Variant report

Variant	rs305375
Chromosome Location	chr10:91122824-91122825
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr10:91115941..91117620-chr10:91122098..91123707,2	MCF-7	breast:

Extended variants
information (count: 44 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:38)

rs_ID	r²[population]
rs10159774	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.96[AMR][1000 genomes];0.94[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs10509570	1.00[CHB][hapmap];0.81[JPT][hapmap];1.00[YRI][hapmap]
rs10749605	0.92[CEU][hapmap];0.91[JPT][hapmap]
rs10749606	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[AMR][1000 genomes];0.95[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs10749607	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs10887943	0.91[JPT][hapmap];1.00[YRI][hapmap]
rs160052	1.00[YRI][hapmap]
rs1888923	0.89[CEU][hapmap];0.91[JPT][hapmap];1.00[YRI][hapmap];0.92[AFR][1000 genomes];0.88[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs215493	0.89[CEU][hapmap];1.00[YRI][hapmap];0.85[AMR][1000 genomes]
rs2484045	0.80[AMR][1000 genomes]
rs303172	0.84[CEU][hapmap]
rs303174	0.85[AMR][1000 genomes]
rs303217	0.96[CEU][hapmap];1.00[YRI][hapmap];0.95[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs304439	0.85[AMR][1000 genomes]
rs304440	0.89[CEU][hapmap];1.00[YRI][hapmap];0.85[AMR][1000 genomes]
rs304448	0.85[CEU][hapmap]
rs304449	0.89[CEU][hapmap];1.00[YRI][hapmap]
rs304451	0.82[AMR][1000 genomes]
rs304478	0.96[CEU][hapmap];1.00[YRI][hapmap];0.95[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs304483	0.86[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs304485	0.89[CEU][hapmap];1.00[YRI][hapmap];0.85[AMR][1000 genomes]
rs304494	0.97[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs304495	0.96[CEU][hapmap];1.00[YRI][hapmap];0.97[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs304504	0.96[CEU][hapmap];1.00[YRI][hapmap];0.97[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs305371	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs305373	1.00[AFR][1000 genomes];0.96[AMR][1000 genomes];0.94[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs305376	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs305377	1.00[YRI][hapmap];0.89[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs4933504	0.81[AFR][1000 genomes];0.86[AMR][1000 genomes]
rs4934471	0.92[CEU][hapmap];0.81[JPT][hapmap];1.00[YRI][hapmap];0.92[AFR][1000 genomes];0.88[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs4934473	0.86[AFR][1000 genomes];0.89[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs4934475	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.96[AMR][1000 genomes];0.93[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs627524	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];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6586184	0.85[AMR][1000 genomes]
rs7094510	0.92[CEU][hapmap];0.91[JPT][hapmap]
rs7095398	0.92[CEU][hapmap];0.91[JPT][hapmap]
rs954439	0.85[CEU][hapmap];0.80[AMR][1000 genomes]
rs975686	0.88[AMR][1000 genomes];0.82[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:4)

SNP	Gene	Cis/trans	Tissue	Source
rs305375	IFIT5	cis	Nerve Tibial	GTEx
rs305375	IFIT5	cis	Artery Tibial	GTEx
rs305375	IFIT5	cis	Skin Sun Exposed Lower leg	GTEx
rs305375	IFIT5	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:25 , 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	chr10:91117400-91124000	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
6	chr10:91119600-91133800	Weak transcription	Pancreas	Pancrea
7	chr10:91120000-91127200	Weak transcription	Duodenum Mucosa	Duodenum
8	chr10:91120400-91127000	Weak transcription	Cortex derived primary cultured neurospheres	brain
9	chr10:91121000-91127200	Weak transcription	Fetal Intestine Large	intestine
10	chr10:91121600-91123000	Weak transcription	GM12878-XiMat	blood
11	chr10:91121800-91125000	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
12	chr10:91122000-91123400	Enhancers	Fetal Adrenal Gland	Adrenal Gland
13	chr10:91122000-91124000	Enhancers	K562	blood
14	chr10:91122000-91125200	Enhancers	Fetal Heart	heart
15	chr10:91122200-91124200	Enhancers	Primary hematopoietic stem cells	blood
16	chr10:91122200-91124200	Enhancers	Primary hematopoietic stem cells short term culture	blood
17	chr10:91122200-91125000	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
18	chr10:91122600-91123800	Weak transcription	Spleen	Spleen
19	chr10:91122600-91127400	Weak transcription	Placenta	Placenta
20	chr10:91122600-91127400	Weak transcription	Right Atrium	heart
21	chr10:91122600-91128600	Weak transcription	Ovary	ovary
22	chr10:91122800-91123200	Enhancers	Primary T cells from cord blood	blood
23	chr10:91122800-91124000	Enhancers	Right Ventricle	heart
24	chr10:91122800-91124200	Enhancers	Primary T helper cells fromperipheralblood	blood
25	chr10:91122800-91127200	Weak transcription	Fetal Intestine Small	intestine

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