Variant report

Variant	rs2406598
Chromosome Location	chr5:52332089-52332090
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 30 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:23)

rs_ID	r²[population]
rs10051913	0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10068849	0.91[AFR][1000 genomes]
rs11955860	0.99[AFR][1000 genomes];0.91[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs12520747	0.93[CEU][hapmap];0.94[YRI][hapmap];0.90[AFR][1000 genomes];0.82[EUR][1000 genomes]
rs1421933	0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs1421938	0.97[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs1549276	0.95[EUR][1000 genomes]
rs2056403	0.86[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2112290	0.89[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs2216729	0.96[CEU][hapmap];0.82[YRI][hapmap];0.89[AFR][1000 genomes];0.82[EUR][1000 genomes]
rs26678	0.81[CEU][hapmap]
rs3212434	0.89[AFR][1000 genomes];0.82[EUR][1000 genomes]
rs3212452	0.88[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs3212469	0.82[AFR][1000 genomes];0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs3212476	0.82[AFR][1000 genomes];0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs3212530	0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs3797499	0.92[AFR][1000 genomes];0.82[EUR][1000 genomes]
rs7719848	0.96[CEU][hapmap];0.93[EUR][1000 genomes]
rs7731858	0.97[AFR][1000 genomes];0.91[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs7736005	0.84[AFR][1000 genomes];0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs988557	0.96[CEU][hapmap];0.90[YRI][hapmap];0.89[AFR][1000 genomes];0.82[EUR][1000 genomes]
rs988558	0.96[CEU][hapmap];0.91[YRI][hapmap];0.89[AFR][1000 genomes];0.82[EUR][1000 genomes]
rs988559	0.89[AFR][1000 genomes];0.82[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:7 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv462187	chr5:51758804-52333420	Enhancers Weak transcription Strong transcription Flanking Active TSS Bivalent/Poised TSS Active TSS Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	43 gene(s)	inside rSNPs	diseases
2	nsv598163	chr5:51758804-52333420	Strong transcription Weak transcription Enhancers Active TSS Genic enhancers Flanking Active TSS Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	43 gene(s)	inside rSNPs	diseases
3	nsv471013	chr5:51779197-52339114	Weak transcription Enhancers Flanking Active TSS Active TSS Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer Strong transcription Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	43 gene(s)	inside rSNPs	diseases
4	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
5	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
6	nsv880425	chr5:52291279-52345868	Enhancers Weak transcription Flanking Active TSS Genic enhancers Active TSS Strong transcription Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer	Chromatin interactive region	2 gene(s)	inside rSNPs	diseases
7	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

No data

Chromatin state (count:55 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:52307000-52333800	Weak transcription	Gastric	stomach
2	chr5:52314200-52348000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
3	chr5:52317600-52333600	Weak transcription	Colonic Mucosa	Colon
4	chr5:52322200-52333200	Weak transcription	Fetal Stomach	stomach
5	chr5:52323600-52332600	Weak transcription	Stomach Smooth Muscle	stomach
6	chr5:52324200-52334200	Weak transcription	Spleen	Spleen
7	chr5:52324400-52356400	Weak transcription	Brain Anterior Caudate	brain
8	chr5:52324600-52332400	Weak transcription	Cortex derived primary cultured neurospheres	brain
9	chr5:52327600-52333000	Weak transcription	Rectal Smooth Muscle	rectum
10	chr5:52327800-52332200	Weak transcription	Esophagus	oesophagus
11	chr5:52327800-52333800	Weak transcription	Sigmoid Colon	Sigmoid Colon
12	chr5:52327800-52334400	Weak transcription	Pancreas	Pancrea
13	chr5:52327800-52344200	Weak transcription	Rectal Mucosa Donor 29	rectum
14	chr5:52328000-52332600	Weak transcription	Colon Smooth Muscle	Colon
15	chr5:52328000-52332800	Weak transcription	Brain Inferior Temporal Lobe	brain
16	chr5:52328000-52333000	Weak transcription	HSMM	muscle
17	chr5:52328000-52369200	Weak transcription	Fetal Intestine Small	intestine
18	chr5:52328400-52333000	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
19	chr5:52328400-52333000	Weak transcription	Duodenum Mucosa	Duodenum
20	chr5:52328400-52333800	Weak transcription	Brain Cingulate Gyrus	brain
21	chr5:52328600-52335200	Genic enhancers	Breast Myoepithelial Primary Cells	Breast
22	chr5:52328800-52332600	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
23	chr5:52328800-52333200	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
24	chr5:52328800-52335800	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
25	chr5:52328800-52348000	Weak transcription	Fetal Intestine Large	intestine
26	chr5:52329000-52332800	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
27	chr5:52329000-52334200	Weak transcription	Lung	lung
28	chr5:52329200-52332200	Weak transcription	Small Intestine	intestine
29	chr5:52329200-52332800	Weak transcription	Stomach Mucosa	stomach
30	chr5:52329400-52335600	Weak transcription	Dnd41	blood
31	chr5:52330000-52332800	Genic enhancers	HMEC	breast
32	chr5:52330200-52332400	Genic enhancers	NHEK	skin
33	chr5:52330200-52333200	Enhancers	A549	lung
34	chr5:52331000-52333000	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
35	chr5:52331000-52333800	Enhancers	Hela-S3	cervix
36	chr5:52331000-52336200	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
37	chr5:52331000-52337000	Weak transcription	Fetal Kidney	kidney
38	chr5:52331400-52333000	Weak transcription	Brain Substantia Nigra	brain
39	chr5:52331400-52333000	Weak transcription	Fetal Lung	lung
40	chr5:52331600-52333400	Genic enhancers	HepG2	liver
41	chr5:52331800-52333400	Enhancers	NHDF-Ad	bronchial
42	chr5:52331800-52333600	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
43	chr5:52331800-52333800	Enhancers	NHLF	lung
44	chr5:52331800-52334400	Genic enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
45	chr5:52331800-52334800	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
46	chr5:52331800-52334800	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
47	chr5:52331800-52335200	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
48	chr5:52331800-52337200	Enhancers	HUVEC	blood vessel
49	chr5:52332000-52332200	Enhancers	Right Atrium	heart
50	chr5:52332000-52332400	Weak transcription	Muscle Satellite Cultured Cells	--

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