Variant report

Variant	rs3740027
Chromosome Location	chr10:91069136-91069137
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 46 )
Associated
traits (count: 6 )

rSNPs within LD-proxies of this variant (count:41)

rs_ID	r²[population]
rs10509572	0.81[CEU][hapmap];0.89[GIH][hapmap];0.84[LWK][hapmap];0.91[MKK][hapmap];0.91[TSI][hapmap];0.81[YRI][hapmap];0.84[AMR][1000 genomes]
rs10887950	0.83[GIH][hapmap]
rs10887959	0.82[LWK][hapmap]
rs11203063	0.92[ASW][hapmap];0.95[CEU][hapmap];1.00[GIH][hapmap];0.90[LWK][hapmap];0.94[MEX][hapmap];0.95[MKK][hapmap];0.91[TSI][hapmap];0.90[YRI][hapmap];0.90[AFR][1000 genomes];0.97[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs11203066	0.92[AFR][1000 genomes];0.98[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs11203070	0.87[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs11203072	0.89[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs11203090	0.84[AMR][1000 genomes]
rs11203099	0.81[CEU][hapmap];0.89[GIH][hapmap];0.82[LWK][hapmap];0.91[MKK][hapmap];0.88[TSI][hapmap];0.82[AMR][1000 genomes]
rs11203115	0.82[LWK][hapmap]
rs11819073	0.84[AMR][1000 genomes]
rs12244233	0.81[CEU][hapmap];0.89[GIH][hapmap];0.86[MKK][hapmap];0.88[TSI][hapmap]
rs12248331	0.90[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs12255504	0.81[CEU][hapmap];0.81[YRI][hapmap];0.90[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs12772449	0.87[AFR][1000 genomes];0.95[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs1332330	0.85[CEU][hapmap];0.86[AFR][1000 genomes];0.97[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs1591051	0.81[CEU][hapmap];0.81[YRI][hapmap];0.85[AMR][1000 genomes]
rs17120001	0.84[AMR][1000 genomes]
rs17120004	0.84[AMR][1000 genomes]
rs2070845	0.90[CEU][hapmap];0.89[CHB][hapmap];0.92[JPT][hapmap];0.95[YRI][hapmap];0.90[AFR][1000 genomes];0.93[AMR][1000 genomes];0.93[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2274878	0.81[MEX][hapmap];0.82[TSI][hapmap]
rs34032344	0.84[AFR][1000 genomes];0.95[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs34234196	0.84[AMR][1000 genomes]
rs34712773	0.84[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs35830608	0.84[AMR][1000 genomes]
rs3780878	0.81[CEU][hapmap];0.89[GIH][hapmap];0.87[LWK][hapmap];0.87[MEX][hapmap];0.91[MKK][hapmap];0.88[TSI][hapmap];0.81[YRI][hapmap];0.90[AMR][1000 genomes]
rs4630205	0.87[MEX][hapmap]
rs6586182	0.84[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs6586183	0.81[CEU][hapmap];0.84[MKK][hapmap];0.91[TSI][hapmap];0.84[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs6586188	0.81[MEX][hapmap]
rs7073534	0.84[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs7085361	0.84[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs7088579	0.81[CEU][hapmap];0.89[GIH][hapmap];0.82[LWK][hapmap];0.84[MKK][hapmap];0.88[TSI][hapmap];0.81[YRI][hapmap];0.84[AMR][1000 genomes]
rs7090346	0.81[CEU][hapmap]
rs71479013	0.84[AMR][1000 genomes]
rs7897619	0.81[CEU][hapmap];0.89[GIH][hapmap];0.88[MKK][hapmap];0.91[TSI][hapmap];0.84[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs7897873	0.81[CEU][hapmap];0.84[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs7910389	0.90[AMR][1000 genomes]
rs7916812	0.81[CEU][hapmap];0.83[GIH][hapmap];0.87[MEX][hapmap];0.81[TSI][hapmap];0.82[AMR][1000 genomes]
rs884407	0.84[AMR][1000 genomes]
rs9733018	0.91[AFR][1000 genomes];0.98[AMR][1000 genomes];0.94[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:6)

SNP	Gene	Cis/trans	Tissue	Source
rs3740027	IFIT5	cis	multi-tissue	Pritchard
rs3740027	IDE	cis	parietal	SCAN
rs3740027	IFIT5	cis	lymphoblastoid	seeQTL
rs3740027	C10orf116	cis	cerebellum	SCAN
rs3740027	IFIT5	Cis_1M	lymphoblastoid	RTeQTL
rs3740027	IFIT1	cis	cerebellum	SCAN

Chromatin state (count:71 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr10:91055800-91070000	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
2	chr10:91063200-91074600	Weak transcription	Fetal Intestine Small	intestine
3	chr10:91063200-91076000	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
4	chr10:91063400-91069800	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
5	chr10:91063400-91072600	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
6	chr10:91063800-91069200	Weak transcription	Esophagus	oesophagus
7	chr10:91063800-91069200	Weak transcription	Pancreas	Pancrea
8	chr10:91063800-91069200	Weak transcription	Right Atrium	heart
9	chr10:91063800-91070400	Weak transcription	Fetal Kidney	kidney
10	chr10:91063800-91074200	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
11	chr10:91064000-91072800	Weak transcription	Placenta Amnion	Placenta Amnion
12	chr10:91064200-91086600	Weak transcription	Hela-S3	cervix
13	chr10:91065400-91069800	Strong transcription	Primary B cells from cord blood	blood
14	chr10:91065600-91069200	Strong transcription	Primary T cells fromperipheralblood	blood
15	chr10:91065600-91069400	Strong transcription	Primary B cells from peripheral blood	blood
16	chr10:91065600-91069400	Strong transcription	Primary T helper cells fromperipheralblood	blood
17	chr10:91065600-91069400	Strong transcription	Fetal Muscle Trunk	muscle
18	chr10:91065800-91069200	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
19	chr10:91065800-91069200	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
20	chr10:91065800-91069200	Strong transcription	Stomach Smooth Muscle	stomach
21	chr10:91065800-91069400	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
22	chr10:91065800-91069400	Strong transcription	Liver	Liver
23	chr10:91065800-91069400	Strong transcription	Left Ventricle	heart
24	chr10:91066200-91069400	Strong transcription	Breast Myoepithelial Primary Cells	Breast
25	chr10:91066200-91070800	Weak transcription	Fetal Intestine Large	intestine
26	chr10:91066400-91069200	Weak transcription	Primary hematopoietic stem cells short term culture	blood
27	chr10:91066400-91069400	ZNF genes & repeats	Primary T helper naive cells fromperipheralblood	blood
28	chr10:91066400-91074200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
29	chr10:91066600-91069200	Weak transcription	NHLF	lung
30	chr10:91066600-91070400	Weak transcription	Fetal Thymus	thymus
31	chr10:91066600-91073200	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
32	chr10:91066600-91074200	Weak transcription	Brain Inferior Temporal Lobe	brain
33	chr10:91066600-91074600	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
34	chr10:91066600-91075400	Weak transcription	Primary T killer memory cells from peripheral blood	blood
35	chr10:91066800-91070000	Weak transcription	Right Ventricle	heart
36	chr10:91066800-91072000	Weak transcription	Lung	lung
37	chr10:91066800-91073400	Weak transcription	Brain Substantia Nigra	brain
38	chr10:91067000-91069200	Weak transcription	NHDF-Ad	bronchial
39	chr10:91067000-91074000	Weak transcription	Brain Hippocampus Middle	brain
40	chr10:91067000-91074400	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
41	chr10:91067200-91069200	Strong transcription	Monocytes-CD14+_RO01746	blood
42	chr10:91067200-91069400	Weak transcription	GM12878-XiMat	blood
43	chr10:91067200-91070400	Weak transcription	Fetal Stomach	stomach
44	chr10:91067200-91073400	Weak transcription	Brain Cingulate Gyrus	brain
45	chr10:91067200-91076000	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
46	chr10:91067400-91069200	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
47	chr10:91067400-91072800	Weak transcription	Fetal Brain Male	brain
48	chr10:91067600-91069400	Weak transcription	Osteobl	bone
49	chr10:91067600-91071000	Weak transcription	Spleen	Spleen
50	chr10:91067600-91071000	Weak transcription	HSMM	muscle

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