Muscle	Colon
29	chr1:223102600-223103600	Weak transcription	Rectal Smooth Muscle	rectum
30	chr1:223102600-223103800	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
31	chr1:223102600-223104400	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
32	chr1:223102600-223104400	Weak transcription	HUES64 Cell Line	embryonic stem cell
33	chr1:223102600-223104400	Weak transcription	Fetal Kidney	kidney
34	chr1:223102600-223109000	Weak transcription	Right Ventricle	heart
35	chr1:223102600-223109200	Weak transcription	Stomach Smooth Muscle	stomach
36	chr1:223102600-223117800	Weak transcription	Psoas Muscle	Psoas
37	chr1:223102600-223121200	Weak transcription	iPS-20b Cell Line	embryonic stem cell
38	chr1:223102800-223116200	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
39	chr1:223102800-223124400	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
40	chr1:223103000-223103600	Enhancers	Liver	Liver
41	chr1:223103000-223105600	Enhancers	Fetal Lung	lung
42	chr1:223103200-223116200	Weak transcription	Duodenum Smooth Muscle	Duodenum
43	chr1:223103400-223103600	Enhancers	Ovary	ovary
44	chr1:223103400-223103800	Enhancers	Fetal Adrenal Gland	Adrenal Gland
45	chr1:223103400-223105000	Enhancers	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived

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