Variant report

Variant	rs627524
Chromosome Location	chr10:91116790-91116791
allele	A/C
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: 43 )
Associated
traits (count: 5 )

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

rs_ID	r²[population]
rs10159774	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.93[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];0.96[MEX][hapmap];0.88[MKK][hapmap];0.95[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.96[AMR][1000 genomes];0.95[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[CHD][hapmap];0.89[GIH][hapmap];1.00[JPT][hapmap];0.96[MEX][hapmap];0.98[TSI][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];0.97[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs10887943	1.00[JPT][hapmap];1.00[YRI][hapmap]
rs160052	1.00[YRI][hapmap]
rs1888923	1.00[ASW][hapmap];0.89[CEU][hapmap];0.81[CHD][hapmap];0.91[JPT][hapmap];0.87[LWK][hapmap];0.96[MEX][hapmap];0.89[TSI][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];0.92[MEX][hapmap];0.93[MKK][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];0.84[GIH][hapmap];0.96[MEX][hapmap];1.00[MKK][hapmap];0.93[TSI][hapmap];1.00[YRI][hapmap];0.95[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs304439	0.85[AMR][1000 genomes]
rs304440	0.88[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];0.87[GIH][hapmap];0.92[MEX][hapmap];1.00[MKK][hapmap];0.93[TSI][hapmap];1.00[YRI][hapmap];0.95[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs304483	0.86[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs304485	0.89[CEU][hapmap];1.00[YRI][hapmap];0.85[AMR][1000 genomes]
rs304494	0.97[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs304495	0.96[CEU][hapmap];1.00[YRI][hapmap];0.97[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs304504	0.96[CEU][hapmap];0.87[GIH][hapmap];0.92[MEX][hapmap];0.90[MKK][hapmap];0.95[TSI][hapmap];1.00[YRI][hapmap];0.97[AMR][1000 genomes];0.91[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];0.97[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs305373	1.00[AFR][1000 genomes];0.96[AMR][1000 genomes];0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs305375	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]
rs305376	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs305377	1.00[YRI][hapmap];0.89[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs4933504	0.81[AFR][1000 genomes];0.86[AMR][1000 genomes]
rs4934471	1.00[ASW][hapmap];0.92[CEU][hapmap];0.81[JPT][hapmap];0.87[LWK][hapmap];0.96[MEX][hapmap];0.87[TSI][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]
rs6586184	0.85[AMR][1000 genomes]
rs7094510	0.82[ASW][hapmap];0.92[CEU][hapmap];0.81[CHD][hapmap];0.91[JPT][hapmap];0.80[TSI][hapmap]
rs7095398	0.92[CEU][hapmap];0.91[JPT][hapmap]
rs954439	0.85[CEU][hapmap];0.84[MEX][hapmap];0.80[TSI][hapmap];0.80[AMR][1000 genomes]
rs975686	0.88[AMR][1000 genomes];0.82[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:5)

SNP	Gene	Cis/trans	Tissue	Source
rs627524	IFIT5	Cis_1M	lymphoblastoid	RTeQTL
rs627524	IFIT5	cis	Artery Tibial	GTEx
rs627524	IFIT1	cis	cerebellum	SCAN
rs627524	IFIT5	cis	Skin Sun Exposed Lower leg	GTEx
rs627524	IFIT5	cis	Nerve Tibial	GTEx

Chromatin state (count:34 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr10:91108600-91122200	Weak transcription	Spleen	Spleen
2	chr10:91112200-91116800	Weak transcription	H1 Cell Line	embryonic stem cell
3	chr10:91112400-91116800	Weak transcription	Fetal Stomach	stomach
4	chr10:91112400-91120000	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
5	chr10:91112400-91122400	Weak transcription	Esophagus	oesophagus
6	chr10:91112400-91127400	Weak transcription	Left Ventricle	heart
7	chr10:91113000-91116800	Weak transcription	Fetal Kidney	kidney
8	chr10:91113000-91119200	Weak transcription	Lung	lung
9	chr10:91113200-91122200	Weak transcription	Placenta	Placenta
10	chr10:91113400-91116800	Weak transcription	Fetal Heart	heart
11	chr10:91114400-91117000	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
12	chr10:91114600-91117200	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
13	chr10:91114600-91117400	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
14	chr10:91114800-91116800	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
15	chr10:91114800-91117200	Enhancers	NHLF	lung
16	chr10:91114800-91117400	Enhancers	NHDF-Ad	bronchial
17	chr10:91115000-91117200	Enhancers	Osteobl	bone
18	chr10:91115400-91117200	Enhancers	Brain Germinal Matrix	brain
19	chr10:91115400-91117400	Enhancers	Fetal Lung	lung
20	chr10:91116000-91117000	Enhancers	Fetal Adrenal Gland	Adrenal Gland
21	chr10:91116000-91117200	Enhancers	Fetal Muscle Leg	muscle
22	chr10:91116200-91122000	Weak transcription	K562	blood
23	chr10:91116400-91117200	Enhancers	Foreskin Fibroblast Primary Cells skin02	Skin
24	chr10:91116400-91119000	Enhancers	Primary hematopoietic stem cells short term culture	blood
25	chr10:91116600-91116800	Enhancers	NH-A	brain
26	chr10:91116600-91117000	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
27	chr10:91116600-91117000	Enhancers	GM12878-XiMat	blood
28	chr10:91116600-91117200	Enhancers	H9 Cell Line	embryonic stem cell
29	chr10:91116600-91117200	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
30	chr10:91116600-91117200	Enhancers	Cortex derived primary cultured neurospheres	brain
31	chr10:91116600-91117200	Enhancers	Fetal Intestine Small	intestine
32	chr10:91116600-91117800	Enhancers	iPS-18 Cell Line	embryonic stem cell
33	chr10:91116600-91118000	Enhancers	Primary hematopoietic stem cells	blood
34	chr10:91116600-91120000	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--

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