Variant report

Variant	rs305374
Chromosome Location	chr10:91120287-91120288
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 37 )
Associated
traits (count: 5 )

rSNPs within LD-proxies of this variant (count:31)

rs_ID	r²[population]
rs10509571	0.86[CHB][hapmap];0.84[YRI][hapmap]
rs10788641	0.89[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.82[AMR][1000 genomes];0.89[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs10887945	0.81[EUR][1000 genomes]
rs10887946	0.89[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.82[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs10887947	0.89[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.84[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs10887948	0.88[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs11203065	0.81[EUR][1000 genomes]
rs11203078	0.89[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.85[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1141862	0.88[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs12220939	0.82[EUR][1000 genomes]
rs191027	0.97[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2274878	0.95[CHB][hapmap];0.83[YRI][hapmap]
rs303210	0.83[CEU][hapmap]
rs303215	0.83[CEU][hapmap]
rs304437	0.83[CEU][hapmap]
rs304441	0.83[CEU][hapmap]
rs304493	0.83[CEU][hapmap];0.96[YRI][hapmap];0.88[AMR][1000 genomes]
rs304498	0.83[AMR][1000 genomes]
rs304501	0.94[CEU][hapmap];0.92[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs304502	0.83[CEU][hapmap]
rs304505	0.83[CEU][hapmap]
rs304506	0.83[CEU][hapmap]
rs304508	0.94[CEU][hapmap];0.92[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs4339948	0.86[CHB][hapmap];0.84[YRI][hapmap]
rs4630205	0.95[CHB][hapmap]
rs627127	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs627496	0.92[AMR][1000 genomes];0.92[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6586188	0.95[CHB][hapmap]
rs781501	0.84[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7916812	0.87[YRI][hapmap]
rs812451	0.89[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[EUR][1000 genomes];0.96[ASN][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
rs305374	IFIT5	cis	Nerve Tibial	GTEx
rs305374	IFIT5	cis	Esophagus Mucosa	GTEx
rs305374	IFIT5	cis	Artery Tibial	GTEx
rs305374	IFIT5	cis	Esophagus Muscularis	GTEx
rs305374	IFIT5	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:24 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr10:91108600-91122200	Weak transcription	Spleen	Spleen
2	chr10:91112400-91122400	Weak transcription	Esophagus	oesophagus
3	chr10:91112400-91127400	Weak transcription	Left Ventricle	heart
4	chr10:91113200-91122200	Weak transcription	Placenta	Placenta
5	chr10:91116200-91122000	Weak transcription	K562	blood
6	chr10:91117000-91122000	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
7	chr10:91117000-91127800	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
8	chr10:91117200-91122000	Weak transcription	Fetal Heart	heart
9	chr10:91117200-91127400	Weak transcription	H9 Cell Line	embryonic stem cell
10	chr10:91117200-91127400	Weak transcription	Fetal Muscle Leg	muscle
11	chr10:91117400-91124000	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
12	chr10:91118000-91122200	Weak transcription	Primary hematopoietic stem cells	blood
13	chr10:91119000-91122200	Weak transcription	Primary hematopoietic stem cells short term culture	blood
14	chr10:91119200-91121000	Enhancers	Fetal Intestine Large	intestine
15	chr10:91119400-91120600	Enhancers	Fetal Intestine Small	intestine
16	chr10:91119400-91120600	Enhancers	Stomach Mucosa	stomach
17	chr10:91119400-91122200	Weak transcription	Right Atrium	heart
18	chr10:91119600-91133800	Weak transcription	Pancreas	Pancrea
19	chr10:91119800-91120400	Enhancers	Cortex derived primary cultured neurospheres	brain
20	chr10:91120000-91120600	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
21	chr10:91120000-91121200	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
22	chr10:91120000-91127200	Weak transcription	Duodenum Mucosa	Duodenum
23	chr10:91120200-91120400	Weak transcription	Fetal Kidney	kidney
24	chr10:91120200-91122200	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links