Variant report

Variant	rs1888923
Chromosome Location	chr10:91070950-91070951
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	chr10:91064364..91065915-chr10:91069467..91071005,2	MCF-7	breast:

Extended variants
information (count: 36 )
Associated
traits (count: 3 )

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

rs_ID	r²[population]
rs10159774	1.00[ASW][hapmap];0.89[CEU][hapmap];0.91[JPT][hapmap];0.87[LWK][hapmap];1.00[MEX][hapmap];0.89[TSI][hapmap];1.00[YRI][hapmap];0.92[AFR][1000 genomes];0.92[AMR][1000 genomes];0.84[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs10509570	1.00[YRI][hapmap]
rs10749605	0.89[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.82[GIH][hapmap];1.00[JPT][hapmap];0.84[MEX][hapmap];0.83[TSI][hapmap];0.80[AMR][1000 genomes];0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10749606	0.89[CEU][hapmap];0.81[CHD][hapmap];0.91[JPT][hapmap];1.00[MEX][hapmap];0.91[TSI][hapmap];0.89[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs10749607	0.89[CEU][hapmap];0.91[JPT][hapmap];1.00[YRI][hapmap];0.92[AFR][1000 genomes];0.92[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs10887943	1.00[CHB][hapmap];0.91[JPT][hapmap];1.00[YRI][hapmap];0.97[ASN][1000 genomes]
rs160052	1.00[YRI][hapmap]
rs215493	0.87[MEX][hapmap];1.00[YRI][hapmap]
rs303217	0.85[CEU][hapmap];0.92[MEX][hapmap];0.82[TSI][hapmap];1.00[YRI][hapmap];0.83[AMR][1000 genomes]
rs304440	1.00[YRI][hapmap]
rs304449	1.00[YRI][hapmap]
rs304478	0.85[CEU][hapmap];0.87[MEX][hapmap];0.82[TSI][hapmap];1.00[YRI][hapmap];0.83[AMR][1000 genomes]
rs304485	1.00[YRI][hapmap]
rs304494	0.85[AMR][1000 genomes]
rs304495	0.85[CEU][hapmap];1.00[YRI][hapmap];0.85[AMR][1000 genomes]
rs304504	0.85[CEU][hapmap];0.87[MEX][hapmap];0.84[TSI][hapmap];1.00[YRI][hapmap];0.85[AMR][1000 genomes]
rs305371	0.92[CEU][hapmap];0.91[JPT][hapmap];1.00[YRI][hapmap];0.92[AFR][1000 genomes];0.90[AMR][1000 genomes];0.86[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs305373	0.92[AFR][1000 genomes];0.88[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs305375	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]
rs305376	0.92[AFR][1000 genomes];0.88[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs305377	1.00[YRI][hapmap];0.82[AFR][1000 genomes];0.88[AMR][1000 genomes]
rs4933504	0.88[AFR][1000 genomes];0.98[AMR][1000 genomes];0.94[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs4934471	1.00[ASW][hapmap];0.96[CEU][hapmap];1.00[CHB][hapmap];0.81[CHD][hapmap];1.00[GIH][hapmap];0.91[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];0.98[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4934473	0.99[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4934475	0.88[CEU][hapmap];0.91[JPT][hapmap];1.00[YRI][hapmap];0.92[AFR][1000 genomes];0.92[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs627524	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]
rs6586184	0.88[AMR][1000 genomes]
rs7094510	0.82[ASW][hapmap];0.89[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];0.84[MEX][hapmap];0.91[TSI][hapmap];0.91[AMR][1000 genomes];0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7095398	0.89[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];0.84[MEX][hapmap];0.83[TSI][hapmap];0.83[AMR][1000 genomes];0.84[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs954439	0.89[CEU][hapmap];0.87[GIH][hapmap];0.88[MEX][hapmap];0.91[TSI][hapmap];0.91[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs975686	1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][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:3)

SNP	Gene	Cis/trans	Tissue	Source
rs1888923	IFIT5	cis	Artery Tibial	GTEx
rs1888923	IFIT5	cis	Skin Sun Exposed Lower leg	GTEx
rs1888923	IFIT5	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:39 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr10:91063200-91074600	Weak transcription	Fetal Intestine Small	intestine
2	chr10:91063200-91076000	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
3	chr10:91063400-91072600	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
4	chr10:91063800-91074200	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
5	chr10:91064000-91072800	Weak transcription	Placenta Amnion	Placenta Amnion
6	chr10:91064200-91086600	Weak transcription	Hela-S3	cervix
7	chr10:91066400-91074200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
8	chr10:91066600-91073200	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
9	chr10:91066600-91074200	Weak transcription	Brain Inferior Temporal Lobe	brain
10	chr10:91066600-91074600	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
11	chr10:91066600-91075400	Weak transcription	Primary T killer memory cells from peripheral blood	blood
12	chr10:91066800-91072000	Weak transcription	Lung	lung
13	chr10:91066800-91073400	Weak transcription	Brain Substantia Nigra	brain
14	chr10:91067000-91074000	Weak transcription	Brain Hippocampus Middle	brain
15	chr10:91067000-91074400	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
16	chr10:91067200-91073400	Weak transcription	Brain Cingulate Gyrus	brain
17	chr10:91067200-91076000	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
18	chr10:91067400-91072800	Weak transcription	Fetal Brain Male	brain
19	chr10:91067600-91071000	Weak transcription	Spleen	Spleen
20	chr10:91067600-91071000	Weak transcription	HSMM	muscle
21	chr10:91067600-91076000	Weak transcription	Brain Anterior Caudate	brain
22	chr10:91067800-91071000	Weak transcription	Rectal Mucosa Donor 29	rectum
23	chr10:91067800-91073000	Weak transcription	Primary hematopoietic stem cells	blood
24	chr10:91067800-91074200	Weak transcription	Brain Angular Gyrus	brain
25	chr10:91067800-91074600	Weak transcription	Fetal Lung	lung
26	chr10:91068000-91071400	Weak transcription	Primary T cells from cord blood	blood
27	chr10:91069000-91074000	Weak transcription	Cortex derived primary cultured neurospheres	brain
28	chr10:91069000-91074200	Weak transcription	Fetal Muscle Leg	muscle
29	chr10:91069200-91071000	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
30	chr10:91069200-91071200	Weak transcription	Monocytes-CD14+_RO01746	blood
31	chr10:91069200-91074200	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
32	chr10:91069400-91071000	Weak transcription	Primary T helper cells fromperipheralblood	blood
33	chr10:91069400-91071000	Weak transcription	Fetal Muscle Trunk	muscle
34	chr10:91069400-91071400	Weak transcription	Primary B cells from peripheral blood	blood
35	chr10:91069400-91071400	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
36	chr10:91069400-91074200	Weak transcription	Breast Myoepithelial Primary Cells	Breast
37	chr10:91069400-91076600	Weak transcription	Left Ventricle	heart
38	chr10:91069800-91071600	Weak transcription	Primary B cells from cord blood	blood
39	chr10:91070200-91071000	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell

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