Variant report

Variant	rs303172
Chromosome Location	chr10:91179829-91179830
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr10:91179113..91181163-chr10:91223513..91225946,2	MCF-7	breast:

Extended variants
information (count: 31 )
Associated
traits (count: 6 )

rSNPs within LD-proxies of this variant (count:28)

rs_ID	r²[population]
rs10159774	0.84[CEU][hapmap]
rs10749606	0.84[CEU][hapmap]
rs10749607	0.84[CEU][hapmap]
rs215493	0.96[CEU][hapmap];1.00[CHB][hapmap];0.84[CHD][hapmap];0.95[GIH][hapmap];0.94[JPT][hapmap];1.00[TSI][hapmap];0.90[AMR][1000 genomes];0.96[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2458877	0.83[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2484045	0.91[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs303169	0.81[CEU][hapmap]
rs303170	0.98[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs303174	0.90[AMR][1000 genomes];0.95[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs303217	0.88[CEU][hapmap];0.84[CHD][hapmap];0.86[GIH][hapmap];0.89[JPT][hapmap];0.83[TSI][hapmap];0.81[AMR][1000 genomes];0.84[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs304439	0.90[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs304440	0.96[CEU][hapmap];0.94[JPT][hapmap];0.90[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs304443	0.83[AMR][1000 genomes];0.96[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs304448	1.00[CEU][hapmap];1.00[CHB][hapmap];0.96[CHD][hapmap];1.00[GIH][hapmap];0.94[JPT][hapmap];1.00[MEX][hapmap];0.98[TSI][hapmap];0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs304449	0.96[CEU][hapmap];1.00[CHB][hapmap];0.94[JPT][hapmap];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs304451	0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs304478	0.88[CEU][hapmap];0.80[CHD][hapmap];0.84[GIH][hapmap];0.84[JPT][hapmap];0.81[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs304483	0.87[AMR][1000 genomes];0.91[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs304485	0.96[CEU][hapmap];1.00[CHB][hapmap];0.89[JPT][hapmap];0.90[AMR][1000 genomes];0.96[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs304494	0.83[EUR][1000 genomes]
rs304495	0.88[CEU][hapmap];0.84[JPT][hapmap];0.83[EUR][1000 genomes]
rs304504	0.88[CEU][hapmap];0.80[CHD][hapmap];0.84[GIH][hapmap];0.84[JPT][hapmap];0.80[TSI][hapmap];0.83[EUR][1000 genomes]
rs305371	0.84[CEU][hapmap]
rs305375	0.84[CEU][hapmap]
rs305377	0.84[JPT][hapmap]
rs4934475	0.84[CEU][hapmap]
rs559198	0.89[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs627524	0.84[CEU][hapmap]

Variant overlapped rSNPs/rCNVs (count:3 , 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

mRNA abundance (count:6)

SNP	Gene	Cis/trans	Tissue	Source
rs303172	IFIT5	cis	Artery Tibial	GTEx
rs303172	IFIT5	cis	Skin Sun Exposed Lower leg	GTEx
rs303172	IFIT5	cis	cerebellum	SCAN
rs303172	IFIT5	cis	Esophagus Mucosa	GTEx
rs303172	IFIT5	cis	Nerve Tibial	GTEx
rs303172	IFIT5	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:100 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr10:91175400-91180200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
2	chr10:91175400-91187600	Weak transcription	HUVEC	blood vessel
3	chr10:91175600-91181200	Enhancers	Primary T helper naive cells fromperipheralblood	blood
4	chr10:91175600-91181200	Weak transcription	Placenta Amnion	Placenta Amnion
5	chr10:91175600-91183800	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
6	chr10:91175600-91188200	Weak transcription	Skeletal Muscle Male	skeletal muscle
7	chr10:91175600-91191800	Weak transcription	Psoas Muscle	Psoas
8	chr10:91175600-91191800	Weak transcription	Hela-S3	cervix
9	chr10:91175800-91182600	Weak transcription	Thymus	Thymus
10	chr10:91176000-91180000	Weak transcription	Colonic Mucosa	Colon
11	chr10:91176200-91186400	Weak transcription	Skeletal Muscle Female	skeletal muscle
12	chr10:91176600-91182800	Weak transcription	Esophagus	oesophagus
13	chr10:91177000-91181400	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
14	chr10:91177200-91181600	Strong transcription	Fetal Intestine Large	intestine
15	chr10:91177200-91181800	Strong transcription	Monocytes-CD14+_RO01746	blood
16	chr10:91177400-91182000	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
17	chr10:91177600-91184000	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
18	chr10:91178000-91183600	Weak transcription	Primary hematopoietic stem cells	blood
19	chr10:91178000-91186000	Weak transcription	HMEC	breast
20	chr10:91178000-91186200	Weak transcription	HSMMtube	muscle
21	chr10:91178000-91186400	Weak transcription	Fetal Stomach	stomach
22	chr10:91178000-91187800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
23	chr10:91178200-91180200	Weak transcription	Breast Myoepithelial Primary Cells	Breast
24	chr10:91178200-91180200	Weak transcription	Placenta	Placenta
25	chr10:91178200-91180200	Weak transcription	NHEK	skin
26	chr10:91178200-91180600	Weak transcription	Fetal Heart	heart
27	chr10:91178200-91182200	Weak transcription	Rectal Mucosa Donor 31	rectum
28	chr10:91178200-91183800	Weak transcription	HepG2	liver
29	chr10:91178200-91184800	Weak transcription	Duodenum Smooth Muscle	Duodenum
30	chr10:91178200-91186400	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
31	chr10:91178200-91191800	Weak transcription	Aorta	Aorta
32	chr10:91178200-91197600	Weak transcription	Pancreas	Pancrea
33	chr10:91178400-91180000	Weak transcription	Primary T cells fromperipheralblood	blood
34	chr10:91178400-91180000	Weak transcription	Fetal Muscle Leg	muscle
35	chr10:91178400-91180000	Weak transcription	Sigmoid Colon	Sigmoid Colon
36	chr10:91178400-91180000	Weak transcription	HSMM	muscle
37	chr10:91178400-91180400	Weak transcription	Left Ventricle	heart
38	chr10:91178400-91180400	Active TSS	GM12878-XiMat	blood
39	chr10:91178400-91180800	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
40	chr10:91178400-91180800	Weak transcription	Fetal Muscle Trunk	muscle
41	chr10:91178400-91181400	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
42	chr10:91178400-91181600	Weak transcription	Brain Angular Gyrus	brain
43	chr10:91178400-91182000	Weak transcription	Rectal Mucosa Donor 29	rectum
44	chr10:91178400-91182800	Weak transcription	Colon Smooth Muscle	Colon
45	chr10:91178400-91183000	Weak transcription	Fetal Thymus	thymus
46	chr10:91178400-91183800	Weak transcription	Duodenum Mucosa	Duodenum
47	chr10:91178400-91184800	Weak transcription	Lung	lung
48	chr10:91178400-91185600	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
49	chr10:91178400-91186200	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
50	chr10:91178400-91186200	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin

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