Variant report

Variant	rs2054988
Chromosome Location	chr3:56593170-56593171
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 75 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:73)

rs_ID	r²[population]
rs10212341	0.90[YRI][hapmap]
rs10222449	0.89[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs10222462	0.83[AMR][1000 genomes];0.89[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs1045926	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.97[YRI][hapmap];0.85[AMR][1000 genomes];0.82[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs10865998	0.89[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs10865999	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.80[AFR][1000 genomes];0.85[AMR][1000 genomes];0.82[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs10866000	0.82[ASN][1000 genomes]
rs11130536	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.84[AFR][1000 genomes];0.86[ASN][1000 genomes]
rs11130538	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.83[ASN][1000 genomes]
rs11706624	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.86[AFR][1000 genomes];0.89[AMR][1000 genomes];0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs11715395	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.97[YRI][hapmap];0.84[ASN][1000 genomes]
rs11921326	0.83[AFR][1000 genomes];0.86[ASN][1000 genomes]
rs12490749	0.86[ASN][1000 genomes]
rs12636392	0.81[AMR][1000 genomes];0.89[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs12636773	0.98[AMR][1000 genomes];0.90[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12715490	0.99[AMR][1000 genomes];0.90[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs13094666	0.83[ASN][1000 genomes]
rs13097030	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1352766	0.93[AFR][1000 genomes];0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs1388251	0.81[AMR][1000 genomes];0.89[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs1491166	0.95[CEU][hapmap];0.95[CHB][hapmap];0.95[JPT][hapmap];0.86[YRI][hapmap];0.87[AMR][1000 genomes];0.92[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs17056878	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[AMR][1000 genomes];0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs17216740	0.81[AFR][1000 genomes];0.84[ASN][1000 genomes]
rs2004199	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.82[AFR][1000 genomes];0.89[AMR][1000 genomes];0.87[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2029464	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.84[AFR][1000 genomes];0.86[ASN][1000 genomes]
rs2035798	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2054987	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2291499	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.84[AFR][1000 genomes];0.80[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2291501	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.80[AFR][1000 genomes];0.85[AMR][1000 genomes];0.82[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2317133	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.82[AFR][1000 genomes];0.87[AMR][1000 genomes];0.85[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2317245	0.85[ASN][1000 genomes]
rs282533	0.83[CHB][hapmap]
rs28407059	0.85[AMR][1000 genomes];0.90[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs3732512	0.86[ASN][1000 genomes]
rs4093514	0.98[AFR][1000 genomes];0.98[EUR][1000 genomes]
rs4681746	0.95[CHB][hapmap];0.96[JPT][hapmap]
rs4681951	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.89[AFR][1000 genomes];0.93[AMR][1000 genomes];0.93[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs4681963	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.83[AFR][1000 genomes];0.83[ASN][1000 genomes]
rs4974220	0.99[AMR][1000 genomes];0.88[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4974224	0.89[AFR][1000 genomes];0.98[EUR][1000 genomes]
rs6765870	0.90[AFR][1000 genomes];0.97[EUR][1000 genomes]
rs6774323	0.83[ASN][1000 genomes]
rs6784100	0.89[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs6785479	0.88[AFR][1000 genomes];0.93[AMR][1000 genomes];0.92[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs6790915	0.87[EUR][1000 genomes]
rs6798118	0.81[AFR][1000 genomes];0.93[AMR][1000 genomes];0.93[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs6799576	0.87[AMR][1000 genomes];0.88[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6802051	0.84[AFR][1000 genomes];0.86[ASN][1000 genomes]
rs6804262	0.81[ASN][1000 genomes]
rs6805469	0.81[AFR][1000 genomes];0.93[AMR][1000 genomes];0.93[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs72877266	0.88[AMR][1000 genomes];0.88[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7612599	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.82[AFR][1000 genomes];0.87[AMR][1000 genomes];0.85[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs7618024	0.95[CHB][hapmap];1.00[JPT][hapmap]
rs7626378	0.88[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7629559	0.80[AFR][1000 genomes];0.89[AMR][1000 genomes];0.89[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs7647272	0.89[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs9811046	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[AMR][1000 genomes];0.88[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs9820759	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.83[ASN][1000 genomes]
rs9822876	0.81[CHB][hapmap]
rs9836539	0.89[EUR][1000 genomes]
rs9840528	0.95[CEU][hapmap];0.82[ASN][1000 genomes]
rs9842283	1.00[CEU][hapmap];0.95[CHB][hapmap];0.95[JPT][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];0.96[EUR][1000 genomes]
rs9845096	0.84[AFR][1000 genomes];0.84[ASN][1000 genomes]
rs9845655	0.83[ASN][1000 genomes]
rs9846282	0.90[AMR][1000 genomes];0.83[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs9858728	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.83[ASN][1000 genomes]
rs9862490	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[AMR][1000 genomes];0.84[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs9881005	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs9881154	0.82[ASN][1000 genomes]
rs9881789	0.85[AFR][1000 genomes];0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs9881961	0.93[AFR][1000 genomes];0.92[AMR][1000 genomes];0.95[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs9985253	1.00[CEU][hapmap];0.97[YRI][hapmap];0.91[AFR][1000 genomes];0.93[AMR][1000 genomes];0.95[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs9985254	0.83[AFR][1000 genomes];0.93[AMR][1000 genomes];0.95[EUR][1000 genomes];0.88[ASN][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	esv3347557	chr3:56466500-56619322	Enhancers Strong transcription Weak transcription Flanking Active TSS Bivalent/Poised TSS Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
2	nsv876817	chr3:56517253-56649282	Weak transcription ZNF genes & repeats Strong transcription Enhancers Genic enhancers Active TSS Flanking Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	8 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	chr3:56590400-56593400	Active TSS	GM12878-XiMat	blood
2	chr3:56591800-56593200	Flanking Active TSS	Primary T cells from cord blood	blood
3	chr3:56591800-56596000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
4	chr3:56591800-56599800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
5	chr3:56592000-56593200	Flanking Active TSS	Dnd41	blood
6	chr3:56592000-56615600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
7	chr3:56592200-56593400	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
8	chr3:56592200-56609400	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
9	chr3:56592400-56593400	Enhancers	Primary T helper cells fromperipheralblood	blood
10	chr3:56592400-56593400	Weak transcription	Placenta	Placenta
11	chr3:56592400-56593600	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
12	chr3:56592400-56593600	Weak transcription	Primary T cells fromperipheralblood	blood
13	chr3:56592400-56593800	Enhancers	Primary T helper naive cells fromperipheralblood	blood
14	chr3:56592400-56593800	Enhancers	Primary T cells effector/memory enriched fromperipheralblood	blood
15	chr3:56592400-56593800	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
16	chr3:56592400-56594000	Weak transcription	Primary monocytes fromperipheralblood	blood
17	chr3:56592400-56594000	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
18	chr3:56592400-56594000	Weak transcription	Fetal Thymus	thymus
19	chr3:56592400-56594200	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
20	chr3:56592400-56594600	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
21	chr3:56592400-56594800	Weak transcription	Primary B cells from peripheral blood	blood
22	chr3:56592400-56594800	Weak transcription	HSMM	muscle
23	chr3:56592400-56596000	Weak transcription	Fetal Muscle Trunk	muscle
24	chr3:56592400-56596000	Weak transcription	Fetal Stomach	stomach
25	chr3:56592400-56596800	Weak transcription	Fetal Muscle Leg	muscle
26	chr3:56592400-56599800	Weak transcription	Fetal Lung	lung
27	chr3:56592400-56600000	Weak transcription	Ovary	ovary
28	chr3:56592400-56601200	Weak transcription	Placenta Amnion	Placenta Amnion
29	chr3:56592400-56601400	Weak transcription	Left Ventricle	heart
30	chr3:56592400-56601800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
31	chr3:56592400-56601800	Weak transcription	Lung	lung
32	chr3:56592400-56602000	Weak transcription	H9 Cell Line	embryonic stem cell
33	chr3:56592400-56602800	Weak transcription	Esophagus	oesophagus
34	chr3:56592400-56602800	Weak transcription	Gastric	stomach
35	chr3:56592400-56602800	Weak transcription	Spleen	Spleen
36	chr3:56592400-56603000	Weak transcription	Pancreas	Pancrea
37	chr3:56592400-56607400	Weak transcription	Psoas Muscle	Psoas
38	chr3:56592400-56615600	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
39	chr3:56592400-56639800	Weak transcription	Right Ventricle	heart
40	chr3:56592400-56644800	Weak transcription	Small Intestine	intestine
41	chr3:56592600-56593200	Weak transcription	HUES6 Cell Line	embryonic stem cell
42	chr3:56592600-56593200	Enhancers	Brain Substantia Nigra	brain
43	chr3:56592600-56593200	Enhancers	Colon Smooth Muscle	Colon
44	chr3:56592600-56593200	Enhancers	Fetal Kidney	kidney
45	chr3:56592600-56593200	Enhancers	HUVEC	blood vessel
46	chr3:56592600-56593600	Enhancers	Primary T helper 17 cells PMA-I stimulated	--
47	chr3:56592600-56593600	Weak transcription	Monocytes-CD14+_RO01746	blood
48	chr3:56592600-56593800	Enhancers	Primary T killer naive cells fromperipheralblood	blood
49	chr3:56592600-56593800	Enhancers	Hela-S3	cervix
50	chr3:56592600-56594200	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived

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