Variant report

Variant	rs40402
Chromosome Location	chr5:14818366-14818367
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 34 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:28)

rs_ID	r²[population]
rs1620976	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1679138	0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1812659	0.87[AMR][1000 genomes];0.96[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs2448493	0.87[AMR][1000 genomes];0.87[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2453320	0.85[ASN][1000 genomes]
rs258220	0.86[CEU][hapmap];1.00[CHB][hapmap];0.87[AMR][1000 genomes];0.86[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs258232	0.85[ASN][1000 genomes]
rs25946	0.84[CHB][hapmap]
rs26304	1.00[CEU][hapmap];0.94[CHB][hapmap];1.00[JPT][hapmap];0.84[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs26305	0.84[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs26306	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs27353	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.84[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs30613	0.94[CHB][hapmap];0.84[ASN][1000 genomes]
rs31907	0.84[AMR][1000 genomes];0.84[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs31910	0.92[CEU][hapmap];0.94[CHB][hapmap];0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs31911	0.93[CEU][hapmap];0.88[CHB][hapmap];0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs31917	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.80[YRI][hapmap];0.83[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs31987	0.82[CEU][hapmap];0.94[CHB][hapmap];0.83[AMR][1000 genomes];0.83[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs31988	0.83[AMR][1000 genomes];0.84[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs31989	0.82[CEU][hapmap];0.94[CHB][hapmap];0.80[JPT][hapmap];0.83[AMR][1000 genomes];0.84[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs31990	0.83[AMR][1000 genomes];0.84[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs379016	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.80[YRI][hapmap];0.83[AFR][1000 genomes];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs412056	0.89[CEU][hapmap];0.94[CHB][hapmap];0.87[AMR][1000 genomes];0.87[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs42274	0.83[AMR][1000 genomes];0.83[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs826351	0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs826355	0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs826356	1.00[CEU][hapmap];0.89[CHB][hapmap];1.00[JPT][hapmap];0.92[AMR][1000 genomes];0.94[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs826358	1.00[CEU][hapmap];1.00[CHB][hapmap];0.88[JPT][hapmap];0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:6 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1018187	chr5:14385164-15127103	Strong transcription Flanking Bivalent TSS/Enh Weak transcription Enhancers Genic enhancers Active TSS Flanking Active TSS ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	61 gene(s)	inside rSNPs	diseases
2	nsv948447	chr5:14771247-14852610	Enhancers Genic enhancers Weak transcription Flanking Active TSS Active TSS Strong transcription ZNF genes & repeats	TF binding region CpG island Chromatin interactive region miRNA	3 gene(s)	inside rSNPs	diseases
3	nsv830212	chr5:14784197-14966683	Enhancers Weak transcription Flanking Active TSS Active TSS Strong transcription ZNF genes & repeats Bivalent/Poised TSS Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	20 gene(s)	inside rSNPs	diseases
4	esv2753381	chr5:14814900-14882800	Strong transcription Active TSS Weak transcription Flanking Active TSS Enhancers ZNF genes & repeats Genic enhancers Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	15 gene(s)	inside rSNPs	diseases
5	esv2755533	chr5:14814900-14882800	Enhancers Flanking Active TSS Bivalent/Poised TSS Genic enhancers Weak transcription Active TSS Flanking Bivalent TSS/Enh Strong transcription Transcr. at gene 5' and 3' Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA	15 gene(s)	inside rSNPs	diseases
6	esv2755538	chr5:14814900-14927500	Enhancers Weak transcription Flanking Bivalent TSS/Enh Active TSS Flanking Active TSS Genic enhancers Bivalent/Poised TSS Strong transcription Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA	18 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:65 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:14796400-14821800	Weak transcription	Duodenum Smooth Muscle	Duodenum
2	chr5:14811400-14821400	Weak transcription	Fetal Heart	heart
3	chr5:14811600-14819400	Weak transcription	Esophagus	oesophagus
4	chr5:14811600-14825000	Weak transcription	Breast Myoepithelial Primary Cells	Breast
5	chr5:14811600-14827400	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
6	chr5:14811600-14827600	Weak transcription	Rectal Mucosa Donor 29	rectum
7	chr5:14811600-14843800	Weak transcription	Fetal Intestine Large	intestine
8	chr5:14811600-14861200	Weak transcription	Colonic Mucosa	Colon
9	chr5:14812000-14849600	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
10	chr5:14812200-14820600	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
11	chr5:14812600-14821000	Weak transcription	Sigmoid Colon	Sigmoid Colon
12	chr5:14814000-14824800	Weak transcription	HepG2	liver
13	chr5:14814000-14835000	Weak transcription	Primary T helper naive cells from peripheral blood	blood
14	chr5:14814200-14819200	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
15	chr5:14814200-14820200	Weak transcription	Primary T cells from cord blood	blood
16	chr5:14814200-14820600	Weak transcription	Fetal Intestine Small	intestine
17	chr5:14814200-14827000	Weak transcription	Dnd41	blood
18	chr5:14814400-14842200	Weak transcription	Thymus	Thymus
19	chr5:14814800-14826800	Weak transcription	Primary T cells fromperipheralblood	blood
20	chr5:14815800-14818400	Enhancers	HMEC	breast
21	chr5:14816200-14821400	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
22	chr5:14816200-14824600	Enhancers	Fetal Brain Male	brain
23	chr5:14816400-14819000	Weak transcription	Primary T helper cells PMA-I stimulated	--
24	chr5:14816400-14820400	Weak transcription	Rectal Mucosa Donor 31	rectum
25	chr5:14816800-14819200	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
26	chr5:14817000-14819000	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
27	chr5:14817000-14819000	Weak transcription	Brain Anterior Caudate	brain
28	chr5:14817000-14820000	Enhancers	NHDF-Ad	bronchial
29	chr5:14817000-14821400	Weak transcription	HUVEC	blood vessel
30	chr5:14817200-14819000	Weak transcription	Psoas Muscle	Psoas
31	chr5:14817200-14819000	Enhancers	Osteobl	bone
32	chr5:14817400-14819200	Weak transcription	Aorta	Aorta
33	chr5:14817400-14819200	Weak transcription	Right Ventricle	heart
34	chr5:14817400-14819400	Weak transcription	Left Ventricle	heart
35	chr5:14817400-14819600	Enhancers	Primary B cells from peripheral blood	blood
36	chr5:14817400-14821400	Weak transcription	Pancreatic Islets	Pancreatic Islet
37	chr5:14817400-14829600	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
38	chr5:14817400-14842400	Weak transcription	Lung	lung
39	chr5:14817600-14819200	Weak transcription	HSMMtube	muscle
40	chr5:14817600-14820600	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
41	chr5:14817600-14823800	Weak transcription	Liver	Liver
42	chr5:14817800-14818800	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
43	chr5:14817800-14819000	Weak transcription	Brain Angular Gyrus	brain
44	chr5:14817800-14819000	Weak transcription	Skeletal Muscle Male	skeletal muscle
45	chr5:14817800-14819200	Weak transcription	Adipose Nuclei	Adipose
46	chr5:14817800-14819200	Weak transcription	HSMM	muscle
47	chr5:14817800-14819400	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
48	chr5:14817800-14819600	Enhancers	GM12878-XiMat	blood
49	chr5:14817800-14820600	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
50	chr5:14817800-14820600	Weak transcription	Fetal Brain Female	brain

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