Variant report

Variant	rs2406599
Chromosome Location	chr5:52361219-52361220
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 40 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:25)

rs_ID	r²[population]
rs1109527	1.00[CEU][hapmap];0.94[YRI][hapmap];0.94[AFR][1000 genomes];0.94[EUR][1000 genomes]
rs1421933	0.80[ASN][1000 genomes]
rs1421934	0.89[AFR][1000 genomes];0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[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]
rs1549276	0.84[YRI][hapmap]
rs1833557	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2056403	0.82[ASN][1000 genomes]
rs2287872	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][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	0.88[YRI][hapmap]
rs30099	0.88[CEU][hapmap];0.86[EUR][1000 genomes]
rs30727	0.86[EUR][1000 genomes]
rs3212469	0.80[ASN][1000 genomes]
rs3212476	0.80[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	0.89[YRI][hapmap]
rs996765	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:15 , 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	nsv880766	chr5:52350521-52362765	Weak transcription Strong transcription Enhancers Genic enhancers Flanking Active TSS	Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
10	nsv881626	chr5:52350521-52370174	Strong transcription Weak transcription Flanking Active TSS Enhancers Genic enhancers ZNF genes & repeats	Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
11	nsv880601	chr5:52350521-52375927	Weak transcription Enhancers Genic enhancers Strong transcription Flanking Active TSS ZNF genes & repeats	Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
12	nsv880945	chr5:52351437-52362765	Strong transcription Weak transcription Enhancers Genic enhancers Flanking Active TSS	Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
13	nsv598168	chr5:52355516-52373810	Weak transcription Enhancers Strong transcription Genic enhancers Flanking Active TSS ZNF genes & repeats	Chromatin interactive region	n/a	inside rSNPs	diseases
14	nsv881522	chr5:52357916-52370521	Flanking Active TSS Genic enhancers Weak transcription Strong transcription Enhancers ZNF genes & repeats	Chromatin interactive region	n/a	inside rSNPs	diseases
15	nsv880866	chr5:52358262-52378295	Strong transcription Weak transcription Genic enhancers Enhancers ZNF genes & repeats Flanking Active TSS	Chromatin interactive region	n/a	inside rSNPs	diseases

No data

Chromatin state (count:68 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:52328000-52369200	Weak transcription	Fetal Intestine Small	intestine
2	chr5:52333800-52369800	Weak transcription	Colonic Mucosa	Colon
3	chr5:52333800-52392600	Weak transcription	Duodenum Smooth Muscle	Duodenum
4	chr5:52334800-52380800	Weak transcription	Stomach Mucosa	stomach
5	chr5:52334800-52391200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
6	chr5:52336400-52399800	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
7	chr5:52337400-52369000	Weak transcription	Brain Inferior Temporal Lobe	brain
8	chr5:52337400-52370200	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
9	chr5:52341200-52396400	Strong transcription	HMEC	breast
10	chr5:52341400-52396400	Strong transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
11	chr5:52342000-52367200	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
12	chr5:52342400-52363600	Weak transcription	Rectal Smooth Muscle	rectum
13	chr5:52342600-52383800	Strong transcription	NHEK	skin
14	chr5:52343200-52361800	Strong transcription	HepG2	liver
15	chr5:52343400-52392800	Weak transcription	Left Ventricle	heart
16	chr5:52344000-52369200	Weak transcription	Pancreas	Pancrea
17	chr5:52346200-52386800	Weak transcription	Stomach Smooth Muscle	stomach
18	chr5:52346600-52369200	Weak transcription	Brain Angular Gyrus	brain
19	chr5:52347200-52370000	Weak transcription	HUES64 Cell Line	embryonic stem cell
20	chr5:52347600-52387000	Weak transcription	Fetal Stomach	stomach
21	chr5:52347800-52369200	Weak transcription	Cortex derived primary cultured neurospheres	brain
22	chr5:52347800-52395000	Weak transcription	Psoas Muscle	Psoas
23	chr5:52348600-52371000	Weak transcription	HUES48 Cell Line	embryonic stem cell
24	chr5:52348600-52394800	Weak transcription	HUES6 Cell Line	embryonic stem cell
25	chr5:52349000-52370200	Weak transcription	Dnd41	blood
26	chr5:52349400-52361400	Weak transcription	A549	lung
27	chr5:52349400-52362800	Weak transcription	Brain Substantia Nigra	brain
28	chr5:52349400-52379600	Weak transcription	Fetal Muscle Leg	muscle
29	chr5:52349600-52362800	Strong transcription	Breast Myoepithelial Primary Cells	Breast
30	chr5:52349600-52369000	Weak transcription	Lung	lung
31	chr5:52349600-52371400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
32	chr5:52352400-52363200	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
33	chr5:52352400-52379200	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
34	chr5:52352400-52389800	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
35	chr5:52353000-52364600	Strong transcription	Rectal Mucosa Donor 29	rectum
36	chr5:52353000-52367800	Weak transcription	Aorta	Aorta
37	chr5:52354200-52368800	Weak transcription	Brain Cingulate Gyrus	brain
38	chr5:52354200-52372000	Weak transcription	ES-I3 Cell Line	embryonic stem cell
39	chr5:52355600-52371000	Weak transcription	iPS-18 Cell Line	embryonic stem cell
40	chr5:52356800-52370800	Weak transcription	Brain Anterior Caudate	brain
41	chr5:52356800-52394000	Weak transcription	Fetal Kidney	kidney
42	chr5:52357000-52367200	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
43	chr5:52357200-52369200	Weak transcription	Esophagus	oesophagus
44	chr5:52357200-52371400	Weak transcription	Gastric	stomach
45	chr5:52357400-52367800	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
46	chr5:52357400-52369000	Weak transcription	Brain Hippocampus Middle	brain
47	chr5:52357400-52370400	Weak transcription	iPS-20b Cell Line	embryonic stem cell
48	chr5:52358200-52361800	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
49	chr5:52358200-52364000	Weak transcription	Sigmoid Colon	Sigmoid Colon
50	chr5:52358400-52365400	Weak transcription	Fetal Intestine Large	intestine

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