Variant report

Variant	rs5027774
Chromosome Location	chr10:50462845-50462846
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr10:50461288..50465074-chr10:50465528..50469172,3	K562	blood:
2	chr10:50462244..50464154-chr10:50465883..50467890,2	K562	blood:

Extended variants
information (count: 28 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:25)

rs_ID	r²[population]
rs10745254	0.83[AFR][1000 genomes]
rs10745255	0.84[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs10745256	0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs10776548	0.83[AFR][1000 genomes]
rs10776554	0.89[AMR][1000 genomes];0.96[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs10776557	1.00[CEU][hapmap];1.00[CHB][hapmap];0.94[CHD][hapmap];0.94[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.97[TSI][hapmap];0.91[AMR][1000 genomes];0.94[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs10857453	0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs10857462	1.00[CHB][hapmap];1.00[JPT][hapmap];0.84[ASN][1000 genomes]
rs11101071	0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1122558	0.83[AMR][1000 genomes];0.89[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs1962330	0.90[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1987086	0.90[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2377946	0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2889797	0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs3954175	0.93[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[AMR][1000 genomes];0.85[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs4838378	0.85[AMR][1000 genomes];0.89[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs4838475	0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4838476	0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4838489	0.83[AMR][1000 genomes];0.89[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs4838492	1.00[CHB][hapmap];1.00[JPT][hapmap];0.84[ASN][1000 genomes]
rs7098639	0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs7098667	0.85[AMR][1000 genomes];0.89[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs7893248	0.81[ASN][1000 genomes]
rs7909185	0.91[AMR][1000 genomes];0.94[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs7913739	0.87[AMR][1000 genomes];0.85[EUR][1000 genomes];0.88[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv895375	chr10:50306386-51028871	Weak transcription Active TSS Strong transcription Enhancers Flanking Active TSS Bivalent Enhancer Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	33 gene(s)	inside rSNPs	diseases
2	nsv534410	chr10:50317458-50826916	Weak transcription Bivalent Enhancer Enhancers Active TSS Strong transcription Flanking Active TSS Bivalent/Poised TSS Genic enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	30 gene(s)	inside rSNPs	diseases
3	esv3398622	chr10:50460546-50464244	Enhancers Weak transcription Flanking Active TSS ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	Chromatin interactive region	n/a	inside rSNPs	diseases

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs5027774	SYT15	cis	parietal	SCAN
rs5027774	NCOA4	cis	parietal	SCAN
rs5027774	LRRC18	cis	parietal	SCAN
rs5027774	TIMM23	cis	cerebellum	SCAN

Chromatin state (count:40 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr10:50460600-50463200	Enhancers	Left Ventricle	heart
2	chr10:50460800-50467000	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
3	chr10:50461200-50463800	Enhancers	Primary T helper 17 cells PMA-I stimulated	--
4	chr10:50461200-50464000	Enhancers	Primary T killer naive cells fromperipheralblood	blood
5	chr10:50461400-50463800	Enhancers	Thymus	Thymus
6	chr10:50461400-50464200	Enhancers	Fetal Thymus	thymus
7	chr10:50461400-50466000	Enhancers	Primary B cells from peripheral blood	blood
8	chr10:50461600-50463200	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
9	chr10:50461600-50464000	Weak transcription	Psoas Muscle	Psoas
10	chr10:50462000-50463200	Flanking Active TSS	Primary hematopoietic stem cells	blood
11	chr10:50462000-50463200	Enhancers	Primary T helper cells PMA-I stimulated	--
12	chr10:50462000-50463200	Enhancers	Primary mononuclear cells fromperipheralblood	Blood
13	chr10:50462000-50463200	Enhancers	Skeletal Muscle Female	skeletal muscle
14	chr10:50462000-50463400	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
15	chr10:50462000-50463400	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Female	--
16	chr10:50462000-50463400	Enhancers	Spleen	Spleen
17	chr10:50462000-50463600	Enhancers	Primary T helper naive cells from peripheral blood	blood
18	chr10:50462000-50463600	Enhancers	Primary T killer memory cells from peripheral blood	blood
19	chr10:50462200-50463200	Flanking Active TSS	Primary T cells from cord blood	blood
20	chr10:50462200-50463200	Enhancers	Duodenum Mucosa	Duodenum
21	chr10:50462200-50463400	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
22	chr10:50462200-50463400	Enhancers	Primary T helper cells fromperipheralblood	blood
23	chr10:50462200-50463400	Enhancers	Primary T cells effector/memory enriched fromperipheralblood	blood
24	chr10:50462200-50463800	Enhancers	Primary monocytes fromperipheralblood	blood
25	chr10:50462200-50464800	Bivalent Enhancer	Primary T cells fromperipheralblood	blood
26	chr10:50462400-50463200	Flanking Active TSS	Primary B cells from cord blood	blood
27	chr10:50462400-50463400	Enhancers	Fetal Muscle Trunk	muscle
28	chr10:50462400-50463600	Flanking Active TSS	Primary hematopoietic stem cells short term culture	blood
29	chr10:50462600-50463200	Enhancers	iPS DF 19.11 Cell Line	embryonic stem cell
30	chr10:50462600-50463200	Enhancers	Lung	lung
31	chr10:50462600-50463400	Enhancers	Primary neutrophils fromperipheralblood	blood
32	chr10:50462600-50463400	Enhancers	Primary T regulatory cells fromperipheralblood	blood
33	chr10:50462600-50464200	Enhancers	Fetal Muscle Leg	muscle
34	chr10:50462800-50463000	Enhancers	iPS-15b Cell Line	embryonic stem cell
35	chr10:50462800-50463000	Bivalent Enhancer	Fetal Adrenal Gland	Adrenal Gland
36	chr10:50462800-50463000	Enhancers	Fetal Heart	heart
37	chr10:50462800-50463000	Enhancers	Right Atrium	heart
38	chr10:50462800-50463200	Flanking Active TSS	Dnd41	blood
39	chr10:50462800-50463200	Flanking Active TSS	Monocytes-CD14+_RO01746	blood
40	chr10:50462800-50463600	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell

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