Variant report

Variant	rs3212608
Chromosome Location	chr5:52375536-52375537
allele	A/C/G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 31 )
Associated
traits (count: 0)

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

rs_ID	r²[population]
rs10940289	0.86[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12109479	0.83[AFR][1000 genomes];0.90[AMR][1000 genomes];0.89[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2233213	0.83[AFR][1000 genomes];0.90[AMR][1000 genomes];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2233216	0.83[AFR][1000 genomes];0.90[AMR][1000 genomes];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2233220	0.83[AFR][1000 genomes];0.90[AMR][1000 genomes];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3212427	0.86[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs3212428	0.86[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs3212437	0.86[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs3212454	0.86[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3212460	0.86[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3212462	0.86[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3212477	0.86[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3212534	1.00[AFR][1000 genomes];0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3212538	1.00[AFR][1000 genomes];0.91[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3212541	0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3212602	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3212639	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3816326	0.83[AFR][1000 genomes];0.90[AMR][1000 genomes];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3928414	0.97[EUR][1000 genomes]
rs41308283	0.83[AFR][1000 genomes];0.90[AMR][1000 genomes];0.89[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs7732191	0.86[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs9968622	0.86[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs9968673	0.86[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[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	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
5	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
6	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
7	nsv881684	chr5:52366905-52376916	Weak transcription Enhancers Strong transcription Flanking Active TSS ZNF genes & repeats Genic enhancers	Chromatin interactive region	n/a	inside rSNPs	diseases
8	nsv598170	chr5:52373696-52376916	Strong transcription Weak transcription Enhancers Genic enhancers	Chromatin interactive region	n/a	inside rSNPs	diseases

No data

Chromatin state (count:73 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:52333800-52392600	Weak transcription	Duodenum Smooth Muscle	Duodenum
2	chr5:52334800-52380800	Weak transcription	Stomach Mucosa	stomach
3	chr5:52334800-52391200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
4	chr5:52336400-52399800	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
5	chr5:52341200-52396400	Strong transcription	HMEC	breast
6	chr5:52341400-52396400	Strong transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
7	chr5:52342600-52383800	Strong transcription	NHEK	skin
8	chr5:52343400-52392800	Weak transcription	Left Ventricle	heart
9	chr5:52346200-52386800	Weak transcription	Stomach Smooth Muscle	stomach
10	chr5:52347600-52387000	Weak transcription	Fetal Stomach	stomach
11	chr5:52347800-52395000	Weak transcription	Psoas Muscle	Psoas
12	chr5:52348600-52394800	Weak transcription	HUES6 Cell Line	embryonic stem cell
13	chr5:52349400-52379600	Weak transcription	Fetal Muscle Leg	muscle
14	chr5:52352400-52379200	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
15	chr5:52352400-52389800	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
16	chr5:52356800-52394000	Weak transcription	Fetal Kidney	kidney
17	chr5:52359400-52380000	Weak transcription	Muscle Satellite Cultured Cells	--
18	chr5:52360200-52388800	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
19	chr5:52361200-52392800	Weak transcription	Small Intestine	intestine
20	chr5:52362200-52387800	Strong transcription	HepG2	liver
21	chr5:52362400-52382400	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
22	chr5:52363200-52376400	Strong transcription	Rectal Mucosa Donor 31	rectum
23	chr5:52363400-52382600	Strong transcription	Breast Myoepithelial Primary Cells	Breast
24	chr5:52365800-52394800	Weak transcription	Right Ventricle	heart
25	chr5:52366000-52382800	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
26	chr5:52367400-52386200	Strong transcription	HUVEC	blood vessel
27	chr5:52367400-52388000	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
28	chr5:52367600-52381200	Strong transcription	Rectal Mucosa Donor 29	rectum
29	chr5:52367600-52385000	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
30	chr5:52367800-52386000	Strong transcription	NH-A	brain
31	chr5:52368000-52386200	Weak transcription	Aorta	Aorta
32	chr5:52368800-52376400	Strong transcription	Duodenum Mucosa	Duodenum
33	chr5:52369000-52381000	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
34	chr5:52369000-52392800	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
35	chr5:52369400-52382600	Weak transcription	Brain Angular Gyrus	brain
36	chr5:52369400-52383600	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
37	chr5:52369600-52375800	Weak transcription	Esophagus	oesophagus
38	chr5:52369800-52379800	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
39	chr5:52370400-52394600	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
40	chr5:52370400-52404600	Weak transcription	Brain Germinal Matrix	brain
41	chr5:52370800-52376400	Weak transcription	iPS-20b Cell Line	embryonic stem cell
42	chr5:52371400-52375800	Weak transcription	HUES48 Cell Line	embryonic stem cell
43	chr5:52371800-52376000	Weak transcription	Brain Inferior Temporal Lobe	brain
44	chr5:52372000-52382600	Weak transcription	Brain Anterior Caudate	brain
45	chr5:52372000-52394800	Weak transcription	Colonic Mucosa	Colon
46	chr5:52372000-52394800	Weak transcription	Rectal Smooth Muscle	rectum
47	chr5:52372200-52375800	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
48	chr5:52372200-52375800	Weak transcription	Brain Hippocampus Middle	brain
49	chr5:52372200-52375800	Weak transcription	Sigmoid Colon	Sigmoid Colon
50	chr5:52372200-52375800	Weak transcription	Dnd41	blood

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