Variant report

Variant	rs28408106
Chromosome Location	chr5:74708513-74708514
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 68 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:63)

rs_ID	r²[population]
rs10036682	0.80[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs10038945	0.89[EUR][1000 genomes]
rs10041470	0.95[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs10055011	0.86[AFR][1000 genomes];0.95[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs10059022	0.83[AFR][1000 genomes];0.95[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs10061689	0.89[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs10067900	0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs10074747	0.80[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs10076819	0.93[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs10077427	0.93[EUR][1000 genomes]
rs10078671	0.89[EUR][1000 genomes]
rs10474437	0.80[AFR][1000 genomes];0.91[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs12173076	0.92[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs13360099	0.80[AFR][1000 genomes];0.91[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs13361353	0.93[EUR][1000 genomes]
rs1469051	0.85[EUR][1000 genomes]
rs1553234	0.93[EUR][1000 genomes]
rs1820049	0.88[EUR][1000 genomes]
rs1909719	0.83[AFR][1000 genomes];0.80[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs2287710	0.86[AFR][1000 genomes];0.88[EUR][1000 genomes]
rs28612248	0.80[AFR][1000 genomes];0.90[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs28668361	0.89[EUR][1000 genomes]
rs28874007	0.91[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs3804231	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4703671	0.86[AMR][1000 genomes];0.98[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs4703675	0.86[AFR][1000 genomes];0.80[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs4704213	0.90[AMR][1000 genomes];1.00[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs4704229	0.86[AFR][1000 genomes];0.80[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs56859362	0.91[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs5744544	0.88[EUR][1000 genomes]
rs5744545	0.86[EUR][1000 genomes]
rs5744636	0.86[AFR][1000 genomes];0.80[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs5744667	0.87[EUR][1000 genomes]
rs5744704	0.89[EUR][1000 genomes]
rs5744709	0.88[EUR][1000 genomes]
rs5744712	0.88[EUR][1000 genomes]
rs57907925	0.85[EUR][1000 genomes]
rs58519566	0.86[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs58841453	0.86[AFR][1000 genomes];0.80[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs61303403	0.81[EUR][1000 genomes]
rs6891560	0.95[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs72633963	0.89[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs72633964	0.91[AFR][1000 genomes];0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs72633965	0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs72633966	0.84[AFR][1000 genomes];0.93[AMR][1000 genomes];0.93[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs72633967	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];0.93[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs72633968	0.90[EUR][1000 genomes]
rs72633969	0.93[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs72633970	0.91[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs72633971	0.90[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs72633972	0.81[AFR][1000 genomes];0.80[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs72633973	0.93[EUR][1000 genomes]
rs72633974	0.86[AFR][1000 genomes];0.80[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs72633975	0.89[EUR][1000 genomes]
rs72633976	0.87[EUR][1000 genomes]
rs72633977	0.81[EUR][1000 genomes]
rs7356633	0.90[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7726478	0.94[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs904743	0.85[EUR][1000 genomes]
rs9293652	0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9293654	0.81[AFR][1000 genomes];0.88[EUR][1000 genomes]
rs9293655	0.83[AFR][1000 genomes];0.80[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs979182	0.85[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:5 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv882193	chr5:74656175-74917862	ZNF genes & repeats Weak transcription Enhancers Strong transcription Active TSS Flanking Active TSS Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	15 gene(s)	inside rSNPs	diseases
2	nsv882194	chr5:74656175-74946455	Strong transcription Genic enhancers Weak transcription Enhancers Active TSS Flanking Active TSS ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	15 gene(s)	inside rSNPs	diseases
3	nsv882195	chr5:74678937-74896798	Weak transcription Enhancers ZNF genes & repeats Active TSS Strong transcription Genic enhancers Flanking Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	12 gene(s)	inside rSNPs	diseases
4	nsv882196	chr5:74678937-74917862	Weak transcription Enhancers Strong transcription Flanking Bivalent TSS/Enh Flanking Active TSS Bivalent Enhancer Active TSS ZNF genes & repeats Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	13 gene(s)	inside rSNPs	diseases
5	nsv882197	chr5:74692776-74946455	Enhancers Weak transcription ZNF genes & repeats Strong transcription Genic enhancers Active TSS Flanking Active TSS 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 target site	13 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:120 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:74656400-74725600	Weak transcription	Placenta Amnion	Placenta Amnion
2	chr5:74656800-74731400	Weak transcription	Rectal Smooth Muscle	rectum
3	chr5:74659800-74720600	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
4	chr5:74660000-74722800	Weak transcription	Fetal Heart	heart
5	chr5:74667000-74723200	Strong transcription	Monocytes-CD14+_RO01746	blood
6	chr5:74670800-74709400	Weak transcription	Pancreas	Pancrea
7	chr5:74670800-74720600	Weak transcription	Right Ventricle	heart
8	chr5:74670800-74731400	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
9	chr5:74671000-74722800	Weak transcription	Hela-S3	cervix
10	chr5:74674400-74761400	Weak transcription	Esophagus	oesophagus
11	chr5:74675400-74720800	Weak transcription	Small Intestine	intestine
12	chr5:74676200-74721000	Weak transcription	Brain Hippocampus Middle	brain
13	chr5:74677400-74722800	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
14	chr5:74677600-74709200	Weak transcription	Gastric	stomach
15	chr5:74677600-74734200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
16	chr5:74677800-74721000	Weak transcription	NH-A	brain
17	chr5:74677800-74725000	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
18	chr5:74677800-74731400	Weak transcription	Aorta	Aorta
19	chr5:74678000-74720600	Weak transcription	Colonic Mucosa	Colon
20	chr5:74678000-74730800	Weak transcription	Psoas Muscle	Psoas
21	chr5:74680600-74721000	Weak transcription	HMEC	breast
22	chr5:74680800-74722600	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
23	chr5:74681000-74723200	Weak transcription	HUVEC	blood vessel
24	chr5:74681400-74718400	Weak transcription	Brain Germinal Matrix	brain
25	chr5:74681800-74720600	Weak transcription	Fetal Brain Male	brain
26	chr5:74684000-74709000	Weak transcription	Spleen	Spleen
27	chr5:74684000-74720400	Weak transcription	Primary T helper naive cells from peripheral blood	blood
28	chr5:74684000-74720800	Weak transcription	Thymus	Thymus
29	chr5:74684000-74731200	Weak transcription	HSMMtube	muscle
30	chr5:74685800-74709200	Weak transcription	Dnd41	blood
31	chr5:74685800-74711800	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
32	chr5:74692000-74709000	Weak transcription	HepG2	liver
33	chr5:74695200-74718200	Weak transcription	Colon Smooth Muscle	Colon
34	chr5:74695400-74721000	Weak transcription	Brain Anterior Caudate	brain
35	chr5:74695400-74721000	Weak transcription	Brain Inferior Temporal Lobe	brain
36	chr5:74695400-74723200	Weak transcription	Skeletal Muscle Male	skeletal muscle
37	chr5:74695600-74721000	Weak transcription	Brain Angular Gyrus	brain
38	chr5:74696000-74715800	Weak transcription	Ovary	ovary
39	chr5:74696200-74713800	Weak transcription	Fetal Brain Female	brain
40	chr5:74696800-74709000	Weak transcription	Sigmoid Colon	Sigmoid Colon
41	chr5:74697000-74714000	Weak transcription	Skeletal Muscle Female	skeletal muscle
42	chr5:74697000-74720400	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
43	chr5:74697200-74714000	Weak transcription	Primary hematopoietic stem cells short term culture	blood
44	chr5:74697400-74714200	Weak transcription	Stomach Smooth Muscle	stomach
45	chr5:74697800-74710000	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
46	chr5:74698000-74711200	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
47	chr5:74698000-74712200	Weak transcription	Duodenum Mucosa	Duodenum
48	chr5:74698000-74714000	Weak transcription	Fetal Kidney	kidney
49	chr5:74699400-74715800	Weak transcription	Primary hematopoietic stem cells	blood
50	chr5:74699600-74710600	Weak transcription	HSMM	muscle

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