Variant report

Variant	rs10887959
Chromosome Location	chr10:91181853-91181854
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	chr10:91172166..91175121-chr10:91181406..91183145,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000152778	Chromatin interaction
ENSG00000107798	Chromatin interaction

Extended variants
information (count: 45 )
Associated
traits (count: 9 )

rSNPs within LD-proxies of this variant (count:42)

rs_ID	r²[population]
rs10509572	0.85[CEU][hapmap];1.00[CHB][hapmap];0.92[CHD][hapmap];0.81[JPT][hapmap];0.92[LWK][hapmap];0.82[MEX][hapmap];0.95[YRI][hapmap];0.83[ASN][1000 genomes]
rs10788642	0.83[AFR][1000 genomes];0.88[AMR][1000 genomes];0.91[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs10887950	0.85[ASW][hapmap];0.85[CEU][hapmap];0.89[CHD][hapmap];0.95[LWK][hapmap];0.88[MEX][hapmap];0.92[MKK][hapmap];0.88[TSI][hapmap];1.00[YRI][hapmap];0.82[AFR][1000 genomes];0.80[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs10887953	0.90[CEU][hapmap];0.87[CHB][hapmap];1.00[YRI][hapmap];0.82[AFR][1000 genomes];0.87[AMR][1000 genomes];0.86[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs10887957	0.86[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs11203063	0.80[CEU][hapmap];0.87[JPT][hapmap];0.92[LWK][hapmap];0.85[YRI][hapmap]
rs11203090	0.83[ASN][1000 genomes]
rs11203099	0.85[CEU][hapmap];0.93[CHB][hapmap];0.92[CHD][hapmap];0.81[JPT][hapmap];0.95[LWK][hapmap];0.82[MEX][hapmap];1.00[YRI][hapmap];0.84[ASN][1000 genomes]
rs11203105	0.83[AFR][1000 genomes];0.88[AMR][1000 genomes];0.88[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs11203106	0.83[AFR][1000 genomes];0.88[AMR][1000 genomes];0.88[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs11203109	0.90[CEU][hapmap];0.87[CHB][hapmap];1.00[YRI][hapmap];0.83[AFR][1000 genomes];0.88[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs11203112	0.85[AFR][1000 genomes];0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs11203115	0.92[ASW][hapmap];0.95[CEU][hapmap];1.00[CHB][hapmap];0.92[CHD][hapmap];0.84[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];0.88[MEX][hapmap];0.98[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.87[AFR][1000 genomes];0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs11203119	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs11819073	0.82[ASN][1000 genomes]
rs12244233	0.85[CEU][hapmap];1.00[CHB][hapmap];0.89[CHD][hapmap];0.81[JPT][hapmap];0.82[LWK][hapmap]
rs12255504	0.85[CEU][hapmap];1.00[CHB][hapmap];0.87[JPT][hapmap];0.85[YRI][hapmap]
rs12356008	0.85[AFR][1000 genomes];0.93[AMR][1000 genomes];0.95[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs12781453	0.80[AMR][1000 genomes];0.89[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs12781505	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[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];0.95[YRI][hapmap];0.81[ASN][1000 genomes]
rs17120001	0.83[ASN][1000 genomes]
rs17120004	0.83[ASN][1000 genomes]
rs17120325	0.90[CEU][hapmap];1.00[YRI][hapmap]
rs17121248	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]
rs2274878	0.81[LWK][hapmap]
rs303212	0.90[YRI][hapmap]
rs34234196	0.83[ASN][1000 genomes]
rs35359667	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs35830608	0.83[ASN][1000 genomes]
rs3740027	0.82[LWK][hapmap]
rs3780878	0.85[CEU][hapmap];1.00[CHB][hapmap];0.88[CHD][hapmap];0.87[JPT][hapmap];0.95[LWK][hapmap];0.85[YRI][hapmap]
rs6586183	0.85[CEU][hapmap];1.00[CHB][hapmap];0.88[CHD][hapmap];0.87[JPT][hapmap];0.87[LWK][hapmap]
rs6586196	0.85[CEU][hapmap]
rs7088579	0.85[CEU][hapmap];0.93[CHB][hapmap];0.92[CHD][hapmap];0.81[JPT][hapmap];0.95[LWK][hapmap];0.82[MEX][hapmap];0.95[YRI][hapmap];0.82[ASN][1000 genomes]
rs7090346	0.95[CEU][hapmap];0.87[CHB][hapmap];0.92[CHD][hapmap];1.00[GIH][hapmap];0.82[JPT][hapmap];1.00[MEX][hapmap];0.97[TSI][hapmap];0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs71479013	0.83[ASN][1000 genomes]
rs7897619	0.85[CEU][hapmap];1.00[CHB][hapmap];0.88[CHD][hapmap];0.87[JPT][hapmap];0.87[LWK][hapmap]
rs7897873	0.84[CEU][hapmap];1.00[CHB][hapmap];0.86[JPT][hapmap]
rs7916812	1.00[CHB][hapmap];0.88[CHD][hapmap];0.93[JPT][hapmap];0.85[LWK][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:9)

SNP	Gene	Cis/trans	Tissue	Source
rs10887959	IFIT5	cis	multi-tissue	Pritchard
rs10887959	IFIT5	cis	brain	seeQTL
rs10887959	IFIT5	cis	lymphoblastoid	seeQTL
rs10887959	IFIT5	cis	Liver	GTEx
rs10887959	C11orf9	trans	cerebellum	SCAN
rs10887959	CH25H	cis	cerebellum	SCAN
rs10887959	IFIT1B	cis	lymphoblastoid	seeQTL
rs10887959	IFIT5	cis	Lymphoblastoid	GTEx
rs10887959	C10orf116	cis	cerebellum	SCAN

Chromatin state (count:93 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr10:91175400-91187600	Weak transcription	HUVEC	blood vessel
2	chr10:91175600-91183800	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
3	chr10:91175600-91188200	Weak transcription	Skeletal Muscle Male	skeletal muscle
4	chr10:91175600-91191800	Weak transcription	Psoas Muscle	Psoas
5	chr10:91175600-91191800	Weak transcription	Hela-S3	cervix
6	chr10:91175800-91182600	Weak transcription	Thymus	Thymus
7	chr10:91176200-91186400	Weak transcription	Skeletal Muscle Female	skeletal muscle
8	chr10:91176600-91182800	Weak transcription	Esophagus	oesophagus
9	chr10:91177400-91182000	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
10	chr10:91177600-91184000	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
11	chr10:91178000-91183600	Weak transcription	Primary hematopoietic stem cells	blood
12	chr10:91178000-91186000	Weak transcription	HMEC	breast
13	chr10:91178000-91186200	Weak transcription	HSMMtube	muscle
14	chr10:91178000-91186400	Weak transcription	Fetal Stomach	stomach
15	chr10:91178000-91187800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
16	chr10:91178200-91182200	Weak transcription	Rectal Mucosa Donor 31	rectum
17	chr10:91178200-91183800	Weak transcription	HepG2	liver
18	chr10:91178200-91184800	Weak transcription	Duodenum Smooth Muscle	Duodenum
19	chr10:91178200-91186400	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
20	chr10:91178200-91191800	Weak transcription	Aorta	Aorta
21	chr10:91178200-91197600	Weak transcription	Pancreas	Pancrea
22	chr10:91178400-91182000	Weak transcription	Rectal Mucosa Donor 29	rectum
23	chr10:91178400-91182800	Weak transcription	Colon Smooth Muscle	Colon
24	chr10:91178400-91183000	Weak transcription	Fetal Thymus	thymus
25	chr10:91178400-91183800	Weak transcription	Duodenum Mucosa	Duodenum
26	chr10:91178400-91184800	Weak transcription	Lung	lung
27	chr10:91178400-91185600	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
28	chr10:91178400-91186200	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
29	chr10:91178400-91186200	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
30	chr10:91178400-91186200	Weak transcription	NHLF	lung
31	chr10:91178400-91186200	Weak transcription	Osteobl	bone
32	chr10:91178400-91187200	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
33	chr10:91178400-91188000	Weak transcription	Right Ventricle	heart
34	chr10:91178400-91191600	Weak transcription	A549	lung
35	chr10:91178600-91186200	Weak transcription	NH-A	brain
36	chr10:91178800-91186200	Weak transcription	NHDF-Ad	bronchial
37	chr10:91178800-91186400	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
38	chr10:91179000-91183000	Weak transcription	Brain Germinal Matrix	brain
39	chr10:91179000-91186200	Weak transcription	Muscle Satellite Cultured Cells	--
40	chr10:91179400-91183000	Weak transcription	Brain Substantia Nigra	brain
41	chr10:91179400-91183600	Weak transcription	Cortex derived primary cultured neurospheres	brain
42	chr10:91179400-91184200	Weak transcription	Fetal Kidney	kidney
43	chr10:91179400-91186400	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
44	chr10:91179400-91187600	Weak transcription	iPS-20b Cell Line	embryonic stem cell
45	chr10:91179400-91187800	Weak transcription	ES-I3 Cell Line	embryonic stem cell
46	chr10:91179400-91187800	Weak transcription	HUES48 Cell Line	embryonic stem cell
47	chr10:91179400-91187800	Weak transcription	HUES64 Cell Line	embryonic stem cell
48	chr10:91179600-91182000	Weak transcription	Brain Hippocampus Middle	brain
49	chr10:91179600-91182800	Weak transcription	Fetal Brain Male	brain
50	chr10:91179600-91183200	Weak transcription	Brain Inferior Temporal Lobe	brain

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