Variant report

Variant	rs9293809
Chromosome Location	chr5:79565071-79565072
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 17 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:15)

rs_ID	r²[population]
rs10035563	0.91[AMR][1000 genomes];0.93[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10041270	0.95[CEU][hapmap];0.94[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];0.98[AMR][1000 genomes];0.92[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10051472	0.80[AMR][1000 genomes];0.88[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs10056958	0.82[JPT][hapmap]
rs10065865	0.88[ASN][1000 genomes]
rs10462573	0.87[ASN][1000 genomes]
rs1126176	0.83[CHB][hapmap];0.84[ASN][1000 genomes]
rs11960022	0.96[AFR][1000 genomes];0.97[AMR][1000 genomes];0.94[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4998063	0.92[JPT][hapmap]
rs55649733	0.97[ASN][1000 genomes]
rs56850090	0.87[ASN][1000 genomes]
rs6872359	1.00[CHB][hapmap];0.83[CHD][hapmap];1.00[JPT][hapmap];0.96[ASN][1000 genomes]
rs7707520	0.97[ASN][1000 genomes]
rs9293807	0.90[ASW][hapmap];1.00[CHB][hapmap];0.92[CHD][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MKK][hapmap];0.83[TSI][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs9293808	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:2 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv432748	chr5:79300434-79577760	Enhancers Genic enhancers Weak transcription Bivalent Enhancer Flanking Active TSS Strong transcription ZNF genes & repeats Bivalent/Poised TSS Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	22 gene(s)	inside rSNPs	diseases
2	nsv948807	chr5:79549207-79805765	Genic enhancers Enhancers Flanking Active TSS Weak transcription Strong transcription Active TSS ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	49 gene(s)	inside rSNPs	diseases

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs9293809	SERINC5	cis	parietal	SCAN
rs9293809	HOMER1	cis	parietal	SCAN
rs9293809	CKMT2	cis	parietal	SCAN
rs9293809	ZBED3	cis	parietal	SCAN

Chromatin state (count:38 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:79553400-79577800	Weak transcription	Right Atrium	heart
2	chr5:79553600-79568200	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
3	chr5:79560800-79565400	Weak transcription	Primary neutrophils fromperipheralblood	blood
4	chr5:79561600-79569800	Enhancers	Primary T cells from cord blood	blood
5	chr5:79562400-79566000	Enhancers	Primary T helper cells PMA-I stimulated	--
6	chr5:79563600-79569200	Enhancers	Primary T cells fromperipheralblood	blood
7	chr5:79563800-79567800	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
8	chr5:79563800-79567800	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
9	chr5:79563800-79567800	Enhancers	Primary T helper cells fromperipheralblood	blood
10	chr5:79563800-79568000	Enhancers	Primary T killer memory cells from peripheral blood	blood
11	chr5:79563800-79569400	Enhancers	Primary T helper naive cells fromperipheralblood	blood
12	chr5:79563800-79569400	Enhancers	Fetal Thymus	thymus
13	chr5:79564000-79566600	Weak transcription	Placenta	Placenta
14	chr5:79564200-79565600	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
15	chr5:79564400-79566600	Enhancers	Thymus	Thymus
16	chr5:79564600-79565200	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
17	chr5:79564600-79565200	Enhancers	Dnd41	blood
18	chr5:79564600-79565400	Enhancers	iPS-18 Cell Line	embryonic stem cell
19	chr5:79564600-79565400	Enhancers	Primary B cells from cord blood	blood
20	chr5:79564600-79565400	Enhancers	Primary hematopoietic stem cells short term culture	blood
21	chr5:79564600-79565400	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
22	chr5:79564600-79565400	Enhancers	Duodenum Smooth Muscle	Duodenum
23	chr5:79564600-79565400	Enhancers	Rectal Mucosa Donor 29	rectum
24	chr5:79564600-79565600	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
25	chr5:79564600-79566000	Enhancers	Fetal Adrenal Gland	Adrenal Gland
26	chr5:79564600-79566400	Enhancers	Primary hematopoietic stem cells	blood
27	chr5:79564600-79567600	Enhancers	Primary T helper 17 cells PMA-I stimulated	--
28	chr5:79564600-79567800	Enhancers	Primary T helper naive cells from peripheral blood	blood
29	chr5:79564600-79568000	Enhancers	Primary T killer naive cells fromperipheralblood	blood
30	chr5:79564800-79565200	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
31	chr5:79564800-79565200	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
32	chr5:79564800-79565200	Enhancers	HepG2	liver
33	chr5:79564800-79565200	Enhancers	Monocytes-CD14+_RO01746	blood
34	chr5:79564800-79565400	Enhancers	ES-I3 Cell Line	embryonic stem cell
35	chr5:79564800-79565600	Enhancers	Fetal Stomach	stomach
36	chr5:79564800-79566400	Enhancers	Cortex derived primary cultured neurospheres	brain
37	chr5:79565000-79565200	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
38	chr5:79565000-79565400	Enhancers	Fetal Kidney	kidney

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