Variant report

Variant	rs17024278
Chromosome Location	chr2:39962778-39962779
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr2:39962607..39965298-chr2:39967236..39969743,2	K562	blood:
2	chr2:39962720..39965298-chr2:39968180..39969743,3	K562	blood:
3	chr2:39961424..39963272-chr2:40004019..40005990,2	K562	blood:

Extended variants
information (count: 61 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:59)

rs_ID	r²[population]
rs10490332	1.00[MEX][hapmap]
rs17024157	1.00[AMR][1000 genomes]
rs17024166	0.81[LWK][hapmap];1.00[MEX][hapmap];0.80[YRI][hapmap];1.00[AMR][1000 genomes]
rs17024174	0.82[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs17024175	0.82[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs17024189	0.82[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs17024194	0.82[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs17024197	1.00[AMR][1000 genomes]
rs17024202	1.00[AMR][1000 genomes]
rs17024206	1.00[AMR][1000 genomes]
rs17024260	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs17024275	0.87[AFR][1000 genomes]
rs17024282	1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs17024292	0.80[YRI][hapmap];0.80[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs17024307	1.00[MEX][hapmap]
rs17038962	1.00[ASW][hapmap];1.00[MEX][hapmap];0.85[MKK][hapmap];1.00[YRI][hapmap];1.00[AMR][1000 genomes]
rs2110658	0.81[LWK][hapmap];0.89[YRI][hapmap]
rs57028848	1.00[AMR][1000 genomes]
rs57317087	0.85[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs57564028	1.00[AMR][1000 genomes]
rs58054718	1.00[AMR][1000 genomes]
rs58462460	0.84[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs60131290	1.00[AMR][1000 genomes]
rs72934288	1.00[AMR][1000 genomes]
rs72934295	1.00[AMR][1000 genomes]
rs72934302	0.82[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs72936018	1.00[AMR][1000 genomes]
rs72936030	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs72936031	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs72936034	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs72936037	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs72936041	0.80[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs72936044	0.80[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs72936047	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs72936048	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs72936053	0.81[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs72936058	0.81[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs72936068	0.87[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs72936072	0.84[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs72936073	1.00[AMR][1000 genomes]
rs72936076	0.87[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs72936078	0.87[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs72936079	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs72936085	0.80[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs72936089	1.00[AMR][1000 genomes]
rs72936091	0.80[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs72936095	0.82[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs72936096	0.80[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs72936102	1.00[AMR][1000 genomes]
rs72938105	0.82[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs72938110	0.85[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs72938112	1.00[AMR][1000 genomes]
rs72938118	0.85[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs72938121	1.00[AMR][1000 genomes]
rs72938124	1.00[AMR][1000 genomes]
rs72938132	0.83[AFR][1000 genomes]
rs72938134	1.00[AMR][1000 genomes]
rs72938145	1.00[AMR][1000 genomes]
rs990404	0.82[AFR][1000 genomes];1.00[AMR][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	nsv833870	chr2:39837022-40026024	Flanking Bivalent TSS/Enh Weak transcription Enhancers Strong transcription Active TSS Genic enhancers Bivalent/Poised TSS 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	nsv833881	chr2:39914558-40067256	Weak transcription Enhancers Strong transcription Bivalent Enhancer Active TSS Genic enhancers Flanking Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:124 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:39942000-39963000	Weak transcription	Duodenum Smooth Muscle	Duodenum
2	chr2:39944400-39976600	Weak transcription	Fetal Brain Male	brain
3	chr2:39951000-39963600	Weak transcription	Pancreas	Pancrea
4	chr2:39951000-39964800	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
5	chr2:39951200-39964800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
6	chr2:39951400-39963800	Weak transcription	H9 Cell Line	embryonic stem cell
7	chr2:39952000-39964800	Weak transcription	Rectal Smooth Muscle	rectum
8	chr2:39956000-39962800	Weak transcription	HUVEC	blood vessel
9	chr2:39956200-39966400	Weak transcription	Small Intestine	intestine
10	chr2:39956600-39962800	Weak transcription	Rectal Mucosa Donor 31	rectum
11	chr2:39956600-39963400	Weak transcription	Ovary	ovary
12	chr2:39956800-39964600	Weak transcription	Placenta Amnion	Placenta Amnion
13	chr2:39957400-39971200	Strong transcription	Primary T cells from cord blood	blood
14	chr2:39957600-39963200	Strong transcription	Fetal Lung	lung
15	chr2:39957600-39964200	Strong transcription	Ganglion Eminence derived primary cultured neurospheres	brain
16	chr2:39958400-39963800	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
17	chr2:39958800-39964400	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
18	chr2:39958800-39964600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
19	chr2:39959000-39971200	Strong transcription	Fetal Thymus	thymus
20	chr2:39959400-39966400	Strong transcription	Fetal Intestine Large	intestine
21	chr2:39959400-39967400	Strong transcription	A549	lung
22	chr2:39959400-39971000	Strong transcription	Monocytes-CD14+_RO01746	blood
23	chr2:39959400-39974200	Strong transcription	Primary B cells from cord blood	blood
24	chr2:39959600-39963800	Weak transcription	Esophagus	oesophagus
25	chr2:39959600-39967200	Strong transcription	HepG2	liver
26	chr2:39959800-39967000	Genic enhancers	Breast Myoepithelial Primary Cells	Breast
27	chr2:39960000-39962800	Weak transcription	Right Ventricle	heart
28	chr2:39960000-39963200	Weak transcription	Brain Germinal Matrix	brain
29	chr2:39960000-39964800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
30	chr2:39960000-39964800	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
31	chr2:39960000-39969000	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
32	chr2:39960000-39971000	Strong transcription	K562	blood
33	chr2:39960000-39971200	Strong transcription	Fetal Muscle Trunk	muscle
34	chr2:39960000-39971400	Strong transcription	Primary hematopoietic stem cells short term culture	blood
35	chr2:39960000-39971800	Strong transcription	Primary monocytes fromperipheralblood	blood
36	chr2:39960200-39963800	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
37	chr2:39960200-39963800	Weak transcription	Brain Anterior Caudate	brain
38	chr2:39960200-39965000	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
39	chr2:39960200-39971000	Strong transcription	Fetal Muscle Leg	muscle
40	chr2:39960200-39973800	Strong transcription	Primary hematopoietic stem cells	blood
41	chr2:39960200-39987200	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
42	chr2:39960400-39965000	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
43	chr2:39960400-39970200	Strong transcription	GM12878-XiMat	blood
44	chr2:39960400-39973600	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
45	chr2:39960400-39983000	Weak transcription	Stomach Mucosa	stomach
46	chr2:39960600-39963800	Weak transcription	Brain Cingulate Gyrus	brain
47	chr2:39960600-39963800	Weak transcription	Psoas Muscle	Psoas
48	chr2:39960600-39964600	Strong transcription	Foreskin Fibroblast Primary Cells skin01	Skin
49	chr2:39960800-39962800	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
50	chr2:39960800-39964600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived

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