Variant report

Variant	rs3769860
Chromosome Location	chr2:179666246-179666247
allele	A/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr2:179662340..179664242-chr2:179665023..179667760,3	K562	blood:

Extended variants
information (count: 35 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:33)

rs_ID	r²[population]
rs11902709	1.00[CEU][hapmap];0.92[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs12464157	1.00[AFR][1000 genomes]
rs12464703	1.00[CEU][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs12470905	1.00[CEU][hapmap];0.97[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs12476203	1.00[AFR][1000 genomes]
rs12476289	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs12477340	1.00[AFR][1000 genomes]
rs16866497	1.00[CEU][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs16866532	1.00[CEU][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs17453396	1.00[AFR][1000 genomes]
rs17453403	1.00[AFR][1000 genomes]
rs1883084	1.00[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs1883085	1.00[CEU][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs2253324	1.00[CEU][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs2291304	1.00[CEU][hapmap];1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs2291305	1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs2291308	1.00[CEU][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs2306636	1.00[CEU][hapmap];1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs2562829	1.00[CEU][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs2627040	1.00[CEU][hapmap];0.89[EUR][1000 genomes]
rs2627041	0.92[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs2742347	1.00[CEU][hapmap];0.89[EUR][1000 genomes]
rs2742357	1.00[CEU][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs55863869	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs55913885	1.00[AFR][1000 genomes]
rs56030306	1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];0.94[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs56120016	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs56142888	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs66677602	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs72647839	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs72647889	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs72648917	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs966783	1.00[AFR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:2 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	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
2	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:38 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:179533600-179669200	Weak transcription	Primary T helper naive cells from peripheral blood	blood
2	chr2:179610800-179671400	Weak transcription	Ovary	ovary
3	chr2:179632400-179667800	Weak transcription	iPS-15b Cell Line	embryonic stem cell
4	chr2:179639000-179672000	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
5	chr2:179639400-179671400	Weak transcription	Gastric	stomach
6	chr2:179646000-179684800	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
7	chr2:179647800-179672000	Weak transcription	Fetal Thymus	thymus
8	chr2:179648400-179667200	Weak transcription	HSMM	muscle
9	chr2:179655800-179670800	Weak transcription	H9 Cell Line	embryonic stem cell
10	chr2:179656200-179668400	Weak transcription	Fetal Intestine Small	intestine
11	chr2:179656400-179667600	Weak transcription	Adipose Nuclei	Adipose
12	chr2:179656800-179674400	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
13	chr2:179657800-179668800	Weak transcription	Aorta	Aorta
14	chr2:179658200-179666800	Weak transcription	Psoas Muscle	Psoas
15	chr2:179659200-179671400	Weak transcription	Primary T cells fromperipheralblood	blood
16	chr2:179659400-179698000	Weak transcription	Primary B cells from cord blood	blood
17	chr2:179659800-179671200	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
18	chr2:179660000-179669200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
19	chr2:179662400-179669600	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
20	chr2:179663200-179669400	Weak transcription	Fetal Intestine Large	intestine
21	chr2:179663800-179666800	Strong transcription	Primary T helper cells fromperipheralblood	blood
22	chr2:179663800-179668600	Strong transcription	HSMMtube	muscle
23	chr2:179663800-179669800	Strong transcription	Primary T cells from cord blood	blood
24	chr2:179663800-179671200	Transcr. at gene 5' and 3'	Skeletal Muscle Female	skeletal muscle
25	chr2:179664200-179669600	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
26	chr2:179664600-179672000	Weak transcription	Thymus	Thymus
27	chr2:179664800-179670000	Transcr. at gene 5' and 3'	Skeletal Muscle Male	skeletal muscle
28	chr2:179664800-179673000	Active TSS	Right Atrium	heart
29	chr2:179665400-179666400	Weak transcription	Right Ventricle	heart
30	chr2:179665400-179666800	Weak transcription	Left Ventricle	heart
31	chr2:179665400-179666800	Weak transcription	Pancreas	Pancrea
32	chr2:179665400-179668800	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
33	chr2:179665600-179666600	Weak transcription	Fetal Muscle Trunk	muscle
34	chr2:179665600-179667200	Weak transcription	Primary T helper cells PMA-I stimulated	--
35	chr2:179665600-179668400	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
36	chr2:179665600-179668600	Weak transcription	Primary B cells from peripheral blood	blood
37	chr2:179666000-179668200	Transcr. at gene 5' and 3'	Fetal Heart	heart
38	chr2:179666200-179666800	Active TSS	Fetal Muscle Leg	muscle

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