Variant report

Variant	rs3805557
Chromosome Location	chr5:58284208-58284209
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr5:58277726..58280597-chr5:58283029..58284667,2	K562	blood:

Extended variants
information (count: 43 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:40)

rs_ID	r²[population]
rs10074854	0.93[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.94[AFR][1000 genomes];0.93[AMR][1000 genomes];0.94[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs10461657	1.00[CEU][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.88[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs1463816	0.92[AFR][1000 genomes];0.93[AMR][1000 genomes];0.94[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1498612	0.96[AFR][1000 genomes];0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1532520	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1553114	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.92[LWK][hapmap];1.00[MEX][hapmap];0.88[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs159724	0.84[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs1846369	0.97[AFR][1000 genomes];0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1973450	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1973451	0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2927661	0.94[EUR][1000 genomes]
rs2936190	0.93[CEU][hapmap];0.89[TSI][hapmap];0.86[EUR][1000 genomes]
rs2936193	1.00[CEU][hapmap];0.85[MEX][hapmap];0.85[TSI][hapmap]
rs2936199	0.90[EUR][1000 genomes]
rs2968006	0.93[CEU][hapmap];0.89[TSI][hapmap];0.86[EUR][1000 genomes]
rs2968013	1.00[CEU][hapmap];0.90[EUR][1000 genomes]
rs2968014	0.93[CEU][hapmap];0.85[MEX][hapmap];0.89[TSI][hapmap];0.89[EUR][1000 genomes]
rs2968015	0.89[EUR][1000 genomes]
rs2968017	0.95[EUR][1000 genomes]
rs2968021	1.00[CEU][hapmap];0.98[EUR][1000 genomes]
rs3805553	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]
rs3805554	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3805556	1.00[CEU][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.93[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs412423	0.84[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs4321723	1.00[CEU][hapmap];0.90[EUR][1000 genomes]
rs457959	0.84[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs4621516	0.97[AFR][1000 genomes];0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4629551	1.00[CEU][hapmap];0.88[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs4699930	0.93[CEU][hapmap];0.86[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs4699931	1.00[CEU][hapmap];0.88[EUR][1000 genomes]
rs4700314	1.00[CEU][hapmap];0.93[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs6450496	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[YRI][hapmap];0.97[AFR][1000 genomes];0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6875727	0.89[EUR][1000 genomes]
rs702519	0.84[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs702523	0.88[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs7712725	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[YRI][hapmap];0.97[AFR][1000 genomes];0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7713069	1.00[ASW][hapmap];0.93[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];0.95[YRI][hapmap];0.97[AFR][1000 genomes];0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7713345	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[YRI][hapmap];0.97[AFR][1000 genomes];0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7724713	1.00[ASW][hapmap];0.93[CEU][hapmap];0.93[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.94[LWK][hapmap];1.00[MEX][hapmap];0.87[MKK][hapmap];1.00[TSI][hapmap];0.94[YRI][hapmap];0.94[AFR][1000 genomes];0.93[AMR][1000 genomes];0.94[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7737685	1.00[CEU][hapmap];0.93[CHB][hapmap];1.00[JPT][hapmap];0.91[AMR][1000 genomes];0.93[EUR][1000 genomes];0.99[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:97 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:58266000-58287600	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
2	chr5:58268000-58288400	Weak transcription	Stomach Mucosa	stomach
3	chr5:58268200-58287200	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
4	chr5:58268400-58287400	Strong transcription	Primary hematopoietic stem cells short term culture	blood
5	chr5:58268400-58294400	Weak transcription	NH-A	brain
6	chr5:58268800-58286000	Weak transcription	HepG2	liver
7	chr5:58268800-58286600	Strong transcription	Primary T helper 17 cells PMA-I stimulated	--
8	chr5:58268800-58286800	Strong transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
9	chr5:58268800-58287200	Strong transcription	Primary T helper cells PMA-I stimulated	--
10	chr5:58268800-58287800	Weak transcription	Placenta	Placenta
11	chr5:58268800-58288800	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
12	chr5:58268800-58294600	Weak transcription	Brain Hippocampus Middle	brain
13	chr5:58270200-58297400	Weak transcription	Pancreatic Islets	Pancreatic Islet
14	chr5:58270800-58292600	Weak transcription	Fetal Brain Male	brain
15	chr5:58270800-58295800	Weak transcription	Small Intestine	intestine
16	chr5:58270800-58297000	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
17	chr5:58271000-58285800	Weak transcription	Aorta	Aorta
18	chr5:58271000-58285800	Weak transcription	Pancreas	Pancrea
19	chr5:58271000-58287600	Weak transcription	Esophagus	oesophagus
20	chr5:58271000-58293600	Weak transcription	Brain Inferior Temporal Lobe	brain
21	chr5:58271000-58294600	Weak transcription	Brain Angular Gyrus	brain
22	chr5:58271600-58287200	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
23	chr5:58271600-58294400	Weak transcription	Brain Cingulate Gyrus	brain
24	chr5:58272200-58286000	Weak transcription	Muscle Satellite Cultured Cells	--
25	chr5:58272800-58289000	Weak transcription	HUVEC	blood vessel
26	chr5:58273000-58294400	Weak transcription	Brain Anterior Caudate	brain
27	chr5:58273400-58289200	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
28	chr5:58273800-58294400	Weak transcription	Brain Substantia Nigra	brain
29	chr5:58274400-58285800	Weak transcription	Duodenum Mucosa	Duodenum
30	chr5:58276400-58288800	Strong transcription	Hela-S3	cervix
31	chr5:58276800-58286800	Strong transcription	Fetal Thymus	thymus
32	chr5:58277800-58295600	Weak transcription	Rectal Smooth Muscle	rectum
33	chr5:58278400-58297400	Weak transcription	HSMMtube	muscle
34	chr5:58278400-58299000	Weak transcription	Gastric	stomach
35	chr5:58278600-58284600	Weak transcription	Spleen	Spleen
36	chr5:58278600-58292200	Weak transcription	Brain Germinal Matrix	brain
37	chr5:58279000-58288600	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
38	chr5:58279200-58288000	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
39	chr5:58279200-58314000	Weak transcription	Primary B cells from cord blood	blood
40	chr5:58279400-58285400	Weak transcription	Fetal Brain Female	brain
41	chr5:58279400-58317600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
42	chr5:58279600-58287200	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
43	chr5:58279600-58293000	Weak transcription	Cortex derived primary cultured neurospheres	brain
44	chr5:58279600-58330400	Weak transcription	Fetal Stomach	stomach
45	chr5:58279800-58285800	Weak transcription	Left Ventricle	heart
46	chr5:58279800-58285800	Weak transcription	Lung	lung
47	chr5:58279800-58286800	Weak transcription	Colonic Mucosa	Colon
48	chr5:58279800-58298200	Weak transcription	Sigmoid Colon	Sigmoid Colon
49	chr5:58280000-58287000	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
50	chr5:58280200-58285400	Weak transcription	Colon Smooth Muscle	Colon

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