Variant report

Variant	rs3805553
Chromosome Location	chr5:58288268-58288269
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 44 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:41)

rs_ID	r²[population]
rs10074854	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10461657	0.93[CEU][hapmap];1.00[TSI][hapmap];0.86[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs1463816	0.98[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1498612	0.92[AFR][1000 genomes];0.91[AMR][1000 genomes];0.93[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1532520	0.93[AFR][1000 genomes];0.98[AMR][1000 genomes];0.93[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1553114	1.00[ASW][hapmap];0.93[CEU][hapmap];0.93[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.97[LWK][hapmap];0.93[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];0.98[AMR][1000 genomes];0.94[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs159724	0.81[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs1846369	0.91[AFR][1000 genomes];0.91[AMR][1000 genomes];0.93[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1973450	0.93[AFR][1000 genomes];0.98[AMR][1000 genomes];0.94[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1973451	0.95[AMR][1000 genomes];0.94[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2927661	0.90[EUR][1000 genomes]
rs2936190	1.00[CEU][hapmap];0.89[TSI][hapmap];0.92[EUR][1000 genomes]
rs2936192	0.83[EUR][1000 genomes]
rs2936193	0.93[CEU][hapmap];0.85[TSI][hapmap];0.83[EUR][1000 genomes]
rs2936199	0.92[EUR][1000 genomes]
rs2968006	1.00[CEU][hapmap];0.89[TSI][hapmap];0.92[EUR][1000 genomes]
rs2968013	0.92[CEU][hapmap];0.92[EUR][1000 genomes]
rs2968014	1.00[CEU][hapmap];0.89[TSI][hapmap];0.93[EUR][1000 genomes]
rs2968015	0.93[EUR][1000 genomes]
rs2968017	0.91[EUR][1000 genomes]
rs2968021	0.93[CEU][hapmap];0.94[EUR][1000 genomes]
rs3805554	0.98[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs3805556	0.93[CEU][hapmap];1.00[TSI][hapmap];0.91[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs3805557	1.00[ASW][hapmap];0.93[CEU][hapmap];0.93[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.94[LWK][hapmap];0.81[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.94[AFR][1000 genomes];0.98[AMR][1000 genomes];0.94[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs412423	0.81[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs4321723	0.93[CEU][hapmap];0.92[EUR][1000 genomes]
rs457959	0.81[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs4621516	0.91[AFR][1000 genomes];0.91[AMR][1000 genomes];0.92[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4629551	0.93[CEU][hapmap];0.86[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs4699930	1.00[CEU][hapmap];0.88[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs4699931	0.92[CEU][hapmap];0.91[EUR][1000 genomes]
rs4700314	0.92[CEU][hapmap];0.91[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs6450496	0.93[CEU][hapmap];0.93[CHB][hapmap];1.00[JPT][hapmap];0.95[YRI][hapmap];0.91[AFR][1000 genomes];0.91[AMR][1000 genomes];0.93[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6875727	0.93[EUR][1000 genomes]
rs702519	0.81[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs702523	0.86[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs7712725	0.93[CEU][hapmap];0.93[CHB][hapmap];1.00[JPT][hapmap];0.95[YRI][hapmap];0.91[AFR][1000 genomes];0.91[AMR][1000 genomes];0.92[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7713069	1.00[ASW][hapmap];1.00[CEU][hapmap];0.93[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.95[LWK][hapmap];0.81[MKK][hapmap];1.00[TSI][hapmap];0.95[YRI][hapmap];0.91[AFR][1000 genomes];0.91[AMR][1000 genomes];0.93[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7713345	0.93[CEU][hapmap];0.93[CHB][hapmap];1.00[JPT][hapmap];0.94[YRI][hapmap];0.91[AFR][1000 genomes];0.91[AMR][1000 genomes];0.93[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7724713	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];0.93[MKK][hapmap];1.00[TSI][hapmap];0.94[YRI][hapmap];1.00[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7737685	0.93[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[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	esv2830363	chr5:57893949-58555491	Weak transcription Active TSS Enhancers Flanking Active TSS Transcr. at gene 5' and 3' Strong transcription Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	8 gene(s)	inside rSNPs	diseases
2	nsv830312	chr5:58191579-58382226	Enhancers ZNF genes & repeats Active TSS Weak transcription Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS Strong transcription Flanking Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	3 gene(s)	inside rSNPs	diseases
3	nsv830313	chr5:58273724-58421098	Enhancers Weak transcription Active TSS Flanking Active TSS Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS Strong transcription Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	3 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:82 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:58268000-58288400	Weak transcription	Stomach Mucosa	stomach
2	chr5:58268400-58294400	Weak transcription	NH-A	brain
3	chr5:58268800-58288800	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
4	chr5:58268800-58294600	Weak transcription	Brain Hippocampus Middle	brain
5	chr5:58270200-58297400	Weak transcription	Pancreatic Islets	Pancreatic Islet
6	chr5:58270800-58292600	Weak transcription	Fetal Brain Male	brain
7	chr5:58270800-58295800	Weak transcription	Small Intestine	intestine
8	chr5:58270800-58297000	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
9	chr5:58271000-58293600	Weak transcription	Brain Inferior Temporal Lobe	brain
10	chr5:58271000-58294600	Weak transcription	Brain Angular Gyrus	brain
11	chr5:58271600-58294400	Weak transcription	Brain Cingulate Gyrus	brain
12	chr5:58272800-58289000	Weak transcription	HUVEC	blood vessel
13	chr5:58273000-58294400	Weak transcription	Brain Anterior Caudate	brain
14	chr5:58273400-58289200	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
15	chr5:58273800-58294400	Weak transcription	Brain Substantia Nigra	brain
16	chr5:58276400-58288800	Strong transcription	Hela-S3	cervix
17	chr5:58277800-58295600	Weak transcription	Rectal Smooth Muscle	rectum
18	chr5:58278400-58297400	Weak transcription	HSMMtube	muscle
19	chr5:58278400-58299000	Weak transcription	Gastric	stomach
20	chr5:58278600-58292200	Weak transcription	Brain Germinal Matrix	brain
21	chr5:58279000-58288600	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
22	chr5:58279200-58314000	Weak transcription	Primary B cells from cord blood	blood
23	chr5:58279400-58317600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
24	chr5:58279600-58293000	Weak transcription	Cortex derived primary cultured neurospheres	brain
25	chr5:58279600-58330400	Weak transcription	Fetal Stomach	stomach
26	chr5:58279800-58298200	Weak transcription	Sigmoid Colon	Sigmoid Colon
27	chr5:58280200-58297000	Weak transcription	Fetal Heart	heart
28	chr5:58280200-58297000	Weak transcription	Fetal Kidney	kidney
29	chr5:58280200-58297200	Weak transcription	Psoas Muscle	Psoas
30	chr5:58280200-58299400	Weak transcription	Right Ventricle	heart
31	chr5:58280400-58297600	Weak transcription	Placenta Amnion	Placenta Amnion
32	chr5:58281200-58289200	Strong transcription	Primary T helper cells fromperipheralblood	blood
33	chr5:58281400-58288800	Strong transcription	HSMM	muscle
34	chr5:58281800-58289400	Weak transcription	HUES64 Cell Line	embryonic stem cell
35	chr5:58281800-58289800	Weak transcription	iPS-20b Cell Line	embryonic stem cell
36	chr5:58281800-58321600	Weak transcription	Osteobl	bone
37	chr5:58282400-58288600	Strong transcription	Skeletal Muscle Female	skeletal muscle
38	chr5:58282400-58289200	Weak transcription	ES-I3 Cell Line	embryonic stem cell
39	chr5:58282400-58289600	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
40	chr5:58282400-58290600	Weak transcription	Primary T helper naive cells from peripheral blood	blood
41	chr5:58282400-58306600	Weak transcription	Fetal Intestine Small	intestine
42	chr5:58282600-58290000	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
43	chr5:58283800-58288800	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
44	chr5:58284000-58296200	Weak transcription	Skeletal Muscle Male	skeletal muscle
45	chr5:58284400-58289400	Genic enhancers	A549	lung
46	chr5:58284400-58297600	Weak transcription	Fetal Lung	lung
47	chr5:58284400-58299200	Weak transcription	Primary T killer memory cells from peripheral blood	blood
48	chr5:58285200-58289400	Strong transcription	Primary hematopoietic stem cells	blood
49	chr5:58285400-58288600	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
50	chr5:58286000-58290600	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood

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