Variant report

Variant	rs2609359
Chromosome Location	chr1:223168213-223168214
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	chr1:223168013..223170513-chr1:223178406..223180207,2	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]
rs11487819	0.86[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs2378617	0.92[AMR][1000 genomes];0.94[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2378618	0.87[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs2378619	0.84[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs2609366	0.88[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs2609371	0.84[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs2789910	0.87[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs2789924	0.84[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs2789929	0.84[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs2789931	0.84[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs2789933	0.88[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs2789934	0.85[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs2789937	0.83[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs2789945	0.89[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs2789953	0.87[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs2789954	0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs2789957	0.95[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs2789958	0.88[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs2789972	0.82[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs34188904	0.93[AMR][1000 genomes];0.94[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs34620158	0.87[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs34673329	0.84[EUR][1000 genomes]
rs4317816	0.84[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs4509582	0.81[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs4846783	0.87[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs61837491	0.85[EUR][1000 genomes]
rs67420224	0.84[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs728006	0.84[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs946506	0.87[AMR][1000 genomes];0.94[EUR][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	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
5	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
6	nsv917330	chr1:223141547-223225893	Enhancers Genic enhancers Weak transcription Bivalent Enhancer ZNF genes & repeats Active TSS Flanking Active TSS Transcr. at gene 5' and 3' Strong transcription Flanking Bivalent TSS/Enh	Chromatin interactive region lncRNA	n/a	inside rSNPs	diseases

No data

Chromatin state (count:91 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:223147000-223175800	Weak transcription	Aorta	Aorta
2	chr1:223148200-223168800	Weak transcription	Stomach Smooth Muscle	stomach
3	chr1:223148200-223175600	Weak transcription	Fetal Stomach	stomach
4	chr1:223148600-223168600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
5	chr1:223149200-223168600	Weak transcription	Right Ventricle	heart
6	chr1:223149400-223168600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
7	chr1:223149400-223168600	Weak transcription	Psoas Muscle	Psoas
8	chr1:223149800-223175600	Weak transcription	Ovary	ovary
9	chr1:223150200-223173600	Weak transcription	Fetal Intestine Small	intestine
10	chr1:223152400-223175600	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
11	chr1:223153000-223168600	Weak transcription	Fetal Muscle Leg	muscle
12	chr1:223153200-223168600	Weak transcription	Lung	lung
13	chr1:223153200-223175600	Weak transcription	Esophagus	oesophagus
14	chr1:223155200-223175800	Weak transcription	Colon Smooth Muscle	Colon
15	chr1:223156000-223168800	Weak transcription	Primary hematopoietic stem cells	blood
16	chr1:223156000-223175800	Weak transcription	Rectal Smooth Muscle	rectum
17	chr1:223156600-223175800	Weak transcription	Spleen	Spleen
18	chr1:223157800-223175800	Weak transcription	Gastric	stomach
19	chr1:223158200-223175800	Weak transcription	Adipose Nuclei	Adipose
20	chr1:223158600-223168600	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
21	chr1:223158800-223175800	Weak transcription	Placenta	Placenta
22	chr1:223158800-223175800	Weak transcription	Skeletal Muscle Female	skeletal muscle
23	chr1:223159600-223168400	Weak transcription	Fetal Lung	lung
24	chr1:223160200-223168600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
25	chr1:223160200-223169400	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
26	chr1:223160200-223175600	Weak transcription	Thymus	Thymus
27	chr1:223161800-223168800	Weak transcription	Stomach Mucosa	stomach
28	chr1:223163000-223168600	Weak transcription	Brain Substantia Nigra	brain
29	chr1:223163600-223179800	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
30	chr1:223163800-223175600	Weak transcription	Primary T cells fromperipheralblood	blood
31	chr1:223164000-223168800	Weak transcription	Sigmoid Colon	Sigmoid Colon
32	chr1:223164000-223175800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
33	chr1:223164800-223168400	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
34	chr1:223165000-223168600	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
35	chr1:223165000-223175800	Weak transcription	Fetal Brain Male	brain
36	chr1:223165200-223169200	Strong transcription	Primary B cells from peripheral blood	blood
37	chr1:223165400-223169400	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
38	chr1:223165600-223176000	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
39	chr1:223166200-223168400	Weak transcription	Primary T helper cells PMA-I stimulated	--
40	chr1:223166200-223179400	Weak transcription	Small Intestine	intestine
41	chr1:223166600-223168400	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
42	chr1:223166600-223168800	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
43	chr1:223166600-223169400	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
44	chr1:223166800-223168400	Weak transcription	Fetal Intestine Large	intestine
45	chr1:223166800-223168600	Weak transcription	Left Ventricle	heart
46	chr1:223166800-223169000	Enhancers	NHDF-Ad	bronchial
47	chr1:223166800-223170400	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
48	chr1:223166800-223175000	Weak transcription	Fetal Muscle Trunk	muscle
49	chr1:223167000-223169000	Enhancers	HSMM	muscle
50	chr1:223167000-223175000	Weak transcription	Duodenum Smooth Muscle	Duodenum

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