Variant report

Variant	rs17049374
Chromosome Location	chr2:58367495-58367496
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 36 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:32)

rs_ID	r²[population]
rs17049347	1.00[YRI][hapmap];0.95[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs17049370	1.00[ASW][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.86[MKK][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs17049389	0.91[YRI][hapmap]
rs17049404	0.92[YRI][hapmap];0.83[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs55925609	1.00[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	0.92[YRI][hapmap];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:4 , 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	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
3	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
4	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:90 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:58311200-58382400	Weak transcription	Aorta	Aorta
2	chr2:58315200-58389600	Weak transcription	Primary T killer memory cells from peripheral blood	blood
3	chr2:58318200-58373200	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
4	chr2:58332400-58370800	Weak transcription	Duodenum Mucosa	Duodenum
5	chr2:58340600-58373600	Weak transcription	Primary neutrophils fromperipheralblood	blood
6	chr2:58344400-58386000	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
7	chr2:58346000-58384400	Weak transcription	HUES6 Cell Line	embryonic stem cell
8	chr2:58346600-58373600	Weak transcription	NHEK	skin
9	chr2:58346800-58387200	Weak transcription	Skeletal Muscle Female	skeletal muscle
10	chr2:58347200-58373800	Weak transcription	Hela-S3	cervix
11	chr2:58347800-58369800	Weak transcription	Rectal Mucosa Donor 31	rectum
12	chr2:58347800-58384000	Weak transcription	Fetal Kidney	kidney
13	chr2:58347800-58386600	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
14	chr2:58348400-58373400	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
15	chr2:58348400-58373600	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
16	chr2:58348600-58382400	Weak transcription	Fetal Intestine Large	intestine
17	chr2:58349000-58421200	Weak transcription	Brain Substantia Nigra	brain
18	chr2:58350400-58383800	Weak transcription	K562	blood
19	chr2:58350800-58370800	Weak transcription	Liver	Liver
20	chr2:58351000-58371800	Weak transcription	Sigmoid Colon	Sigmoid Colon
21	chr2:58351000-58382400	Weak transcription	Esophagus	oesophagus
22	chr2:58351000-58384600	Weak transcription	HUES48 Cell Line	embryonic stem cell
23	chr2:58353800-58388200	Weak transcription	Small Intestine	intestine
24	chr2:58358200-58393800	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
25	chr2:58358400-58389000	Weak transcription	Primary T helper naive cells from peripheral blood	blood
26	chr2:58358800-58382400	Weak transcription	Pancreas	Pancrea
27	chr2:58358800-58385200	Weak transcription	Placenta	Placenta
28	chr2:58358800-58385600	Weak transcription	Fetal Thymus	thymus
29	chr2:58359000-58368000	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
30	chr2:58359000-58371400	Weak transcription	Colonic Mucosa	Colon
31	chr2:58359000-58386600	Weak transcription	Duodenum Smooth Muscle	Duodenum
32	chr2:58359000-58387400	Weak transcription	Fetal Muscle Trunk	muscle
33	chr2:58359000-58391400	Weak transcription	Fetal Muscle Leg	muscle
34	chr2:58359000-58399000	Weak transcription	Pancreatic Islets	Pancreatic Islet
35	chr2:58359000-58454000	Weak transcription	Stomach Smooth Muscle	stomach
36	chr2:58359200-58373400	Weak transcription	HMEC	breast
37	chr2:58359200-58381800	Weak transcription	Primary hematopoietic stem cells short term culture	blood
38	chr2:58359200-58382400	Weak transcription	Breast Myoepithelial Primary Cells	Breast
39	chr2:58359200-58382400	Weak transcription	Rectal Smooth Muscle	rectum
40	chr2:58359200-58384400	Weak transcription	Left Ventricle	heart
41	chr2:58359200-58395200	Weak transcription	Fetal Stomach	stomach
42	chr2:58359200-58399200	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
43	chr2:58359400-58385600	Weak transcription	Primary T helper cells PMA-I stimulated	--
44	chr2:58359400-58389400	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
45	chr2:58359600-58385600	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
46	chr2:58359800-58369600	Weak transcription	Primary T helper cells fromperipheralblood	blood
47	chr2:58359800-58384400	Weak transcription	HepG2	liver
48	chr2:58359800-58392000	Weak transcription	Placenta Amnion	Placenta Amnion
49	chr2:58360800-58385000	Weak transcription	HUES64 Cell Line	embryonic stem cell
50	chr2:58360800-58388600	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood

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