Variant report

Variant	rs6762593
Chromosome Location	chr3:49463926-49463927
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 82 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:80)

rs_ID	r²[population]
rs11130197	1.00[YRI][hapmap]
rs11130201	0.89[AFR][1000 genomes]
rs11708174	1.00[ASW][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap]
rs11717485	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs1522929	1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs1568663	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs17080495	1.00[ASW][hapmap];1.00[LWK][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];0.91[YRI][hapmap];0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs17080510	1.00[ASW][hapmap];1.00[LWK][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];0.91[YRI][hapmap];0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs17080567	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs17080664	0.91[YRI][hapmap];0.92[AFR][1000 genomes]
rs1996874	1.00[ASW][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs2131107	0.89[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs2311794	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs2311801	1.00[ASW][hapmap];1.00[LWK][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];0.91[YRI][hapmap];0.86[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs2329024	1.00[ASW][hapmap];1.00[LWK][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.89[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs28615670	1.00[EUR][1000 genomes]
rs3870334	1.00[ASW][hapmap];1.00[LWK][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];0.82[YRI][hapmap];0.86[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs3870340	0.82[ASW][hapmap];1.00[YRI][hapmap];0.94[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs3912831	1.00[YRI][hapmap];0.84[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs4241409	1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs4452334	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs4527417	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs4855856	1.00[YRI][hapmap];0.89[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs4855857	1.00[ASW][hapmap];1.00[LWK][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.89[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs4855870	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs4855872	0.90[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs4855874	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs4855875	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs4855876	0.83[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs4855878	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs4855879	1.00[YRI][hapmap];0.83[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs55677747	0.81[AFR][1000 genomes]
rs55808753	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs55990645	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs56101322	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs56760510	0.86[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs56897974	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs59579780	0.86[AFR][1000 genomes]
rs60011446	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs61749312	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs6446269	0.97[AFR][1000 genomes]
rs6446270	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs6446271	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs6446273	1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs6446276	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs6446278	0.88[YRI][hapmap];0.83[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs6446279	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs6446280	0.92[AFR][1000 genomes]
rs6446281	0.84[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs6446282	0.86[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs6446283	1.00[EUR][1000 genomes]
rs6766297	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs6787665	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs6793124	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs6797164	1.00[YRI][hapmap];0.83[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs72936890	1.00[EUR][1000 genomes]
rs73830703	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs73830704	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs73830705	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs73830706	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs73831434	0.81[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs73831435	0.83[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs73831436	1.00[EUR][1000 genomes]
rs73831437	1.00[EUR][1000 genomes]
rs73831438	0.83[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs73831439	0.86[AFR][1000 genomes]
rs73831440	0.86[AFR][1000 genomes]
rs73831441	0.86[AFR][1000 genomes]
rs73831442	0.92[AFR][1000 genomes]
rs7646393	1.00[YRI][hapmap];0.94[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs8179172	1.00[ASW][hapmap];1.00[LWK][hapmap];1.00[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]
rs9311441	1.00[AFR][1000 genomes]
rs9811460	1.00[EUR][1000 genomes]
rs9814413	1.00[EUR][1000 genomes]
rs9830627	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs9837396	1.00[EUR][1000 genomes]
rs9849446	1.00[EUR][1000 genomes]
rs9861805	0.82[ASW][hapmap];1.00[TSI][hapmap];0.84[YRI][hapmap];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs9869504	1.00[EUR][1000 genomes]
rs9875203	1.00[AMR][1000 genomes];1.00[EUR][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	nsv834687	chr3:49448632-49631788	Flanking Active TSS Strong transcription Enhancers Weak transcription Active TSS Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	56 gene(s)	inside rSNPs	diseases
2	nsv963482	chr3:49459177-49486938	Weak transcription Enhancers Flanking Active TSS Active TSS Strong transcription Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:122 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:49451200-49466200	Weak transcription	Psoas Muscle	Psoas
2	chr3:49455600-49466200	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
3	chr3:49457400-49466000	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
4	chr3:49457600-49465400	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
5	chr3:49459200-49466200	Weak transcription	HUVEC	blood vessel
6	chr3:49459400-49465800	Weak transcription	Muscle Satellite Cultured Cells	--
7	chr3:49459600-49465200	Weak transcription	Hela-S3	cervix
8	chr3:49459600-49465600	Weak transcription	NHDF-Ad	bronchial
9	chr3:49459600-49466200	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
10	chr3:49459600-49466200	Weak transcription	HMEC	breast
11	chr3:49459800-49465600	Weak transcription	NHEK	skin
12	chr3:49460200-49466000	Weak transcription	Pancreatic Islets	Pancreatic Islet
13	chr3:49460400-49464000	Strong transcription	Breast Myoepithelial Primary Cells	Breast
14	chr3:49460400-49464400	Strong transcription	Cortex derived primary cultured neurospheres	brain
15	chr3:49460400-49464400	Strong transcription	Thymus	Thymus
16	chr3:49460400-49465800	Weak transcription	Brain Angular Gyrus	brain
17	chr3:49460400-49465800	Weak transcription	Right Atrium	heart
18	chr3:49460400-49466200	Weak transcription	Primary neutrophils fromperipheralblood	blood
19	chr3:49460600-49464600	Strong transcription	Ganglion Eminence derived primary cultured neurospheres	brain
20	chr3:49460600-49465600	Weak transcription	Esophagus	oesophagus
21	chr3:49460600-49465600	Weak transcription	Rectal Mucosa Donor 31	rectum
22	chr3:49460600-49465600	Weak transcription	A549	lung
23	chr3:49460600-49465800	Weak transcription	Primary hematopoietic stem cells	blood
24	chr3:49460600-49465800	Weak transcription	Brain Substantia Nigra	brain
25	chr3:49460600-49465800	Weak transcription	Fetal Brain Male	brain
26	chr3:49460600-49466000	Weak transcription	ES-I3 Cell Line	embryonic stem cell
27	chr3:49460600-49466000	Weak transcription	H9 Cell Line	embryonic stem cell
28	chr3:49460600-49466000	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
29	chr3:49460600-49466000	Weak transcription	iPS-15b Cell Line	embryonic stem cell
30	chr3:49460600-49466200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
31	chr3:49460600-49466200	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
32	chr3:49460600-49466200	Weak transcription	Small Intestine	intestine
33	chr3:49460600-49466200	Weak transcription	Stomach Mucosa	stomach
34	chr3:49460600-49466200	Weak transcription	HSMM	muscle
35	chr3:49460600-49466200	Weak transcription	Osteobl	bone
36	chr3:49460800-49464000	Strong transcription	Fetal Thymus	thymus
37	chr3:49460800-49465000	Strong transcription	Fetal Stomach	stomach
38	chr3:49460800-49465600	Weak transcription	NH-A	brain
39	chr3:49460800-49465800	Weak transcription	H1 Cell Line	embryonic stem cell
40	chr3:49460800-49466000	Weak transcription	HUES64 Cell Line	embryonic stem cell
41	chr3:49460800-49466000	Weak transcription	iPS-18 Cell Line	embryonic stem cell
42	chr3:49460800-49466000	Weak transcription	iPS-20b Cell Line	embryonic stem cell
43	chr3:49460800-49466200	Weak transcription	HUES48 Cell Line	embryonic stem cell
44	chr3:49460800-49466200	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
45	chr3:49460800-49466200	Weak transcription	Fetal Heart	heart
46	chr3:49460800-49466200	Weak transcription	Fetal Kidney	kidney
47	chr3:49460800-49466200	Weak transcription	HSMMtube	muscle
48	chr3:49461000-49464000	Strong transcription	Fetal Muscle Leg	muscle
49	chr3:49461000-49464400	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
50	chr3:49461200-49464200	Strong transcription	Fetal Muscle Trunk	muscle

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