Variant report

Variant	rs17049353
Chromosome Location	chr2:58348475-58348476
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	chr2:58332265..58336013-chr2:58347138..58350480,3	MCF-7	breast:

Extended variants
information (count: 43 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:38)

rs_ID	r²[population]
rs10176942	1.00[EUR][1000 genomes]
rs12105064	1.00[EUR][1000 genomes];1.00[ASN][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	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs17049341	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17049342	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17049343	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17049344	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17049345	1.00[ASN][1000 genomes]
rs17049350	1.00[EUR][1000 genomes]
rs17049354	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs17049355	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17049364	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[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72951066	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72951082	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs72953108	0.84[AFR][1000 genomes];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:5 , 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	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
3	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
4	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
5	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:66 , 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	chr2:58319400-58358400	Weak transcription	Ovary	ovary
7	chr2:58319800-58349800	Weak transcription	Primary T cells from cord blood	blood
8	chr2:58319800-58350800	Weak transcription	Primary T helper cells fromperipheralblood	blood
9	chr2:58319800-58359000	Weak transcription	Primary T helper cells PMA-I stimulated	--
10	chr2:58319800-58367200	Weak transcription	Rectal Mucosa Donor 29	rectum
11	chr2:58320000-58359000	Weak transcription	Left Ventricle	heart
12	chr2:58322600-58349800	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
13	chr2:58322600-58350400	Weak transcription	Primary B cells from peripheral blood	blood
14	chr2:58323200-58350400	Weak transcription	Primary T cells fromperipheralblood	blood
15	chr2:58323600-58350200	Weak transcription	Liver	Liver
16	chr2:58332400-58370800	Weak transcription	Duodenum Mucosa	Duodenum
17	chr2:58335800-58350600	Weak transcription	Brain Hippocampus Middle	brain
18	chr2:58335800-58358600	Weak transcription	Brain Anterior Caudate	brain
19	chr2:58336400-58365000	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
20	chr2:58337000-58358600	Weak transcription	NHLF	lung
21	chr2:58337200-58358400	Weak transcription	Fetal Muscle Leg	muscle
22	chr2:58338000-58358400	Weak transcription	Fetal Stomach	stomach
23	chr2:58338200-58365400	Weak transcription	Fetal Intestine Small	intestine
24	chr2:58338800-58359000	Weak transcription	HepG2	liver
25	chr2:58339000-58350000	Weak transcription	Dnd41	blood
26	chr2:58340000-58358400	Weak transcription	NH-A	brain
27	chr2:58340200-58349600	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
28	chr2:58340600-58349000	Weak transcription	Osteobl	bone
29	chr2:58340600-58349800	Weak transcription	HUVEC	blood vessel
30	chr2:58340600-58350200	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
31	chr2:58340600-58358400	Weak transcription	HMEC	breast
32	chr2:58340600-58363000	Weak transcription	iPS-18 Cell Line	embryonic stem cell
33	chr2:58340600-58367000	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
34	chr2:58340600-58373600	Weak transcription	Primary neutrophils fromperipheralblood	blood
35	chr2:58341000-58349600	Weak transcription	Primary monocytes fromperipheralblood	blood
36	chr2:58341000-58350000	Weak transcription	Monocytes-CD14+_RO01746	blood
37	chr2:58344400-58386000	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
38	chr2:58346000-58358600	Weak transcription	Fetal Lung	lung
39	chr2:58346000-58384400	Weak transcription	HUES6 Cell Line	embryonic stem cell
40	chr2:58346600-58349000	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
41	chr2:58346600-58358400	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
42	chr2:58346600-58373600	Weak transcription	NHEK	skin
43	chr2:58346800-58387200	Weak transcription	Skeletal Muscle Female	skeletal muscle
44	chr2:58347000-58348600	ZNF genes & repeats	GM12878-XiMat	blood
45	chr2:58347000-58360800	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
46	chr2:58347200-58350200	Weak transcription	Esophagus	oesophagus
47	chr2:58347200-58360200	Weak transcription	Skeletal Muscle Male	skeletal muscle
48	chr2:58347200-58373800	Weak transcription	Hela-S3	cervix
49	chr2:58347600-58352600	Strong transcription	Primary B cells from cord blood	blood
50	chr2:58347800-58348600	Strong transcription	Adipose Nuclei	Adipose

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