Variant report

Variant	rs57654423
Chromosome Location	chr3:52930456-52930457
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 48 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:46)

rs_ID	r²[population]
rs34397833	1.00[AMR][1000 genomes]
rs35981653	1.00[AMR][1000 genomes]
rs56665986	0.84[AFR][1000 genomes]
rs56895623	0.86[AFR][1000 genomes]
rs57273027	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs57465047	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs57561909	0.84[AFR][1000 genomes]
rs57640885	1.00[AMR][1000 genomes]
rs58249114	0.86[AFR][1000 genomes]
rs58888768	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs59224641	0.84[AFR][1000 genomes]
rs59838592	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs60207422	1.00[AMR][1000 genomes]
rs60648378	0.84[AFR][1000 genomes]
rs60805548	1.00[AMR][1000 genomes]
rs61324750	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs61331336	0.86[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs6776862	1.00[AMR][1000 genomes]
rs6798309	0.87[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs6798669	0.86[AFR][1000 genomes]
rs72954390	1.00[AMR][1000 genomes]
rs72954402	1.00[AMR][1000 genomes]
rs72959475	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs72959477	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs72959478	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs72959479	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs72959482	0.98[AFR][1000 genomes]
rs72959487	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs72959494	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs72959499	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs72961704	0.98[AFR][1000 genomes]
rs72961705	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs72961708	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs72961711	1.00[AMR][1000 genomes]
rs72961724	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs72961730	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs72961733	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs72961742	0.87[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs72961752	0.87[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs72965340	0.86[AFR][1000 genomes]
rs72965348	0.86[AFR][1000 genomes]
rs72965358	0.89[AFR][1000 genomes]
rs72965359	0.86[AFR][1000 genomes]
rs72965370	0.87[AFR][1000 genomes]
rs72965381	0.86[AFR][1000 genomes]
rs7618417	0.89[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	esv2762328	chr3:52774884-53002150	Strong transcription Enhancers Active TSS Flanking Active TSS Weak transcription Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	27 gene(s)	inside rSNPs	diseases
2	esv3446915	chr3:52786850-53049217	Strong transcription Active TSS Transcr. at gene 5' and 3' Flanking Active TSS Bivalent Enhancer Weak transcription Enhancers Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	27 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:126 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:52908400-52930600	Weak transcription	A549	lung
2	chr3:52916400-52930600	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
3	chr3:52920400-52930600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
4	chr3:52920400-52930600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
5	chr3:52920400-52930600	Weak transcription	Rectal Mucosa Donor 31	rectum
6	chr3:52921600-52930600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
7	chr3:52925600-52930600	Weak transcription	Esophagus	oesophagus
8	chr3:52927400-52930600	Enhancers	Primary T helper naive cells from peripheral blood	blood
9	chr3:52927600-52930600	Enhancers	Gastric	stomach
10	chr3:52927600-52930600	Enhancers	Pancreas	Pancrea
11	chr3:52927800-52930600	Weak transcription	HSMMtube	muscle
12	chr3:52928200-52930600	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
13	chr3:52928200-52930800	Weak transcription	Sigmoid Colon	Sigmoid Colon
14	chr3:52928400-52930600	Weak transcription	Rectal Smooth Muscle	rectum
15	chr3:52928400-52931000	Weak transcription	Small Intestine	intestine
16	chr3:52928800-52930600	Enhancers	Primary T killer memory cells from peripheral blood	blood
17	chr3:52929200-52930600	Flanking Active TSS	Primary T helper 17 cells PMA-I stimulated	--
18	chr3:52929200-52930600	Enhancers	Lung	lung
19	chr3:52929400-52930600	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
20	chr3:52929400-52930600	Enhancers	Primary T killer naive cells fromperipheralblood	blood
21	chr3:52929400-52930600	Enhancers	Fetal Adrenal Gland	Adrenal Gland
22	chr3:52929400-52930600	Enhancers	Fetal Brain Male	brain
23	chr3:52929400-52930600	Weak transcription	Fetal Muscle Trunk	muscle
24	chr3:52929600-52930600	Weak transcription	Left Ventricle	heart
25	chr3:52929600-52931200	Flanking Active TSS	Primary T regulatory cells fromperipheralblood	blood
26	chr3:52929600-52931200	Flanking Active TSS	Primary T cells effector/memory enriched fromperipheralblood	blood
27	chr3:52929600-52931200	Flanking Active TSS	Monocytes-CD14+_RO01746	blood
28	chr3:52929800-52930600	Enhancers	Adipose Nuclei	Adipose
29	chr3:52929800-52930600	Enhancers	Fetal Lung	lung
30	chr3:52929800-52930600	Enhancers	Fetal Stomach	stomach
31	chr3:52929800-52931000	Flanking Active TSS	Primary T helper cells PMA-I stimulated	--
32	chr3:52929800-52931000	Flanking Active TSS	Brain Angular Gyrus	brain
33	chr3:52929800-52931000	Flanking Active TSS	Brain Anterior Caudate	brain
34	chr3:52929800-52931000	Flanking Active TSS	Thymus	Thymus
35	chr3:52929800-52931200	Flanking Active TSS	Brain Inferior Temporal Lobe	brain
36	chr3:52929800-52931200	Flanking Active TSS	Fetal Thymus	thymus
37	chr3:52929800-52931200	Flanking Active TSS	Skeletal Muscle Male	skeletal muscle
38	chr3:52929800-52931400	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
39	chr3:52929800-52932200	Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
40	chr3:52929800-52932200	Flanking Active TSS	Primary hematopoietic stem cells	blood
41	chr3:52930000-52930600	Enhancers	Primary B cells from cord blood	blood
42	chr3:52930000-52930600	Enhancers	Primary T cells from cord blood	blood
43	chr3:52930000-52930600	Active TSS	Rectal Mucosa Donor 29	rectum
44	chr3:52930000-52930600	Enhancers	HUVEC	blood vessel
45	chr3:52930000-52930800	Enhancers	Fetal Heart	heart
46	chr3:52930000-52930800	Flanking Active TSS	HMEC	breast
47	chr3:52930000-52931000	Flanking Active TSS	Brain Hippocampus Middle	brain
48	chr3:52930000-52931000	Flanking Active TSS	Colon Smooth Muscle	Colon
49	chr3:52930000-52931200	Flanking Active TSS	Brain Substantia Nigra	brain
50	chr3:52930000-52931400	Flanking Active TSS	Primary hematopoietic stem cells short term culture	blood

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