Variant report

Variant	rs304478
Chromosome Location	chr10:91150922-91150923
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 47 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:42)

rs_ID	r²[population]
rs10159774	0.96[CEU][hapmap];0.86[GIH][hapmap];0.87[MEX][hapmap];0.88[MKK][hapmap];0.93[TSI][hapmap];1.00[YRI][hapmap];0.90[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs10509570	1.00[YRI][hapmap]
rs10749605	0.89[CEU][hapmap]
rs10749606	0.96[CEU][hapmap];0.87[MEX][hapmap];0.91[TSI][hapmap];0.87[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs10749607	0.96[CEU][hapmap];1.00[YRI][hapmap];0.90[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs10887943	1.00[YRI][hapmap]
rs160052	1.00[YRI][hapmap]
rs1888923	0.85[CEU][hapmap];0.87[MEX][hapmap];0.82[TSI][hapmap];1.00[YRI][hapmap];0.83[AMR][1000 genomes]
rs215493	0.81[ASW][hapmap];0.93[CEU][hapmap];0.96[CHD][hapmap];0.89[GIH][hapmap];0.89[JPT][hapmap];0.90[LWK][hapmap];0.92[MEX][hapmap];0.93[MKK][hapmap];1.00[YRI][hapmap];0.88[AMR][1000 genomes];0.85[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs2458877	0.81[AMR][1000 genomes];0.86[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs2484045	0.85[AMR][1000 genomes];0.86[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs303170	0.80[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs303172	0.88[CEU][hapmap];0.80[CHD][hapmap];0.84[GIH][hapmap];0.84[JPT][hapmap];0.81[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs303174	0.88[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs303217	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.96[CHD][hapmap];0.98[GIH][hapmap];0.94[JPT][hapmap];1.00[LWK][hapmap];0.96[MEX][hapmap];1.00[MKK][hapmap];0.95[TSI][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs304439	0.88[AMR][1000 genomes];0.86[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs304440	0.92[CEU][hapmap];0.88[JPT][hapmap];1.00[YRI][hapmap];0.88[AMR][1000 genomes];0.86[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs304443	0.81[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs304448	0.89[CEU][hapmap];0.84[CHD][hapmap];0.84[GIH][hapmap];0.89[JPT][hapmap];0.81[TSI][hapmap];0.84[EUR][1000 genomes]
rs304449	0.93[CEU][hapmap];0.89[JPT][hapmap];1.00[YRI][hapmap];0.85[EUR][1000 genomes]
rs304451	0.87[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs304483	0.85[AFR][1000 genomes];0.89[AMR][1000 genomes];0.90[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs304485	0.93[CEU][hapmap];0.94[JPT][hapmap];1.00[YRI][hapmap];0.88[AMR][1000 genomes];0.85[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs304494	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs304495	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs304504	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.81[LWK][hapmap];1.00[MEX][hapmap];0.90[MKK][hapmap];0.98[TSI][hapmap];1.00[YRI][hapmap];0.94[AFR][1000 genomes];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs305371	0.96[CEU][hapmap];1.00[YRI][hapmap];0.92[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs305373	0.90[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs305375	0.96[CEU][hapmap];1.00[YRI][hapmap];0.95[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs305376	0.95[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs305377	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.95[AMR][1000 genomes];0.93[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs4933504	0.81[AMR][1000 genomes]
rs4934471	0.89[CEU][hapmap];0.87[MEX][hapmap];0.85[TSI][hapmap];1.00[YRI][hapmap];0.83[AMR][1000 genomes]
rs4934473	0.84[AMR][1000 genomes]
rs4934475	0.96[CEU][hapmap];1.00[YRI][hapmap];0.90[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs559198	0.80[EUR][1000 genomes]
rs627524	0.96[CEU][hapmap];0.87[GIH][hapmap];0.92[MEX][hapmap];1.00[MKK][hapmap];0.93[TSI][hapmap];1.00[YRI][hapmap];0.95[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs6586184	0.80[AMR][1000 genomes]
rs7094510	0.89[CEU][hapmap]
rs7095398	0.88[CEU][hapmap]
rs954439	0.81[CEU][hapmap]
rs975686	0.83[AMR][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	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	nsv1040375	chr10:91022218-91153074	Enhancers Active TSS Weak transcription Flanking Active TSS Transcr. at gene 5' and 3' Strong transcription Genic enhancers ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	16 gene(s)	inside rSNPs	diseases
5	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:4)

SNP	Gene	Cis/trans	Tissue	Source
rs304478	IFIT5	cis	Nerve Tibial	GTEx
rs304478	IFIT5	Cis_1M	lymphoblastoid	RTeQTL
rs304478	IFIT5	cis	Artery Tibial	GTEx
rs304478	IFIT1	cis	cerebellum	SCAN

Chromatin state (count:51 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr10:91145400-91151000	Weak transcription	GM12878-XiMat	blood
2	chr10:91145400-91151800	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
3	chr10:91145600-91151600	Weak transcription	Primary neutrophils fromperipheralblood	blood
4	chr10:91145800-91151600	Weak transcription	Monocytes-CD14+_RO01746	blood
5	chr10:91146000-91151400	Weak transcription	Primary monocytes fromperipheralblood	blood
6	chr10:91146200-91151400	Weak transcription	Primary hematopoietic stem cells	blood
7	chr10:91146200-91151800	Weak transcription	ES-I3 Cell Line	embryonic stem cell
8	chr10:91146200-91152400	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
9	chr10:91146400-91151600	Weak transcription	Primary hematopoietic stem cells short term culture	blood
10	chr10:91146600-91152000	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
11	chr10:91146800-91151800	Weak transcription	iPS-15b Cell Line	embryonic stem cell
12	chr10:91148000-91151600	Weak transcription	Primary T helper cells PMA-I stimulated	--
13	chr10:91148600-91151600	Weak transcription	A549	lung
14	chr10:91149200-91151000	Enhancers	Brain Hippocampus Middle	brain
15	chr10:91149200-91151600	Weak transcription	NHDF-Ad	bronchial
16	chr10:91149200-91151800	Weak transcription	HUES64 Cell Line	embryonic stem cell
17	chr10:91149200-91151800	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
18	chr10:91149400-91151800	Weak transcription	HUES6 Cell Line	embryonic stem cell
19	chr10:91149600-91151600	Enhancers	Fetal Muscle Leg	muscle
20	chr10:91150000-91151400	Enhancers	Skeletal Muscle Female	skeletal muscle
21	chr10:91150000-91151600	Enhancers	Rectal Smooth Muscle	rectum
22	chr10:91150000-91151800	Enhancers	Cortex derived primary cultured neurospheres	brain
23	chr10:91150000-91151800	Enhancers	Fetal Heart	heart
24	chr10:91150200-91151000	Enhancers	Brain Cingulate Gyrus	brain
25	chr10:91150200-91151200	Enhancers	Fetal Lung	lung
26	chr10:91150200-91151600	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
27	chr10:91150200-91151600	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
28	chr10:91150200-91151600	Enhancers	Colon Smooth Muscle	Colon
29	chr10:91150200-91151600	Enhancers	Skeletal Muscle Male	skeletal muscle
30	chr10:91150400-91151000	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
31	chr10:91150400-91151000	Enhancers	Brain Germinal Matrix	brain
32	chr10:91150400-91151000	Enhancers	Duodenum Smooth Muscle	Duodenum
33	chr10:91150400-91151200	Enhancers	Right Ventricle	heart
34	chr10:91150400-91151600	Enhancers	Brain Dorsolateral Prefrontal Cortex	brain
35	chr10:91150400-91151600	Enhancers	Stomach Smooth Muscle	stomach
36	chr10:91150400-91151800	Enhancers	Left Ventricle	heart
37	chr10:91150400-91152800	Enhancers	Small Intestine	intestine
38	chr10:91150600-91151000	Enhancers	Duodenum Mucosa	Duodenum
39	chr10:91150600-91151400	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
40	chr10:91150600-91151600	Enhancers	Liver	Liver
41	chr10:91150600-91151600	Weak transcription	Brain Angular Gyrus	brain
42	chr10:91150600-91151600	Weak transcription	Brain Inferior Temporal Lobe	brain
43	chr10:91150600-91151800	Weak transcription	Fetal Brain Female	brain
44	chr10:91150800-91151000	Enhancers	NHLF	lung
45	chr10:91150800-91151400	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
46	chr10:91150800-91151400	Weak transcription	Adipose Nuclei	Adipose
47	chr10:91150800-91151600	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
48	chr10:91150800-91151600	Weak transcription	Brain Anterior Caudate	brain
49	chr10:91150800-91151600	Weak transcription	HepG2	liver
50	chr10:91150800-91151800	Weak transcription	Brain Substantia Nigra	brain

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