Variant report

Variant	rs55925609
Chromosome Location	chr2:58329043-58329044
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	chr2:58327413..58329315-chr2:58335366..58337624,2	MCF-7	breast:
2	chr2:58328189..58330016-chr2:58335777..58337900,2	K562	blood:

Extended variants
information (count: 37 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:31)

rs_ID	r²[population]
rs17049347	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs17049370	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs17049374	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs17049404	0.83[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs56878245	1.00[AMR][1000 genomes]
rs58495080	0.83[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs58984910	0.95[AFR][1000 genomes]
rs59264390	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs59299963	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs59871174	1.00[AMR][1000 genomes]
rs60912631	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs61126591	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs61415878	1.00[AMR][1000 genomes]
rs6741122	0.83[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs73942251	1.00[AMR][1000 genomes]
rs73942258	1.00[AMR][1000 genomes]
rs73942281	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs73944812	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs73944819	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs73944823	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs73944825	0.91[AFR][1000 genomes]
rs73944826	0.83[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs73944827	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs73944828	0.83[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs73944835	0.83[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs73944837	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs73944838	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs73944839	1.00[AMR][1000 genomes]
rs73944840	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs7587116	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs7587229	0.95[AFR][1000 genomes];1.00[AMR][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:40 , 50 per page) page: 1

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	chr2:58308600-58333600	Weak transcription	NHDF-Ad	bronchial
4	chr2:58311200-58382400	Weak transcription	Aorta	Aorta
5	chr2:58315200-58389600	Weak transcription	Primary T killer memory cells from peripheral blood	blood
6	chr2:58318200-58373200	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
7	chr2:58318400-58334800	Weak transcription	HSMM	muscle
8	chr2:58319400-58358400	Weak transcription	Ovary	ovary
9	chr2:58319800-58349800	Weak transcription	Primary T cells from cord blood	blood
10	chr2:58319800-58350800	Weak transcription	Primary T helper cells fromperipheralblood	blood
11	chr2:58319800-58359000	Weak transcription	Primary T helper cells PMA-I stimulated	--
12	chr2:58319800-58367200	Weak transcription	Rectal Mucosa Donor 29	rectum
13	chr2:58320000-58334600	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
14	chr2:58320000-58334600	Weak transcription	HUVEC	blood vessel
15	chr2:58320000-58334800	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
16	chr2:58320000-58339600	Weak transcription	Primary hematopoietic stem cells short term culture	blood
17	chr2:58320000-58347600	Weak transcription	Duodenum Smooth Muscle	Duodenum
18	chr2:58320000-58359000	Weak transcription	Left Ventricle	heart
19	chr2:58322200-58334200	Weak transcription	Monocytes-CD14+_RO01746	blood
20	chr2:58322200-58347400	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
21	chr2:58322600-58334400	Weak transcription	Primary monocytes fromperipheralblood	blood
22	chr2:58322600-58349800	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
23	chr2:58322600-58350400	Weak transcription	Primary B cells from peripheral blood	blood
24	chr2:58323200-58335400	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
25	chr2:58323200-58347600	Weak transcription	Breast Myoepithelial Primary Cells	Breast
26	chr2:58323200-58350400	Weak transcription	Primary T cells fromperipheralblood	blood
27	chr2:58323600-58350200	Weak transcription	Liver	Liver
28	chr2:58323800-58334200	Weak transcription	Brain Substantia Nigra	brain
29	chr2:58325800-58333800	Weak transcription	NHEK	skin
30	chr2:58325800-58333800	Weak transcription	Osteobl	bone
31	chr2:58326400-58334000	Weak transcription	Hela-S3	cervix
32	chr2:58326400-58347600	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
33	chr2:58326800-58334000	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
34	chr2:58326800-58334800	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
35	chr2:58327000-58337600	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
36	chr2:58327000-58339600	Weak transcription	K562	blood
37	chr2:58327000-58347600	Weak transcription	Primary hematopoietic stem cells	blood
38	chr2:58327400-58334600	Weak transcription	Primary B cells from cord blood	blood
39	chr2:58328600-58329200	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
40	chr2:58328800-58329400	ZNF genes & repeats	A549	lung

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