Variant report

Variant	rs303216
Chromosome Location	chr10:91155186-91155187
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	POLR2A	chr10:91154957-91155257	GM12878	blood:	n/a	n/a

Variant related genes	Relation type
IFIT1	TF binding region

Extended variants
information (count: 36 )
Associated
traits (count: 6 )

rSNPs within LD-proxies of this variant (count:32)

rs_ID	r²[population]
rs184236	0.90[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs188589	0.91[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs188591	0.87[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs2484046	0.83[AFR][1000 genomes];0.94[AMR][1000 genomes];0.94[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2484047	0.91[AMR][1000 genomes];0.90[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs303171	0.83[AFR][1000 genomes];0.94[AMR][1000 genomes];0.92[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs303173	0.83[AFR][1000 genomes];0.92[AMR][1000 genomes];0.87[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs303209	0.83[AFR][1000 genomes];0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs303210	0.98[AMR][1000 genomes];0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs303213	1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs303215	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs303218	0.91[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs304411	0.83[AFR][1000 genomes];0.91[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs304412	0.84[AMR][1000 genomes]
rs304413	0.81[AMR][1000 genomes]
rs304434	0.83[AFR][1000 genomes];0.94[AMR][1000 genomes];0.94[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs304436	0.92[AMR][1000 genomes];0.94[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs304437	0.83[AFR][1000 genomes];0.95[AMR][1000 genomes];0.95[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs304441	0.83[AFR][1000 genomes];0.95[AMR][1000 genomes];0.95[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs304442	0.83[AFR][1000 genomes];0.95[AMR][1000 genomes];0.95[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs304447	0.91[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs304450	0.83[AFR][1000 genomes];0.94[AMR][1000 genomes];0.94[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs304492	0.90[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs304493	0.82[EUR][1000 genomes]
rs304497	0.86[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs304498	0.83[EUR][1000 genomes]
rs304500	0.89[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs304502	0.83[AFR][1000 genomes];0.90[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs304503	0.83[AFR][1000 genomes];0.90[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs304505	0.92[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs304506	0.92[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs781501	0.86[AMR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1042848	chr10:90466032-91318474	Weak transcription Enhancers Flanking Active TSS Active TSS Bivalent/Poised TSS Bivalent Enhancer Strong transcription Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	66 gene(s)	inside rSNPs	diseases
2	nsv540741	chr10:90466032-91318474	Enhancers Flanking Active TSS Weak transcription Genic enhancers Bivalent Enhancer ZNF genes & repeats Strong transcription Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	66 gene(s)	inside rSNPs	diseases
3	nsv1041964	chr10:90861380-91378356	Flanking Active TSS Enhancers Weak transcription Genic enhancers Bivalent/Poised TSS Active TSS Flanking Bivalent TSS/Enh Strong transcription Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	82 gene(s)	inside rSNPs	diseases
4	esv34085	chr10:91065949-91174175	Enhancers Weak transcription Active TSS Strong transcription Genic enhancers Flanking Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	14 gene(s)	inside rSNPs	diseases

mRNA abundance (count:6)

SNP	Gene	Cis/trans	Tissue	Source
rs303216	IFIT5	cis	Nerve Tibial	GTEx
rs303216	IFIT5	cis	Artery Tibial	GTEx
rs303216	IFIT5	Cis_1M	lymphoblastoid	RTeQTL
rs303216	IFIT5	cis	Esophagus Mucosa	GTEx
rs303216	IFIT5	cis	Esophagus Muscularis	GTEx
rs303216	IFIT1	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:90 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr10:91152800-91173600	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
2	chr10:91152800-91174000	Weak transcription	Gastric	stomach
3	chr10:91153000-91164200	Weak transcription	Esophagus	oesophagus
4	chr10:91153200-91155200	Enhancers	Primary T helper cells PMA-I stimulated	--
5	chr10:91153200-91155400	Enhancers	Breast Myoepithelial Primary Cells	Breast
6	chr10:91153200-91155600	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
7	chr10:91153200-91156200	Weak transcription	Sigmoid Colon	Sigmoid Colon
8	chr10:91153200-91157400	Weak transcription	A549	lung
9	chr10:91153200-91157600	Weak transcription	HepG2	liver
10	chr10:91153200-91157800	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
11	chr10:91153200-91162000	Weak transcription	HSMM	muscle
12	chr10:91153200-91163800	Weak transcription	Spleen	Spleen
13	chr10:91153200-91173600	Weak transcription	Brain Germinal Matrix	brain
14	chr10:91153400-91155200	Enhancers	Cortex derived primary cultured neurospheres	brain
15	chr10:91153400-91155800	Enhancers	Primary T killer memory cells from peripheral blood	blood
16	chr10:91153400-91157400	Weak transcription	Muscle Satellite Cultured Cells	--
17	chr10:91153400-91158000	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
18	chr10:91153400-91162200	Weak transcription	Placenta	Placenta
19	chr10:91153400-91162200	Weak transcription	Lung	lung
20	chr10:91153400-91163400	Weak transcription	Duodenum Mucosa	Duodenum
21	chr10:91153400-91164000	Weak transcription	Pancreas	Pancrea
22	chr10:91153400-91172400	Weak transcription	Thymus	Thymus
23	chr10:91153600-91155400	Enhancers	Primary T helper naive cells fromperipheralblood	blood
24	chr10:91153600-91155400	Enhancers	Primary T helper cells fromperipheralblood	blood
25	chr10:91153600-91157600	Weak transcription	HSMMtube	muscle
26	chr10:91153600-91157800	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
27	chr10:91153600-91162200	Weak transcription	Primary T cells fromperipheralblood	blood
28	chr10:91153600-91162200	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
29	chr10:91153600-91165400	Weak transcription	Fetal Thymus	thymus
30	chr10:91153600-91173600	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
31	chr10:91154000-91155200	Weak transcription	Fetal Muscle Trunk	muscle
32	chr10:91154000-91155400	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
33	chr10:91154000-91155400	Enhancers	Liver	Liver
34	chr10:91154000-91157600	Weak transcription	Rectal Mucosa Donor 31	rectum
35	chr10:91154000-91162200	Weak transcription	Primary T cells from cord blood	blood
36	chr10:91154000-91162200	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
37	chr10:91154000-91162200	Weak transcription	Fetal Stomach	stomach
38	chr10:91154000-91162400	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
39	chr10:91154000-91164200	Weak transcription	Primary B cells from peripheral blood	blood
40	chr10:91154000-91166800	Weak transcription	Right Ventricle	heart
41	chr10:91154200-91155200	Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
42	chr10:91154200-91155200	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
43	chr10:91154200-91155200	Weak transcription	Fetal Heart	heart
44	chr10:91154200-91155200	Enhancers	Stomach Smooth Muscle	stomach
45	chr10:91154200-91155400	Enhancers	Brain Hippocampus Middle	brain
46	chr10:91154200-91155400	Enhancers	Brain Substantia Nigra	brain
47	chr10:91154200-91155400	Enhancers	Colon Smooth Muscle	Colon
48	chr10:91154200-91155400	Enhancers	Skeletal Muscle Female	skeletal muscle
49	chr10:91154200-91157200	Weak transcription	Fetal Lung	lung
50	chr10:91154200-91157400	Weak transcription	Hela-S3	cervix

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