Variant report

Variant	rs2562839
Chromosome Location	chr2:179578730-179578731
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 25 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:21)

rs_ID	r²[population]
rs12622914	0.81[TSI][hapmap]
rs12693164	0.81[TSI][hapmap]
rs12997957	0.81[TSI][hapmap]
rs13390491	0.81[TSI][hapmap]
rs1484116	0.86[CEU][hapmap];0.95[JPT][hapmap];0.94[TSI][hapmap];0.95[EUR][1000 genomes]
rs1484119	0.86[CEU][hapmap];0.90[JPT][hapmap];0.95[EUR][1000 genomes]
rs16866420	0.82[TSI][hapmap]
rs16866465	0.81[TSI][hapmap]
rs17076	0.95[JPT][hapmap]
rs2042996	0.82[TSI][hapmap]
rs2291313	0.86[CEU][hapmap];0.90[JPT][hapmap];0.90[TSI][hapmap];0.92[EUR][1000 genomes]
rs2472751	0.82[TSI][hapmap]
rs2562830	0.93[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[TSI][hapmap];0.88[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2562834	1.00[CHB][hapmap];0.85[CHD][hapmap];1.00[JPT][hapmap];0.94[TSI][hapmap]
rs2562836	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2562838	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.83[MKK][hapmap];1.00[TSI][hapmap];0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2627043	1.00[ASW][hapmap];0.93[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.93[LWK][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];0.96[YRI][hapmap];0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2742327	0.93[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.82[MKK][hapmap];1.00[TSI][hapmap];0.89[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2742331	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4471922	0.86[CEU][hapmap];0.90[JPT][hapmap];0.94[TSI][hapmap];0.92[EUR][1000 genomes]
rs6750145	0.87[TSI][hapmap]

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	esv2757841	chr2:179409072-179608242	Active TSS ZNF genes & repeats Weak transcription Strong transcription Enhancers Genic enhancers Transcr. at gene 5' and 3' Flanking Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	13 gene(s)	inside rSNPs	diseases
2	esv2759103	chr2:179409072-179608242	Weak transcription Strong transcription Enhancers Genic enhancers ZNF genes & repeats Active TSS Transcr. at gene 5' and 3' Flanking Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	13 gene(s)	inside rSNPs	diseases
3	nsv834470	chr2:179555152-179728726	Active TSS Genic enhancers Weak transcription Enhancers Strong transcription Flanking Active TSS ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
4	nsv934108	chr2:179556852-179729925	Weak transcription Genic enhancers Strong transcription ZNF genes & repeats Enhancers Flanking Active TSS Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:36 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:179483200-179655400	Weak transcription	Adipose Nuclei	Adipose
2	chr2:179493000-179620800	Weak transcription	HSMM	muscle
3	chr2:179528200-179601200	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
4	chr2:179529600-179600600	Weak transcription	ES-I3 Cell Line	embryonic stem cell
5	chr2:179533600-179669200	Weak transcription	Primary T helper naive cells from peripheral blood	blood
6	chr2:179538400-179591800	Weak transcription	Fetal Thymus	thymus
7	chr2:179540400-179586800	Weak transcription	H9 Cell Line	embryonic stem cell
8	chr2:179543200-179583400	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
9	chr2:179543400-179596800	Weak transcription	Primary T killer memory cells from peripheral blood	blood
10	chr2:179544800-179579600	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
11	chr2:179545800-179586800	Weak transcription	HUES64 Cell Line	embryonic stem cell
12	chr2:179556800-179592200	Weak transcription	Primary hematopoietic stem cells	blood
13	chr2:179563000-179587400	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
14	chr2:179565400-179600800	Weak transcription	Thymus	Thymus
15	chr2:179566000-179591000	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
16	chr2:179568400-179594000	Strong transcription	Left Ventricle	heart
17	chr2:179568400-179603400	Strong transcription	HSMMtube	muscle
18	chr2:179568800-179596200	Strong transcription	Fetal Muscle Leg	muscle
19	chr2:179569400-179589800	Weak transcription	Lung	lung
20	chr2:179570800-179580800	Strong transcription	Primary T helper naive cells fromperipheralblood	blood
21	chr2:179574200-179586200	Weak transcription	H1 Cell Line	embryonic stem cell
22	chr2:179574200-179590600	Genic enhancers	Skeletal Muscle Female	skeletal muscle
23	chr2:179575200-179580000	Genic enhancers	Fetal Heart	heart
24	chr2:179575200-179601000	Strong transcription	Primary T cells from cord blood	blood
25	chr2:179576200-179583000	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
26	chr2:179576800-179578800	Strong transcription	Psoas Muscle	Psoas
27	chr2:179576800-179579800	Strong transcription	Primary B cells from cord blood	blood
28	chr2:179576800-179585000	Genic enhancers	Skeletal Muscle Male	skeletal muscle
29	chr2:179577000-179580400	Strong transcription	Right Ventricle	heart
30	chr2:179577000-179582800	Weak transcription	Primary B cells from peripheral blood	blood
31	chr2:179577200-179583600	Weak transcription	Primary T cells fromperipheralblood	blood
32	chr2:179577600-179584000	Weak transcription	Primary T helper cells PMA-I stimulated	--
33	chr2:179577800-179640800	Weak transcription	Fetal Intestine Large	intestine
34	chr2:179578000-179578800	Weak transcription	Primary T helper cells fromperipheralblood	blood
35	chr2:179578200-179580400	Strong transcription	Pancreas	Pancrea
36	chr2:179578200-179585200	Strong transcription	Fetal Muscle Trunk	muscle

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