Variant report

Variant	rs17049342
Chromosome Location	chr2:58334666-58334667
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	chr2:58332265..58336013-chr2:58347138..58350480,3	MCF-7	breast:

Extended variants
information (count: 45 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:39)

rs_ID	r²[population]
rs10176942	1.00[EUR][1000 genomes]
rs12105064	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17049241	1.00[EUR][1000 genomes]
rs17049249	1.00[EUR][1000 genomes]
rs17049265	1.00[EUR][1000 genomes]
rs17049267	1.00[EUR][1000 genomes]
rs17049283	1.00[ASN][1000 genomes]
rs17049333	1.00[EUR][1000 genomes]
rs17049337	1.00[EUR][1000 genomes]
rs17049338	0.81[YRI][hapmap];0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs17049341	1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17049343	1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17049344	1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17049345	1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs17049350	1.00[EUR][1000 genomes]
rs17049353	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17049354	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs17049355	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17049364	1.00[YRI][hapmap];0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2030236	1.00[EUR][1000 genomes]
rs57559033	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs60226794	1.00[EUR][1000 genomes]
rs60590670	1.00[EUR][1000 genomes]
rs60956789	1.00[EUR][1000 genomes]
rs61659380	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs6739344	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72947193	1.00[ASN][1000 genomes]
rs72947197	1.00[ASN][1000 genomes]
rs72951065	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72951066	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72951082	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs72953108	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72953132	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs7566805	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7569184	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7579768	1.00[ASN][1000 genomes]
rs7587962	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7588018	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7601556	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[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	nsv525988	chr2:58161520-58427786	Enhancers Weak transcription Flanking Active TSS Active TSS Strong transcription ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	27 gene(s)	inside rSNPs	diseases
2	nsv582097	chr2:58266099-58346966	Enhancers Flanking Active TSS Active TSS Weak transcription Strong transcription ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	26 gene(s)	inside rSNPs	diseases
3	nsv874201	chr2:58269871-58350504	Enhancers Flanking Active TSS Weak transcription Genic enhancers Strong transcription Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	26 gene(s)	inside rSNPs	diseases
4	nsv874202	chr2:58269871-58375688	Active TSS Weak transcription Enhancers Strong transcription ZNF genes & repeats Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	26 gene(s)	inside rSNPs	diseases
5	nsv999042	chr2:58326123-58530903	Enhancers ZNF genes & repeats Weak transcription Flanking Active TSS Active TSS Strong transcription Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	14 gene(s)	inside rSNPs	diseases
6	nsv535734	chr2:58326123-58530903	ZNF genes & repeats Weak transcription Active TSS Strong transcription Flanking Active TSS Enhancers Transcr. at gene 5' and 3' Genic enhancers Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	14 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:56 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:58282600-58350400	Weak transcription	Sigmoid Colon	Sigmoid Colon
2	chr2:58303000-58358800	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
3	chr2:58311200-58382400	Weak transcription	Aorta	Aorta
4	chr2:58315200-58389600	Weak transcription	Primary T killer memory cells from peripheral blood	blood
5	chr2:58318200-58373200	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
6	chr2:58318400-58334800	Weak transcription	HSMM	muscle
7	chr2:58319400-58358400	Weak transcription	Ovary	ovary
8	chr2:58319800-58349800	Weak transcription	Primary T cells from cord blood	blood
9	chr2:58319800-58350800	Weak transcription	Primary T helper cells fromperipheralblood	blood
10	chr2:58319800-58359000	Weak transcription	Primary T helper cells PMA-I stimulated	--
11	chr2:58319800-58367200	Weak transcription	Rectal Mucosa Donor 29	rectum
12	chr2:58320000-58334800	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
13	chr2:58320000-58339600	Weak transcription	Primary hematopoietic stem cells short term culture	blood
14	chr2:58320000-58347600	Weak transcription	Duodenum Smooth Muscle	Duodenum
15	chr2:58320000-58359000	Weak transcription	Left Ventricle	heart
16	chr2:58322200-58347400	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
17	chr2:58322600-58349800	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
18	chr2:58322600-58350400	Weak transcription	Primary B cells from peripheral blood	blood
19	chr2:58323200-58335400	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
20	chr2:58323200-58347600	Weak transcription	Breast Myoepithelial Primary Cells	Breast
21	chr2:58323200-58350400	Weak transcription	Primary T cells fromperipheralblood	blood
22	chr2:58323600-58350200	Weak transcription	Liver	Liver
23	chr2:58326400-58347600	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
24	chr2:58326800-58334800	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
25	chr2:58327000-58337600	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
26	chr2:58327000-58339600	Weak transcription	K562	blood
27	chr2:58327000-58347600	Weak transcription	Primary hematopoietic stem cells	blood
28	chr2:58332400-58370800	Weak transcription	Duodenum Mucosa	Duodenum
29	chr2:58333000-58341800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
30	chr2:58333800-58334800	Enhancers	Muscle Satellite Cultured Cells	--
31	chr2:58333800-58334800	Enhancers	NHLF	lung
32	chr2:58333800-58334800	Enhancers	Osteobl	bone
33	chr2:58333800-58335000	Enhancers	NHEK	skin
34	chr2:58334000-58334800	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
35	chr2:58334000-58334800	Enhancers	Brain Anterior Caudate	brain
36	chr2:58334000-58334800	Enhancers	Hela-S3	cervix
37	chr2:58334000-58335200	Flanking Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
38	chr2:58334000-58336200	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
39	chr2:58334200-58334800	Enhancers	HMEC	breast
40	chr2:58334200-58335400	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
41	chr2:58334400-58334800	Enhancers	Brain Hippocampus Middle	brain
42	chr2:58334400-58334800	Weak transcription	Brain Substantia Nigra	brain
43	chr2:58334400-58335000	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
44	chr2:58334400-58336400	Enhancers	Primary monocytes fromperipheralblood	blood
45	chr2:58334600-58334800	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
46	chr2:58334600-58334800	Enhancers	Primary neutrophils fromperipheralblood	blood
47	chr2:58334600-58334800	Enhancers	NH-A	brain
48	chr2:58334600-58335000	Strong transcription	Primary B cells from cord blood	blood
49	chr2:58334600-58335000	Flanking Active TSS	A549	lung
50	chr2:58334600-58335000	Flanking Active TSS	Monocytes-CD14+_RO01746	blood

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