Variant report

Variant	rs12244233
Chromosome Location	chr10:91124029-91124030
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 66 )
Associated
traits (count: 5 )

rSNPs within LD-proxies of this variant (count:60)

rs_ID	r²[population]
rs10509571	0.86[CEU][hapmap];0.81[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs10509572	0.82[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.96[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.89[LWK][hapmap];0.95[MKK][hapmap];0.97[TSI][hapmap];0.83[YRI][hapmap];0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10788642	0.85[AFR][1000 genomes];0.82[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs10887950	0.90[CEU][hapmap];0.85[CHD][hapmap];0.83[GIH][hapmap];0.83[JPT][hapmap];0.80[TSI][hapmap];0.86[AFR][1000 genomes];0.88[AMR][1000 genomes];0.84[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs10887953	0.95[CEU][hapmap];0.87[CHB][hapmap];0.88[JPT][hapmap];0.86[AFR][1000 genomes];0.82[AMR][1000 genomes];0.82[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs10887957	0.87[ASN][1000 genomes]
rs10887959	0.85[CEU][hapmap];1.00[CHB][hapmap];0.89[CHD][hapmap];0.81[JPT][hapmap];0.82[LWK][hapmap];0.83[ASN][1000 genomes]
rs11203063	0.85[CEU][hapmap];0.81[CHD][hapmap];0.89[GIH][hapmap];0.94[JPT][hapmap];0.90[MKK][hapmap];0.85[TSI][hapmap];0.83[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs11203066	0.82[AFR][1000 genomes];0.85[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs11203070	0.93[AFR][1000 genomes];0.96[AMR][1000 genomes];0.93[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs11203072	0.83[AFR][1000 genomes];0.91[AMR][1000 genomes];0.96[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs11203090	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11203099	0.82[ASW][hapmap];1.00[CEU][hapmap];0.93[CHB][hapmap];0.96[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.86[LWK][hapmap];0.95[MKK][hapmap];0.94[TSI][hapmap];0.89[AFR][1000 genomes];0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs11203105	0.85[AFR][1000 genomes];0.89[ASN][1000 genomes]
rs11203106	0.85[AFR][1000 genomes];0.89[ASN][1000 genomes]
rs11203109	0.95[CEU][hapmap];0.87[CHB][hapmap];0.88[JPT][hapmap];0.85[AFR][1000 genomes];0.83[ASN][1000 genomes]
rs11203112	0.82[AFR][1000 genomes];0.81[ASN][1000 genomes]
rs11203115	0.90[CEU][hapmap];1.00[CHB][hapmap];0.89[CHD][hapmap];0.81[JPT][hapmap];0.82[LWK][hapmap];0.88[ASN][1000 genomes]
rs11203119	0.81[ASN][1000 genomes]
rs11819073	0.87[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs12248331	0.83[AFR][1000 genomes];0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs12255504	1.00[CEU][hapmap];1.00[CHB][hapmap];0.94[JPT][hapmap];0.83[AFR][1000 genomes];0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs12356008	0.82[AFR][1000 genomes];0.86[ASN][1000 genomes]
rs12772449	0.84[AFR][1000 genomes];0.88[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs12781453	0.88[AFR][1000 genomes];0.88[AMR][1000 genomes];0.84[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs12781505	0.84[ASN][1000 genomes]
rs1332330	0.95[CEU][hapmap];0.86[CHB][hapmap];0.94[JPT][hapmap];0.81[AFR][1000 genomes];0.87[AMR][1000 genomes];0.89[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs1591051	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.83[YRI][hapmap];0.92[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs17096301	0.81[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs17120001	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17120004	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17120325	0.95[CEU][hapmap];0.93[JPT][hapmap]
rs17121248	0.85[CEU][hapmap];1.00[CHB][hapmap];0.85[CHD][hapmap];0.81[JPT][hapmap];0.82[ASN][1000 genomes]
rs2070845	0.81[CEU][hapmap];0.87[AMR][1000 genomes]
rs2274878	0.86[CEU][hapmap];0.89[GIH][hapmap];0.88[TSI][hapmap];0.81[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs34032344	0.85[AFR][1000 genomes];0.88[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs34234196	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34712773	0.87[AMR][1000 genomes];0.92[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs35830608	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35833529	0.89[AFR][1000 genomes];0.88[AMR][1000 genomes];0.82[ASN][1000 genomes]
rs3740027	0.81[CEU][hapmap];0.89[GIH][hapmap];0.86[MKK][hapmap];0.88[TSI][hapmap];0.84[AMR][1000 genomes]
rs3780878	1.00[CEU][hapmap];1.00[CHB][hapmap];0.92[CHD][hapmap];1.00[GIH][hapmap];0.94[JPT][hapmap];0.82[LWK][hapmap];0.95[MKK][hapmap];0.94[TSI][hapmap];0.86[AFR][1000 genomes];0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs4339948	0.86[CEU][hapmap];0.81[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs4630205	0.82[CEU][hapmap];0.89[GIH][hapmap]
rs6586182	0.87[AMR][1000 genomes];0.95[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs6586183	1.00[CEU][hapmap];1.00[CHB][hapmap];0.92[CHD][hapmap];0.94[JPT][hapmap];0.88[MKK][hapmap];0.97[TSI][hapmap];0.87[AMR][1000 genomes];0.93[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs6586188	0.89[GIH][hapmap];0.81[EUR][1000 genomes]
rs6586196	0.81[CEU][hapmap]
rs7073534	0.87[AMR][1000 genomes];0.95[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs7085361	0.87[AMR][1000 genomes];0.95[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs7088579	0.82[ASW][hapmap];1.00[CEU][hapmap];0.93[CHB][hapmap];0.96[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.86[LWK][hapmap];0.87[MKK][hapmap];0.94[TSI][hapmap];0.83[YRI][hapmap];0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7090346	0.90[CEU][hapmap];0.87[CHB][hapmap];0.81[CHD][hapmap]
rs7097569	0.90[AFR][1000 genomes];0.88[AMR][1000 genomes];0.84[ASN][1000 genomes]
rs71479013	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7897619	1.00[CEU][hapmap];1.00[CHB][hapmap];0.92[CHD][hapmap];1.00[GIH][hapmap];0.94[JPT][hapmap];0.93[MKK][hapmap];0.91[TSI][hapmap];0.87[AMR][1000 genomes];0.91[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs7897873	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]
rs7910389	0.82[AFR][1000 genomes];0.93[AMR][1000 genomes];0.93[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs7916812	0.90[CEU][hapmap];1.00[CHB][hapmap];0.92[CHD][hapmap];0.94[GIH][hapmap];0.93[JPT][hapmap];0.87[TSI][hapmap];0.85[AMR][1000 genomes];0.84[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs884407	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs9733018	0.81[AFR][1000 genomes];0.85[AMR][1000 genomes];0.84[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:6 , 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
6	nsv528603	chr10:91119644-91124029	Enhancers Weak transcription Flanking Active TSS	TF binding region Chromatin interactive region	1 gene(s)	inside rSNPs	diseases

mRNA abundance (count:5)

SNP	Gene	Cis/trans	Tissue	Source
rs12244233	IFIT5	cis	Lymphoblastoid	GTEx
rs12244233	IFIT1	cis	lymphoblastoid	seeQTL
rs12244233	IFIT5	Cis_1M	lymphoblastoid	RTeQTL
rs12244233	IFIT5	cis	lymphoblastoid	seeQTL
rs12244233	IFIT5	cis	multi-tissue	Pritchard

Chromatin state (count:37 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr10:91112400-91127400	Weak transcription	Left Ventricle	heart
2	chr10:91117000-91127800	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
3	chr10:91117200-91127400	Weak transcription	H9 Cell Line	embryonic stem cell
4	chr10:91117200-91127400	Weak transcription	Fetal Muscle Leg	muscle
5	chr10:91119600-91133800	Weak transcription	Pancreas	Pancrea
6	chr10:91120000-91127200	Weak transcription	Duodenum Mucosa	Duodenum
7	chr10:91120400-91127000	Weak transcription	Cortex derived primary cultured neurospheres	brain
8	chr10:91121000-91127200	Weak transcription	Fetal Intestine Large	intestine
9	chr10:91121800-91125000	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
10	chr10:91122000-91125200	Enhancers	Fetal Heart	heart
11	chr10:91122200-91124200	Enhancers	Primary hematopoietic stem cells	blood
12	chr10:91122200-91124200	Enhancers	Primary hematopoietic stem cells short term culture	blood
13	chr10:91122200-91125000	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
14	chr10:91122600-91127400	Weak transcription	Placenta	Placenta
15	chr10:91122600-91127400	Weak transcription	Right Atrium	heart
16	chr10:91122600-91128600	Weak transcription	Ovary	ovary
17	chr10:91122800-91124200	Enhancers	Primary T helper cells fromperipheralblood	blood
18	chr10:91122800-91127200	Weak transcription	Fetal Intestine Small	intestine
19	chr10:91123000-91124800	Enhancers	Monocytes-CD14+_RO01746	blood
20	chr10:91123600-91124200	Enhancers	Primary T helper cells PMA-I stimulated	--
21	chr10:91123600-91124200	Flanking Active TSS	GM12878-XiMat	blood
22	chr10:91123600-91124200	Enhancers	HSMMtube	muscle
23	chr10:91123600-91124400	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
24	chr10:91123600-91125000	Enhancers	Primary monocytes fromperipheralblood	blood
25	chr10:91123800-91124200	Enhancers	Primary B cells from peripheral blood	blood
26	chr10:91123800-91124200	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
27	chr10:91123800-91124200	Enhancers	Primary T helper 17 cells PMA-I stimulated	--
28	chr10:91123800-91124200	Enhancers	Skeletal Muscle Female	skeletal muscle
29	chr10:91123800-91124400	Enhancers	Psoas Muscle	Psoas
30	chr10:91123800-91128800	Weak transcription	Colon Smooth Muscle	Colon
31	chr10:91124000-91125000	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
32	chr10:91124000-91127200	Weak transcription	Brain Inferior Temporal Lobe	brain
33	chr10:91124000-91127200	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
34	chr10:91124000-91128000	Weak transcription	NHLF	lung
35	chr10:91124000-91129000	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
36	chr10:91124000-91129000	Weak transcription	Skeletal Muscle Male	skeletal muscle
37	chr10:91124000-91130400	Weak transcription	K562	blood

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