Variant report

Variant	rs7629559
Chromosome Location	chr3:56642851-56642852
allele	C/T
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:72)

rs_ID	r²[population]
rs1045926	0.93[AFR][1000 genomes];0.96[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10865998	0.82[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs10865999	0.97[AFR][1000 genomes];0.96[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10866000	0.82[AMR][1000 genomes];0.85[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs11130536	0.85[AFR][1000 genomes];0.87[AMR][1000 genomes];0.90[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs11130538	0.83[AMR][1000 genomes];0.85[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs11706624	0.86[AFR][1000 genomes];0.83[AMR][1000 genomes];0.83[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs11714608	0.80[AMR][1000 genomes]
rs11715395	0.93[AFR][1000 genomes];0.85[AMR][1000 genomes];0.89[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs11719656	0.87[ASN][1000 genomes]
rs11921326	0.83[AFR][1000 genomes];0.89[AMR][1000 genomes];0.89[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12488218	0.87[ASN][1000 genomes]
rs12490749	0.95[AFR][1000 genomes];0.89[AMR][1000 genomes];0.91[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12493637	0.81[ASN][1000 genomes]
rs12636773	0.87[AMR][1000 genomes];0.82[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs12715490	0.88[AMR][1000 genomes];0.82[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs13094666	0.93[ASN][1000 genomes]
rs13097030	0.80[AFR][1000 genomes];0.89[AMR][1000 genomes];0.90[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs13097288	0.86[ASN][1000 genomes]
rs1352766	0.85[AFR][1000 genomes];0.96[AMR][1000 genomes];0.93[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1491166	0.81[AMR][1000 genomes];0.81[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs17056878	0.83[AMR][1000 genomes];0.83[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs17216740	0.82[AFR][1000 genomes];0.85[AMR][1000 genomes];0.87[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2004199	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2029464	0.85[AFR][1000 genomes];0.89[AMR][1000 genomes];0.91[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2029465	0.82[ASN][1000 genomes]
rs2035798	0.88[AFR][1000 genomes];0.89[AMR][1000 genomes];0.90[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2054987	0.88[AFR][1000 genomes];0.89[AMR][1000 genomes];0.89[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2054988	0.80[AFR][1000 genomes];0.89[AMR][1000 genomes];0.89[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2291499	0.85[AFR][1000 genomes];0.89[AMR][1000 genomes];0.91[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2291501	0.97[AFR][1000 genomes];0.96[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2317133	0.98[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2317245	0.95[AFR][1000 genomes];0.89[AMR][1000 genomes];0.91[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs35998149	0.82[ASN][1000 genomes]
rs3732512	0.86[AMR][1000 genomes];0.80[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4093514	0.80[AFR][1000 genomes];0.91[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs4681951	0.82[AFR][1000 genomes];0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4681963	0.83[AFR][1000 genomes];0.83[AMR][1000 genomes];0.87[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs4974220	0.88[AMR][1000 genomes];0.80[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs4974224	0.87[AFR][1000 genomes];0.91[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs57800049	0.80[AMR][1000 genomes]
rs66529035	0.87[ASN][1000 genomes]
rs6765870	0.88[AFR][1000 genomes];0.89[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs6774323	0.92[AFR][1000 genomes];0.83[AMR][1000 genomes];0.87[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs6784100	0.82[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs6785479	0.84[AFR][1000 genomes];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6798118	0.91[AFR][1000 genomes];0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6799576	0.81[AMR][1000 genomes];0.87[ASN][1000 genomes]
rs6802051	0.85[AFR][1000 genomes];0.87[AMR][1000 genomes];0.89[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6804262	0.81[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs6805469	0.92[AFR][1000 genomes];0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs72877266	0.82[AMR][1000 genomes];0.85[ASN][1000 genomes]
rs7432897	0.81[ASN][1000 genomes]
rs7612599	0.98[AFR][1000 genomes];0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7618024	0.81[ASN][1000 genomes]
rs7626378	0.87[AFR][1000 genomes];0.89[AMR][1000 genomes];0.90[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs9811046	0.83[AMR][1000 genomes];0.88[ASN][1000 genomes]
rs9820759	0.80[AFR][1000 genomes];0.93[ASN][1000 genomes]
rs9836539	0.82[EUR][1000 genomes]
rs9840528	0.87[AFR][1000 genomes];0.83[AMR][1000 genomes];0.84[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs9842283	0.89[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs9845096	0.83[AFR][1000 genomes];0.85[AMR][1000 genomes];0.87[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs9845655	0.82[AMR][1000 genomes];0.92[ASN][1000 genomes]
rs9846282	0.97[AMR][1000 genomes];0.88[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs9858728	0.90[AFR][1000 genomes];0.93[ASN][1000 genomes]
rs9862490	0.94[AMR][1000 genomes];0.87[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs9881005	0.88[AFR][1000 genomes];0.89[AMR][1000 genomes];0.90[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs9881154	0.92[ASN][1000 genomes]
rs9881789	0.95[AFR][1000 genomes];0.94[AMR][1000 genomes];0.93[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs9881961	0.85[AFR][1000 genomes];0.94[AMR][1000 genomes];0.91[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs9985253	0.84[AFR][1000 genomes];0.96[AMR][1000 genomes];0.93[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs9985254	0.93[AFR][1000 genomes];0.96[AMR][1000 genomes];0.93[EUR][1000 genomes];0.98[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	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
2	nsv460557	chr3:56594735-56661320	Weak transcription Strong transcription ZNF genes & repeats Genic enhancers Enhancers Active TSS Flanking Active TSS	TF binding region Chromatin interactive region lncRNA miRNA target site	2 gene(s)	inside rSNPs	diseases
3	nsv590362	chr3:56594735-56661320	ZNF genes & repeats Weak transcription Strong transcription Enhancers Genic enhancers Flanking Active TSS Active TSS	TF binding region Chromatin interactive region lncRNA miRNA target site	2 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:123 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:56592400-56644800	Weak transcription	Small Intestine	intestine
2	chr3:56592800-56644600	Weak transcription	Fetal Heart	heart
3	chr3:56603200-56650400	Weak transcription	K562	blood
4	chr3:56606200-56650200	Weak transcription	Colonic Mucosa	Colon
5	chr3:56607800-56650200	Weak transcription	Psoas Muscle	Psoas
6	chr3:56625200-56650400	Weak transcription	NHEK	skin
7	chr3:56625200-56653400	Weak transcription	ES-I3 Cell Line	embryonic stem cell
8	chr3:56626400-56656200	Weak transcription	Stomach Mucosa	stomach
9	chr3:56628600-56649600	Weak transcription	HepG2	liver
10	chr3:56629000-56647400	Weak transcription	HUVEC	blood vessel
11	chr3:56629000-56648000	Weak transcription	NH-A	brain
12	chr3:56629600-56648200	Weak transcription	NHDF-Ad	bronchial
13	chr3:56630000-56654400	Weak transcription	Placenta Amnion	Placenta Amnion
14	chr3:56630600-56645800	Weak transcription	HSMM	muscle
15	chr3:56630800-56645600	Weak transcription	Hela-S3	cervix
16	chr3:56632400-56644800	Weak transcription	A549	lung
17	chr3:56633800-56647800	Weak transcription	HUES64 Cell Line	embryonic stem cell
18	chr3:56634000-56651400	Weak transcription	Fetal Brain Male	brain
19	chr3:56637800-56644200	ZNF genes & repeats	Primary hematopoietic stem cells G-CSF-mobilized Male	--
20	chr3:56640000-56650000	Weak transcription	HMEC	breast
21	chr3:56640200-56644600	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
22	chr3:56640200-56645200	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
23	chr3:56640400-56644600	Weak transcription	iPS-15b Cell Line	embryonic stem cell
24	chr3:56640400-56644800	Weak transcription	Left Ventricle	heart
25	chr3:56640400-56650800	Weak transcription	Colon Smooth Muscle	Colon
26	chr3:56640600-56643000	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
27	chr3:56640600-56644400	Weak transcription	iPS-20b Cell Line	embryonic stem cell
28	chr3:56640600-56644600	Weak transcription	H9 Cell Line	embryonic stem cell
29	chr3:56640600-56644800	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
30	chr3:56640600-56644800	Weak transcription	Brain Inferior Temporal Lobe	brain
31	chr3:56640600-56644800	Weak transcription	Right Ventricle	heart
32	chr3:56640600-56644800	Weak transcription	Skeletal Muscle Male	skeletal muscle
33	chr3:56640600-56645000	Weak transcription	iPS-18 Cell Line	embryonic stem cell
34	chr3:56640600-56646800	Weak transcription	Primary neutrophils fromperipheralblood	blood
35	chr3:56640600-56647200	Weak transcription	HUES48 Cell Line	embryonic stem cell
36	chr3:56640600-56647600	Weak transcription	Skeletal Muscle Female	skeletal muscle
37	chr3:56640600-56647800	Weak transcription	GM12878-XiMat	blood
38	chr3:56640600-56650400	Weak transcription	Rectal Mucosa Donor 31	rectum
39	chr3:56640600-56652600	Weak transcription	Rectal Smooth Muscle	rectum
40	chr3:56640800-56643000	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
41	chr3:56640800-56643000	Weak transcription	Primary B cells from cord blood	blood
42	chr3:56640800-56643000	Weak transcription	Primary hematopoietic stem cells	blood
43	chr3:56640800-56643000	Weak transcription	Pancreatic Islets	Pancreatic Islet
44	chr3:56640800-56643200	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
45	chr3:56640800-56644000	Weak transcription	Fetal Thymus	thymus
46	chr3:56640800-56644600	Weak transcription	Brain Substantia Nigra	brain
47	chr3:56640800-56644800	Weak transcription	H1 Cell Line	embryonic stem cell
48	chr3:56640800-56644800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
49	chr3:56640800-56644800	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
50	chr3:56640800-56644800	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung

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