Variant report

Variant	rs1421932
Chromosome Location	chr5:52349065-52349066
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr5:52342580..52344559-chr5:52347867..52350544,2	K562	blood:

Extended variants
information (count: 57 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:49)

rs_ID	r²[population]
rs1062535	0.94[CHB][hapmap];0.87[JPT][hapmap];0.83[AMR][1000 genomes];0.88[ASN][1000 genomes]
rs1126643	0.94[CHB][hapmap];0.87[JPT][hapmap];0.83[AMR][1000 genomes];0.88[ASN][1000 genomes]
rs12515364	0.83[ASN][1000 genomes]
rs12517446	0.89[AMR][1000 genomes];0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs12518279	0.91[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12520747	0.90[YRI][hapmap]
rs12521915	0.94[CHB][hapmap];0.83[JPT][hapmap];0.83[ASN][1000 genomes]
rs12652168	0.90[ASN][1000 genomes]
rs1421929	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1421930	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1421931	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1833558	0.83[AMR][1000 genomes];0.88[ASN][1000 genomes]
rs1862191	0.89[ASN][1000 genomes]
rs1991013	0.96[AMR][1000 genomes];0.94[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2075615	0.83[AMR][1000 genomes];0.88[ASN][1000 genomes]
rs2075616	0.91[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2075617	0.86[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2216729	0.81[YRI][hapmap]
rs2287871	0.91[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2303122	0.94[CHB][hapmap];0.87[JPT][hapmap];0.84[ASN][1000 genomes]
rs2303123	0.82[AMR][1000 genomes];0.83[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2303127	0.83[AMR][1000 genomes];0.88[ASN][1000 genomes]
rs2897458	0.82[AMR][1000 genomes];0.88[ASN][1000 genomes]
rs2910964	0.83[AMR][1000 genomes];0.88[ASN][1000 genomes]
rs2910965	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2910971	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2974976	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2974978	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2974987	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3212467	0.94[ASN][1000 genomes]
rs3212472	0.93[ASN][1000 genomes]
rs3212508	0.83[AMR][1000 genomes];0.88[ASN][1000 genomes]
rs3212509	0.83[AMR][1000 genomes];0.88[ASN][1000 genomes]
rs3212522	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3212527	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3212533	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3212591	0.91[AMR][1000 genomes];0.95[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs3212600	0.88[ASN][1000 genomes]
rs3212601	0.87[ASN][1000 genomes]
rs3212619	0.85[ASN][1000 genomes]
rs3212640	0.80[AMR][1000 genomes];0.80[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs67719154	0.90[ASN][1000 genomes]
rs6898333	0.94[CHB][hapmap];0.96[JPT][hapmap];0.82[ASN][1000 genomes]
rs7725246	0.94[CHB][hapmap];0.82[ASN][1000 genomes]
rs984966	0.88[ASN][1000 genomes]
rs988557	0.89[YRI][hapmap]
rs988558	0.87[YRI][hapmap]
rs989073	0.93[ASN][1000 genomes]
rs990602	0.80[AMR][1000 genomes];0.80[EUR][1000 genomes];0.94[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:8 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv949005	chr5:52188028-52808229	Flanking Bivalent TSS/Enh Enhancers Weak transcription Active TSS Flanking Active TSS Strong transcription Transcr. at gene 5' and 3' ZNF genes & repeats Genic enhancers Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	35 gene(s)	inside rSNPs	diseases
2	nsv830296	chr5:52209528-52410253	Strong transcription Enhancers Flanking Active TSS Weak transcription Genic enhancers Flanking Bivalent TSS/Enh Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	27 gene(s)	inside rSNPs	diseases
3	nsv881652	chr5:52323568-52385312	Weak transcription Genic enhancers Enhancers Strong transcription Flanking Active TSS Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
4	nsv880389	chr5:52333420-52375199	Enhancers Weak transcription Strong transcription Active TSS Genic enhancers Flanking Active TSS ZNF genes & repeats Transcr. at gene 5' and 3'	Chromatin interactive region	3 gene(s)	inside rSNPs	diseases
5	nsv881071	chr5:52334774-52362765	Weak transcription Flanking Active TSS Enhancers Strong transcription Active TSS Genic enhancers	Chromatin interactive region	3 gene(s)	inside rSNPs	diseases
6	nsv881388	chr5:52339234-52375536	Weak transcription Strong transcription Enhancers Genic enhancers Flanking Active TSS ZNF genes & repeats	Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
7	nsv880600	chr5:52342760-52362765	Weak transcription Enhancers Strong transcription Genic enhancers Flanking Active TSS	Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
8	nsv880861	chr5:52347692-52362765	Strong transcription Enhancers Weak transcription Genic enhancers Flanking Active TSS	Chromatin interactive region	1 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:64 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:52324400-52356400	Weak transcription	Brain Anterior Caudate	brain
2	chr5:52328000-52369200	Weak transcription	Fetal Intestine Small	intestine
3	chr5:52333800-52369800	Weak transcription	Colonic Mucosa	Colon
4	chr5:52333800-52392600	Weak transcription	Duodenum Smooth Muscle	Duodenum
5	chr5:52334000-52360800	Weak transcription	Small Intestine	intestine
6	chr5:52334800-52380800	Weak transcription	Stomach Mucosa	stomach
7	chr5:52334800-52391200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
8	chr5:52336400-52399800	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
9	chr5:52337200-52353400	Weak transcription	Rectal Mucosa Donor 31	rectum
10	chr5:52337400-52355200	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
11	chr5:52337400-52369000	Weak transcription	Brain Inferior Temporal Lobe	brain
12	chr5:52337400-52370200	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
13	chr5:52341200-52396400	Strong transcription	HMEC	breast
14	chr5:52341400-52359000	Weak transcription	NHDF-Ad	bronchial
15	chr5:52341400-52396400	Strong transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
16	chr5:52341800-52358800	Weak transcription	Osteobl	bone
17	chr5:52342000-52367200	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
18	chr5:52342400-52363600	Weak transcription	Rectal Smooth Muscle	rectum
19	chr5:52342600-52383800	Strong transcription	NHEK	skin
20	chr5:52343000-52359000	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
21	chr5:52343200-52350800	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
22	chr5:52343200-52351800	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
23	chr5:52343200-52361800	Strong transcription	HepG2	liver
24	chr5:52343400-52350000	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
25	chr5:52343400-52357200	Strong transcription	HUVEC	blood vessel
26	chr5:52343400-52392800	Weak transcription	Left Ventricle	heart
27	chr5:52344000-52369200	Weak transcription	Pancreas	Pancrea
28	chr5:52344200-52356000	Weak transcription	iPS-20b Cell Line	embryonic stem cell
29	chr5:52344400-52356400	Weak transcription	Esophagus	oesophagus
30	chr5:52344400-52356400	Weak transcription	Gastric	stomach
31	chr5:52345600-52350800	Strong transcription	Hela-S3	cervix
32	chr5:52346200-52386800	Weak transcription	Stomach Smooth Muscle	stomach
33	chr5:52346400-52349800	Strong transcription	Duodenum Mucosa	Duodenum
34	chr5:52346600-52369200	Weak transcription	Brain Angular Gyrus	brain
35	chr5:52347000-52353000	Weak transcription	Rectal Mucosa Donor 29	rectum
36	chr5:52347200-52370000	Weak transcription	HUES64 Cell Line	embryonic stem cell
37	chr5:52347600-52387000	Weak transcription	Fetal Stomach	stomach
38	chr5:52347800-52349200	Strong transcription	Muscle Satellite Cultured Cells	--
39	chr5:52347800-52349600	Genic enhancers	Breast Myoepithelial Primary Cells	Breast
40	chr5:52347800-52350200	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
41	chr5:52347800-52369200	Weak transcription	Cortex derived primary cultured neurospheres	brain
42	chr5:52347800-52395000	Weak transcription	Psoas Muscle	Psoas
43	chr5:52348000-52349200	Enhancers	Primary hematopoietic stem cells short term culture	blood
44	chr5:52348000-52349400	Enhancers	Brain Substantia Nigra	brain
45	chr5:52348000-52349600	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
46	chr5:52348000-52349600	Strong transcription	Fetal Intestine Large	intestine
47	chr5:52348000-52349600	Strong transcription	Sigmoid Colon	Sigmoid Colon
48	chr5:52348000-52349600	Strong transcription	Spleen	Spleen
49	chr5:52348200-52349600	Strong transcription	Foreskin Fibroblast Primary Cells skin01	Skin
50	chr5:52348200-52349600	Strong transcription	Foreskin Fibroblast Primary Cells skin02	Skin

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