Variant report

Variant	rs4339948
Chromosome Location	chr10:91092850-91092851
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr10:91086403..91089519-chr10:91091273..91094339,4	K562	blood:

Variant related genes	Relation type
ENSG00000119917	Chromatin interaction

Extended variants
information (count: 49 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:44)

rs_ID	r²[population]
rs10509571	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10509572	0.86[CEU][hapmap];0.81[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs10788641	0.95[CHB][hapmap]
rs10887946	0.95[CHB][hapmap]
rs10887947	0.86[CHB][hapmap]
rs10887950	0.86[CEU][hapmap]
rs11203063	0.81[CEU][hapmap]
rs11203070	0.84[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs11203072	0.87[AFR][1000 genomes];0.86[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs11203078	0.95[CHB][hapmap]
rs11203090	0.81[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs11203099	0.86[CEU][hapmap];0.82[EUR][1000 genomes]
rs11819073	0.81[AMR][1000 genomes]
rs12244233	0.86[CEU][hapmap]
rs12248331	0.87[AFR][1000 genomes];0.87[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs12255504	0.83[CEU][hapmap];0.87[AFR][1000 genomes];0.87[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs12766862	0.95[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1332330	0.87[CEU][hapmap];0.81[AMR][1000 genomes]
rs1591051	0.83[CEU][hapmap];0.83[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs17096301	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs17120001	0.81[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs17120004	0.81[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs17120325	0.81[CEU][hapmap]
rs2274878	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];0.94[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs305374	0.86[CHB][hapmap];0.84[YRI][hapmap]
rs34234196	0.81[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs34712773	0.81[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs35830608	0.81[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs3780878	0.86[CEU][hapmap];0.83[AFR][1000 genomes];0.87[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs4630205	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs627127	0.95[CHB][hapmap];0.83[YRI][hapmap]
rs6586182	0.81[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs6586183	0.86[CEU][hapmap];0.81[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs6586188	0.91[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.85[AMR][1000 genomes];0.87[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7073534	0.81[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs7085361	0.81[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs7088579	0.86[CEU][hapmap];0.81[AMR][1000 genomes]
rs71479013	0.81[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs7897619	0.86[CEU][hapmap];0.81[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs7897873	0.83[CEU][hapmap];0.81[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs7910389	0.88[AFR][1000 genomes];0.87[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs7916812	0.95[CEU][hapmap];1.00[YRI][hapmap];0.99[AFR][1000 genomes];0.95[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs812451	0.86[CHB][hapmap]
rs884407	0.81[AMR][1000 genomes];0.84[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	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:2)

SNP	Gene	Cis/trans	Tissue	Source
rs4339948	IFIT5	Cis_1M	lymphoblastoid	RTeQTL
rs4339948	IFIT5	cis	multi-tissue	Pritchard

Chromatin state (count:123 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr10:91087200-91093600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
2	chr10:91088000-91099800	Weak transcription	Gastric	stomach
3	chr10:91088200-91093200	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
4	chr10:91088200-91093400	Weak transcription	Esophagus	oesophagus
5	chr10:91090200-91107600	Weak transcription	Pancreas	Pancrea
6	chr10:91091200-91094000	Enhancers	Fetal Brain Male	brain
7	chr10:91091600-91093400	Flanking Active TSS	Primary T helper cells PMA-I stimulated	--
8	chr10:91091600-91094200	Enhancers	HUES6 Cell Line	embryonic stem cell
9	chr10:91091800-91093000	Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
10	chr10:91091800-91093000	Flanking Active TSS	Primary T cells fromperipheralblood	blood
11	chr10:91091800-91093000	Flanking Active TSS	Primary T helper memory cells from peripheral blood 1	blood
12	chr10:91091800-91093000	Flanking Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
13	chr10:91091800-91093000	Flanking Active TSS	Muscle Satellite Cultured Cells	--
14	chr10:91091800-91093000	Flanking Active TSS	Stomach Smooth Muscle	stomach
15	chr10:91091800-91093200	Flanking Active TSS	Primary hematopoietic stem cells	blood
16	chr10:91091800-91093200	Flanking Active TSS	Primary hematopoietic stem cells short term culture	blood
17	chr10:91091800-91093200	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
18	chr10:91091800-91093200	Flanking Active TSS	Brain Hippocampus Middle	brain
19	chr10:91091800-91093200	Active TSS	Ovary	ovary
20	chr10:91091800-91093200	Flanking Active TSS	HepG2	liver
21	chr10:91091800-91093400	Flanking Active TSS	Brain Substantia Nigra	brain
22	chr10:91091800-91093400	Flanking Active TSS	Osteobl	bone
23	chr10:91091800-91093600	Flanking Active TSS	Primary T cells from cord blood	blood
24	chr10:91091800-91093600	Flanking Active TSS	Primary T helper cells fromperipheralblood	blood
25	chr10:91091800-91093600	Flanking Active TSS	NHEK	skin
26	chr10:91091800-91093800	Flanking Active TSS	Primary monocytes fromperipheralblood	blood
27	chr10:91091800-91093800	Flanking Active TSS	Primary B cells from cord blood	blood
28	chr10:91091800-91094000	Flanking Active TSS	Primary neutrophils fromperipheralblood	blood
29	chr10:91091800-91094000	Enhancers	Cortex derived primary cultured neurospheres	brain
30	chr10:91091800-91094000	Active TSS	Foreskin Keratinocyte Primary Cells skin02	Skin
31	chr10:91091800-91094000	Flanking Active TSS	Brain Anterior Caudate	brain
32	chr10:91091800-91094200	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
33	chr10:91091800-91094200	Flanking Active TSS	Primary T helper naive cells from peripheral blood	blood
34	chr10:91091800-91094200	Flanking Active TSS	Adipose Nuclei	Adipose
35	chr10:91091800-91094200	Flanking Active TSS	Liver	Liver
36	chr10:91091800-91094200	Flanking Active TSS	Monocytes-CD14+_RO01746	blood
37	chr10:91092000-91093000	Active TSS	Fetal Muscle Trunk	muscle
38	chr10:91092000-91093000	Flanking Active TSS	Skeletal Muscle Male	skeletal muscle
39	chr10:91092000-91093000	Flanking Active TSS	Hela-S3	cervix
40	chr10:91092000-91093000	Active TSS	NHLF	lung
41	chr10:91092000-91093200	Flanking Active TSS	Foreskin Melanocyte Primary Cells skin03	Skin
42	chr10:91092000-91093200	Active TSS	Right Ventricle	heart
43	chr10:91092000-91093200	Flanking Active TSS	A549	lung
44	chr10:91092000-91093400	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Female	--
45	chr10:91092000-91094000	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
46	chr10:91092000-91094000	Enhancers	iPS-20b Cell Line	embryonic stem cell
47	chr10:91092000-91094000	Flanking Active TSS	Brain Inferior Temporal Lobe	brain
48	chr10:91092000-91094200	Enhancers	ES-I3 Cell Line	embryonic stem cell
49	chr10:91092000-91094200	Enhancers	HUES48 Cell Line	embryonic stem cell
50	chr10:91092000-91094200	Flanking Active TSS	Primary T helper 17 cells PMA-I stimulated	--

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