Variant report

Variant	rs7897873
Chromosome Location	chr10:91090709-91090710
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	GATA3	chr10:91090143-91090872	SK-N-SH	brain:	n/a	chr10:91090552-91090563
2	TCF12	chr10:91090175-91090825	SK-N-SH	brain:	n/a	n/a
3	GATA3	chr10:91090313-91090812	SK-N-SH	brain:	n/a	chr10:91090552-91090563
4	FOXA2	chr10:91090702-91090926	HepG2	liver:	n/a	n/a
5	BHLHE40	chr10:91090650-91090758	GM12878	blood:	n/a	n/a
6	EP300	chr10:91090366-91090723	SK-N-SH_RA	brain:	n/a	chr10:91090377-91090386
7	FOXA1	chr10:91090614-91091048	HepG2	liver:	n/a	n/a
8	POLR2A	chr10:91089798-91091263	GM12891	blood:	n/a	n/a
9	WRNIP1	chr10:91090616-91090911	GM12878	blood:	n/a	n/a
10	POLR2A	chr10:91089877-91091493	GM19099	blood:	n/a	n/a
11	FOXA1	chr10:91090675-91091069	HepG2	liver:	n/a	n/a

Variant related genes	Relation type
IFIT3	TF binding region

Extended variants
information (count: 61 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:56)

rs_ID	r²[population]
rs10509571	0.83[CEU][hapmap];0.81[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs10509572	1.00[CEU][hapmap];1.00[CHB][hapmap];0.93[JPT][hapmap];0.87[AMR][1000 genomes];0.91[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs10788642	0.82[ASN][1000 genomes]
rs10887950	0.90[CEU][hapmap]
rs10887953	0.95[CEU][hapmap];0.86[CHB][hapmap];0.82[JPT][hapmap];0.83[ASN][1000 genomes]
rs10887957	0.81[ASN][1000 genomes]
rs10887959	0.84[CEU][hapmap];1.00[CHB][hapmap];0.86[JPT][hapmap]
rs11203063	0.85[CEU][hapmap];1.00[JPT][hapmap];0.84[AMR][1000 genomes];0.89[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs11203066	0.85[AMR][1000 genomes];0.86[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs11203070	0.90[AMR][1000 genomes];0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs11203072	0.81[AFR][1000 genomes];0.92[AMR][1000 genomes];0.94[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11203090	0.87[AMR][1000 genomes];0.91[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs11203099	1.00[CEU][hapmap];0.92[CHB][hapmap];0.93[JPT][hapmap];0.85[AMR][1000 genomes];0.93[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs11203105	0.83[ASN][1000 genomes]
rs11203106	0.83[ASN][1000 genomes]
rs11203109	0.95[CEU][hapmap];0.86[CHB][hapmap];0.82[JPT][hapmap]
rs11203115	0.90[CEU][hapmap];1.00[CHB][hapmap];0.86[JPT][hapmap];0.82[ASN][1000 genomes]
rs11819073	0.87[AMR][1000 genomes];0.90[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs12244233	1.00[CEU][hapmap];1.00[CHB][hapmap];0.93[JPT][hapmap]
rs12248331	0.81[AFR][1000 genomes];0.93[AMR][1000 genomes];0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12255504	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[AFR][1000 genomes];0.93[AMR][1000 genomes];0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12356008	0.80[ASN][1000 genomes]
rs12766862	0.83[EUR][1000 genomes]
rs12772449	0.82[AMR][1000 genomes];0.86[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs12781453	0.82[ASN][1000 genomes]
rs1332330	0.95[CEU][hapmap];0.85[CHB][hapmap];1.00[JPT][hapmap];0.87[AMR][1000 genomes];0.91[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1591051	1.00[CEU][hapmap];1.00[CHB][hapmap];0.93[JPT][hapmap];0.88[AMR][1000 genomes];0.94[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs17096301	0.81[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs17120001	0.87[AMR][1000 genomes];0.94[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs17120004	0.87[AMR][1000 genomes];0.94[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs17120325	0.95[CEU][hapmap];0.86[JPT][hapmap]
rs17121248	0.84[CEU][hapmap];1.00[CHB][hapmap];0.86[JPT][hapmap]
rs2070845	0.82[CEU][hapmap];0.81[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs2274878	0.86[CEU][hapmap];0.81[AMR][1000 genomes]
rs34032344	0.82[AMR][1000 genomes];0.88[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs34234196	0.87[AMR][1000 genomes];0.94[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs34712773	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35830608	0.87[AMR][1000 genomes];0.91[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs3740027	0.81[CEU][hapmap];0.84[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs3780878	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4339948	0.83[CEU][hapmap];0.81[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs4630205	0.82[CEU][hapmap];0.81[EUR][1000 genomes]
rs59564102	0.85[ASN][1000 genomes]
rs6586182	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6586183	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6586196	0.81[CEU][hapmap]
rs7073534	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7085361	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7088579	1.00[CEU][hapmap];0.92[CHB][hapmap];0.93[JPT][hapmap];0.87[AMR][1000 genomes];0.90[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs7090346	0.90[CEU][hapmap];0.86[CHB][hapmap];0.82[JPT][hapmap]
rs71479013	0.87[AMR][1000 genomes];0.94[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs7897619	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]
rs7910389	0.82[AFR][1000 genomes];0.93[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7916812	0.90[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.85[AMR][1000 genomes];0.83[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs884407	0.87[AMR][1000 genomes];0.94[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs9733018	0.85[AMR][1000 genomes];0.85[EUR][1000 genomes];0.82[ASN][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
rs7897873	IFIT5	Cis_1M	lymphoblastoid	RTeQTL
rs7897873	IFIT5	cis	multi-tissue	Pritchard

Chromatin state (count:121 , 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	chr10:91088000-91091000	Enhancers	ES-I3 Cell Line	embryonic stem cell
3	chr10:91088000-91091200	Enhancers	HUES6 Cell Line	embryonic stem cell
4	chr10:91088000-91099800	Weak transcription	Gastric	stomach
5	chr10:91088200-91091800	Enhancers	Primary B cells from peripheral blood	blood
6	chr10:91088200-91091800	Weak transcription	Fetal Muscle Trunk	muscle
7	chr10:91088200-91092000	Enhancers	Primary T helper 17 cells PMA-I stimulated	--
8	chr10:91088200-91092000	Weak transcription	Aorta	Aorta
9	chr10:91088200-91092400	Weak transcription	H1 Cell Line	embryonic stem cell
10	chr10:91088200-91093200	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
11	chr10:91088200-91093400	Weak transcription	Esophagus	oesophagus
12	chr10:91088400-91090800	Enhancers	Cortex derived primary cultured neurospheres	brain
13	chr10:91088400-91091000	Enhancers	Breast Myoepithelial Primary Cells	Breast
14	chr10:91088400-91091800	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
15	chr10:91088400-91091800	Enhancers	Primary T helper naive cells from peripheral blood	blood
16	chr10:91088400-91091800	Enhancers	Primary T helper cells fromperipheralblood	blood
17	chr10:91088400-91092000	Enhancers	Fetal Intestine Large	intestine
18	chr10:91088400-91092200	Weak transcription	HMEC	breast
19	chr10:91088600-91090800	Enhancers	Skeletal Muscle Female	skeletal muscle
20	chr10:91088600-91091200	Weak transcription	Fetal Brain Male	brain
21	chr10:91088600-91091600	Enhancers	Primary T helper cells PMA-I stimulated	--
22	chr10:91088600-91091800	Weak transcription	K562	blood
23	chr10:91088600-91092200	Weak transcription	HUES64 Cell Line	embryonic stem cell
24	chr10:91088800-91091400	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
25	chr10:91088800-91091400	Weak transcription	Primary B cells from cord blood	blood
26	chr10:91088800-91091800	Enhancers	Dnd41	blood
27	chr10:91088800-91092000	Weak transcription	A549	lung
28	chr10:91088800-91092200	Weak transcription	iPS-15b Cell Line	embryonic stem cell
29	chr10:91088800-91092200	Enhancers	Left Ventricle	heart
30	chr10:91088800-91092600	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
31	chr10:91089000-91091200	Enhancers	Colon Smooth Muscle	Colon
32	chr10:91089000-91091800	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
33	chr10:91089000-91091800	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
34	chr10:91089000-91091800	Enhancers	Fetal Intestine Small	intestine
35	chr10:91089000-91091800	Weak transcription	Pancreatic Islets	Pancreatic Islet
36	chr10:91089000-91091800	Weak transcription	Rectal Mucosa Donor 29	rectum
37	chr10:91089000-91091800	Weak transcription	Rectal Mucosa Donor 31	rectum
38	chr10:91089000-91091800	Weak transcription	HSMMtube	muscle
39	chr10:91089000-91091800	Enhancers	NHDF-Ad	bronchial
40	chr10:91089000-91092000	Weak transcription	HUES48 Cell Line	embryonic stem cell
41	chr10:91089000-91092000	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
42	chr10:91089000-91092000	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
43	chr10:91089000-91092200	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
44	chr10:91089000-91092200	Weak transcription	Fetal Heart	heart
45	chr10:91089200-91090800	Enhancers	Ovary	ovary
46	chr10:91089200-91091000	Enhancers	ES-WA7 Cell Line	embryonic stem cell
47	chr10:91089200-91091000	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
48	chr10:91089200-91091000	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
49	chr10:91089200-91091000	Enhancers	Placenta	Placenta
50	chr10:91089200-91091800	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow

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