Variant report

Variant	rs17049339
Chromosome Location	chr2:58327370-58327371
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 28 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:22)

rs_ID	r²[population]
rs10445895	1.00[ASW][hapmap];0.91[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];0.86[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.85[AMR][1000 genomes];0.93[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs10445896	0.93[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs17049243	0.81[CEU][hapmap];0.83[CHD][hapmap];1.00[JPT][hapmap];0.86[MEX][hapmap]
rs17049247	0.81[CEU][hapmap];1.00[JPT][hapmap]
rs17049270	0.91[CEU][hapmap];1.00[JPT][hapmap];0.88[EUR][1000 genomes]
rs17049296	0.91[CEU][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.88[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs17049298	0.91[CEU][hapmap];1.00[JPT][hapmap];0.86[MEX][hapmap];0.82[AMR][1000 genomes];0.88[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs17049318	0.91[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[YRI][hapmap];0.85[AMR][1000 genomes];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17049334	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.87[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17049351	1.00[ASW][hapmap];0.91[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];0.86[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17049366	0.91[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.96[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2196806	0.91[CEU][hapmap];1.00[CHB][hapmap];0.83[CHD][hapmap];0.90[GIH][hapmap];1.00[JPT][hapmap];0.91[TSI][hapmap];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3771204	0.91[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];0.89[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3771206	0.91[CEU][hapmap];1.00[CHB][hapmap];0.83[CHD][hapmap];0.90[GIH][hapmap];1.00[JPT][hapmap];0.91[TSI][hapmap];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3771211	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];0.86[MEX][hapmap];0.87[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3771212	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs56246409	0.83[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs57471952	0.88[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs59378271	0.85[AMR][1000 genomes];0.88[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs60152647	0.89[AMR][1000 genomes];0.88[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs73942293	0.90[EUR][1000 genomes]
rs7577299	0.91[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[EUR][1000 genomes];0.85[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:44 , 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	chr2:58307600-58328600	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
4	chr2:58308600-58333600	Weak transcription	NHDF-Ad	bronchial
5	chr2:58311200-58382400	Weak transcription	Aorta	Aorta
6	chr2:58315200-58389600	Weak transcription	Primary T killer memory cells from peripheral blood	blood
7	chr2:58318200-58327600	Weak transcription	Placenta	Placenta
8	chr2:58318200-58373200	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
9	chr2:58318400-58334800	Weak transcription	HSMM	muscle
10	chr2:58319400-58358400	Weak transcription	Ovary	ovary
11	chr2:58319800-58349800	Weak transcription	Primary T cells from cord blood	blood
12	chr2:58319800-58350800	Weak transcription	Primary T helper cells fromperipheralblood	blood
13	chr2:58319800-58359000	Weak transcription	Primary T helper cells PMA-I stimulated	--
14	chr2:58319800-58367200	Weak transcription	Rectal Mucosa Donor 29	rectum
15	chr2:58320000-58327600	Weak transcription	Fetal Lung	lung
16	chr2:58320000-58334600	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
17	chr2:58320000-58334600	Weak transcription	HUVEC	blood vessel
18	chr2:58320000-58334800	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
19	chr2:58320000-58339600	Weak transcription	Primary hematopoietic stem cells short term culture	blood
20	chr2:58320000-58347600	Weak transcription	Duodenum Smooth Muscle	Duodenum
21	chr2:58320000-58359000	Weak transcription	Left Ventricle	heart
22	chr2:58322200-58334200	Weak transcription	Monocytes-CD14+_RO01746	blood
23	chr2:58322200-58347400	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
24	chr2:58322600-58334400	Weak transcription	Primary monocytes fromperipheralblood	blood
25	chr2:58322600-58349800	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
26	chr2:58322600-58350400	Weak transcription	Primary B cells from peripheral blood	blood
27	chr2:58323200-58335400	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
28	chr2:58323200-58347600	Weak transcription	Breast Myoepithelial Primary Cells	Breast
29	chr2:58323200-58350400	Weak transcription	Primary T cells fromperipheralblood	blood
30	chr2:58323600-58350200	Weak transcription	Liver	Liver
31	chr2:58323800-58334200	Weak transcription	Brain Substantia Nigra	brain
32	chr2:58325200-58327400	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
33	chr2:58325200-58328600	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
34	chr2:58325800-58333800	Weak transcription	NHEK	skin
35	chr2:58325800-58333800	Weak transcription	Osteobl	bone
36	chr2:58326200-58327600	Strong transcription	A549	lung
37	chr2:58326400-58327400	Strong transcription	Primary B cells from cord blood	blood
38	chr2:58326400-58334000	Weak transcription	Hela-S3	cervix
39	chr2:58326400-58347600	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
40	chr2:58326800-58334000	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
41	chr2:58326800-58334800	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
42	chr2:58327000-58337600	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
43	chr2:58327000-58339600	Weak transcription	K562	blood
44	chr2:58327000-58347600	Weak transcription	Primary hematopoietic stem cells	blood

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