Variant report

Variant	rs17121248
Chromosome Location	chr10:91185696-91185697
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr10:91184701..91187287-chr10:91403234..91405861,2	MCF-7	breast:
2	chr10:91173086..91175345-chr10:91183942..91186085,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000152782	Chromatin interaction
ENSG00000232936	Chromatin interaction
ENSG00000152778	Chromatin interaction
ENSG00000249962	Chromatin interaction
ENSG00000107798	Chromatin interaction

Extended variants
information (count: 42 )
Associated
traits (count: 8 )

rSNPs within LD-proxies of this variant (count:39)

rs_ID	r²[population]
rs10509572	0.85[CEU][hapmap];1.00[CHB][hapmap];0.88[CHD][hapmap];0.81[JPT][hapmap];0.82[MEX][hapmap];0.82[ASN][1000 genomes]
rs10788642	0.85[AMR][1000 genomes];0.89[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs10887950	0.85[CEU][hapmap];0.85[CHD][hapmap];0.88[MEX][hapmap];0.88[TSI][hapmap];0.87[EUR][1000 genomes]
rs10887953	0.90[CEU][hapmap];0.87[CHB][hapmap];0.84[AMR][1000 genomes];0.85[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs10887957	0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs10887959	1.00[CEU][hapmap];1.00[CHB][hapmap];0.96[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs11203063	0.80[CEU][hapmap];0.80[CHD][hapmap];0.87[JPT][hapmap]
rs11203090	0.82[ASN][1000 genomes]
rs11203099	0.85[CEU][hapmap];0.93[CHB][hapmap];0.88[CHD][hapmap];0.81[JPT][hapmap];0.82[MEX][hapmap];0.83[ASN][1000 genomes]
rs11203105	0.85[AMR][1000 genomes];0.87[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs11203106	0.85[AMR][1000 genomes];0.87[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs11203109	0.90[CEU][hapmap];0.87[CHB][hapmap];0.85[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs11203112	0.90[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs11203115	0.95[CEU][hapmap];1.00[CHB][hapmap];0.88[CHD][hapmap];0.84[GIH][hapmap];1.00[JPT][hapmap];0.88[MEX][hapmap];1.00[TSI][hapmap];0.90[AMR][1000 genomes];0.96[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs11203119	0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs11819073	0.81[ASN][1000 genomes]
rs12244233	0.85[CEU][hapmap];1.00[CHB][hapmap];0.85[CHD][hapmap];0.81[JPT][hapmap]
rs12255504	0.85[CEU][hapmap];1.00[CHB][hapmap];0.87[JPT][hapmap]
rs12356008	0.90[AMR][1000 genomes];0.93[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs12781453	0.87[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs12781505	0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1332330	0.80[CEU][hapmap];0.86[CHB][hapmap];0.87[JPT][hapmap]
rs1591051	0.85[CEU][hapmap];1.00[CHB][hapmap];0.81[JPT][hapmap];0.81[ASN][1000 genomes]
rs17120001	0.82[ASN][1000 genomes]
rs17120004	0.82[ASN][1000 genomes]
rs17120325	0.90[CEU][hapmap]
rs34234196	0.82[ASN][1000 genomes]
rs35359667	0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs35830608	0.82[ASN][1000 genomes]
rs3780878	0.85[CEU][hapmap];1.00[CHB][hapmap];0.84[CHD][hapmap];0.87[JPT][hapmap]
rs6586183	0.85[CEU][hapmap];1.00[CHB][hapmap];0.84[CHD][hapmap];0.87[JPT][hapmap]
rs6586196	0.85[CEU][hapmap]
rs7088579	0.85[CEU][hapmap];0.93[CHB][hapmap];0.88[CHD][hapmap];0.81[JPT][hapmap];0.82[MEX][hapmap];0.81[ASN][1000 genomes]
rs7090346	0.95[CEU][hapmap];0.87[CHB][hapmap];0.96[CHD][hapmap];1.00[GIH][hapmap];0.82[JPT][hapmap];1.00[MEX][hapmap];0.97[TSI][hapmap];0.92[AMR][1000 genomes];0.95[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs71479013	0.82[ASN][1000 genomes]
rs7897619	0.85[CEU][hapmap];1.00[CHB][hapmap];0.84[CHD][hapmap];0.87[JPT][hapmap]
rs7897873	0.84[CEU][hapmap];1.00[CHB][hapmap];0.86[JPT][hapmap]
rs7916812	1.00[CHB][hapmap];0.83[CHD][hapmap];0.93[JPT][hapmap]
rs884407	0.81[ASN][1000 genomes]

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:8)

SNP	Gene	Cis/trans	Tissue	Source
rs17121248	IFIT5	cis	lymphoblastoid	seeQTL
rs17121248	IFIT5	cis	multi-tissue	Pritchard
rs17121248	C10orf116	cis	cerebellum	SCAN
rs17121248	C11orf9	trans	cerebellum	SCAN
rs17121248	IFIT5	Cis_1M	lymphoblastoid	RTeQTL
rs17121248	IFIT1	cis	lymphoblastoid	seeQTL
rs17121248	IFIT1B	cis	lymphoblastoid	seeQTL
rs17121248	CH25H	cis	cerebellum	SCAN

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr10:91175400-91187600	Weak transcription	HUVEC	blood vessel
2	chr10:91175600-91188200	Weak transcription	Skeletal Muscle Male	skeletal muscle
3	chr10:91175600-91191800	Weak transcription	Psoas Muscle	Psoas
4	chr10:91175600-91191800	Weak transcription	Hela-S3	cervix
5	chr10:91176200-91186400	Weak transcription	Skeletal Muscle Female	skeletal muscle
6	chr10:91178000-91186000	Weak transcription	HMEC	breast
7	chr10:91178000-91186200	Weak transcription	HSMMtube	muscle
8	chr10:91178000-91186400	Weak transcription	Fetal Stomach	stomach
9	chr10:91178000-91187800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
10	chr10:91178200-91186400	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
11	chr10:91178200-91191800	Weak transcription	Aorta	Aorta
12	chr10:91178200-91197600	Weak transcription	Pancreas	Pancrea
13	chr10:91178400-91186200	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
14	chr10:91178400-91186200	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
15	chr10:91178400-91186200	Weak transcription	NHLF	lung
16	chr10:91178400-91186200	Weak transcription	Osteobl	bone
17	chr10:91178400-91187200	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
18	chr10:91178400-91188000	Weak transcription	Right Ventricle	heart
19	chr10:91178400-91191600	Weak transcription	A549	lung
20	chr10:91178600-91186200	Weak transcription	NH-A	brain
21	chr10:91178800-91186200	Weak transcription	NHDF-Ad	bronchial
22	chr10:91178800-91186400	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
23	chr10:91179000-91186200	Weak transcription	Muscle Satellite Cultured Cells	--
24	chr10:91179400-91186400	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
25	chr10:91179400-91187600	Weak transcription	iPS-20b Cell Line	embryonic stem cell
26	chr10:91179400-91187800	Weak transcription	ES-I3 Cell Line	embryonic stem cell
27	chr10:91179400-91187800	Weak transcription	HUES48 Cell Line	embryonic stem cell
28	chr10:91179400-91187800	Weak transcription	HUES64 Cell Line	embryonic stem cell
29	chr10:91179600-91225600	Weak transcription	Pancreatic Islets	Pancreatic Islet
30	chr10:91181200-91192800	Weak transcription	Left Ventricle	heart
31	chr10:91181400-91186000	Weak transcription	Fetal Heart	heart
32	chr10:91181400-91186200	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
33	chr10:91181400-91186200	Weak transcription	NHEK	skin
34	chr10:91181600-91186200	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
35	chr10:91181600-91186200	Weak transcription	HSMM	muscle
36	chr10:91181800-91186200	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
37	chr10:91181800-91186400	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
38	chr10:91182000-91186400	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
39	chr10:91182000-91186400	Weak transcription	Fetal Lung	lung
40	chr10:91182000-91187200	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
41	chr10:91182200-91187400	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
42	chr10:91182200-91191200	Weak transcription	Sigmoid Colon	Sigmoid Colon
43	chr10:91182200-91191400	Weak transcription	Breast Myoepithelial Primary Cells	Breast
44	chr10:91183800-91186400	Enhancers	HepG2	liver
45	chr10:91184400-91186200	Enhancers	Liver	Liver
46	chr10:91184600-91186000	Weak transcription	Fetal Kidney	kidney
47	chr10:91184600-91186200	Enhancers	Fetal Intestine Large	intestine
48	chr10:91184600-91186200	Enhancers	Fetal Intestine Small	intestine
49	chr10:91185600-91185800	Enhancers	Primary T helper naive cells fromperipheralblood	blood
50	chr10:91185600-91186400	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived

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