Variant report

Variant	rs1833557
Chromosome Location	chr5:52349661-52349662
allele	A/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: 33 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:24)

rs_ID	r²[population]
rs1109527	1.00[CEU][hapmap];0.89[YRI][hapmap];0.93[AFR][1000 genomes];0.94[EUR][1000 genomes]
rs1421933	0.81[ASN][1000 genomes]
rs1421934	0.95[AFR][1000 genomes];0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs152089	0.88[CEU][hapmap];0.81[EUR][1000 genomes]
rs153138	0.82[EUR][1000 genomes]
rs153140	0.82[EUR][1000 genomes]
rs1541689	1.00[CEU][hapmap];0.86[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs2056403	0.82[ASN][1000 genomes]
rs2287872	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs2406599	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs25826	0.80[EUR][1000 genomes]
rs26346	0.85[EUR][1000 genomes]
rs27406	0.86[EUR][1000 genomes]
rs27420	0.82[EUR][1000 genomes]
rs27915	0.82[YRI][hapmap]
rs30099	0.88[CEU][hapmap];0.86[EUR][1000 genomes]
rs30727	0.86[EUR][1000 genomes]
rs3212469	0.81[ASN][1000 genomes]
rs3212476	0.81[ASN][1000 genomes]
rs3212530	0.82[ASN][1000 genomes]
rs3212616	0.90[AFR][1000 genomes];0.86[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs43188	0.85[EUR][1000 genomes]
rs7719848	0.83[YRI][hapmap]
rs996765	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:9 , 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
9	nsv881331	chr5:52349661-52353959	Weak transcription Strong transcription Enhancers	Chromatin interactive region	1 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:61 , 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	chr5:52347800-52350200	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
39	chr5:52347800-52369200	Weak transcription	Cortex derived primary cultured neurospheres	brain
40	chr5:52347800-52395000	Weak transcription	Psoas Muscle	Psoas
41	chr5:52348200-52359000	Strong transcription	NH-A	brain
42	chr5:52348600-52371000	Weak transcription	HUES48 Cell Line	embryonic stem cell
43	chr5:52348600-52394800	Weak transcription	HUES6 Cell Line	embryonic stem cell
44	chr5:52348800-52349800	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
45	chr5:52348800-52349800	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
46	chr5:52348800-52353800	Weak transcription	Brain Cingulate Gyrus	brain
47	chr5:52348800-52356000	Weak transcription	Brain Hippocampus Middle	brain
48	chr5:52349000-52370200	Weak transcription	Dnd41	blood
49	chr5:52349200-52354600	Weak transcription	Muscle Satellite Cultured Cells	--
50	chr5:52349400-52361400	Weak transcription	A549	lung

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