Variant report

Variant	rs304447
Chromosome Location	chr10:91178804-91178805
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 30 )
Associated
traits (count: 13 )

rSNPs within LD-proxies of this variant (count:27)

rs_ID	r²[population]
rs184236	1.00[ASW][hapmap];1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.91[JPT][hapmap];0.98[LWK][hapmap];1.00[MEX][hapmap];0.93[MKK][hapmap];1.00[TSI][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]
rs188589	1.00[CEU][hapmap];0.95[CHB][hapmap];0.93[CHD][hapmap];1.00[GIH][hapmap];0.85[JPT][hapmap];0.90[MEX][hapmap];1.00[TSI][hapmap];0.98[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs188591	0.88[EUR][1000 genomes]
rs2484046	0.94[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2484047	0.90[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs303171	0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs303173	0.86[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs303209	0.95[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs303210	0.83[CEU][hapmap];0.86[CHB][hapmap];0.93[CHD][hapmap];1.00[GIH][hapmap];0.93[TSI][hapmap];0.94[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs303213	0.95[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs303215	0.83[CEU][hapmap];0.86[CHB][hapmap];0.91[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs303216	0.91[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs303218	0.97[GIH][hapmap];0.93[TSI][hapmap];0.90[EUR][1000 genomes]
rs304411	0.94[CEU][hapmap];0.95[CHB][hapmap];0.93[CHD][hapmap];1.00[GIH][hapmap];0.86[JPT][hapmap];0.93[TSI][hapmap];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs304434	0.94[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs304436	0.92[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs304437	0.83[CEU][hapmap];0.95[CHB][hapmap];0.95[CHD][hapmap];1.00[GIH][hapmap];0.81[JPT][hapmap];0.96[TSI][hapmap];0.94[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs304441	0.83[CEU][hapmap];0.86[CHB][hapmap];0.94[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs304442	0.94[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs304450	0.94[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs304492	0.89[EUR][1000 genomes]
rs304493	0.82[CEU][hapmap];0.81[TSI][hapmap]
rs304500	0.95[GIH][hapmap];0.93[TSI][hapmap];0.88[EUR][1000 genomes]
rs304502	0.83[CEU][hapmap];0.85[CHB][hapmap];0.93[CHD][hapmap];0.86[GIH][hapmap];0.90[TSI][hapmap];0.88[EUR][1000 genomes]
rs304503	0.89[EUR][1000 genomes]
rs304505	0.83[CEU][hapmap];0.81[CHB][hapmap];0.93[CHD][hapmap];0.97[GIH][hapmap];0.93[TSI][hapmap];0.89[EUR][1000 genomes]
rs304506	0.83[CEU][hapmap];0.86[CHB][hapmap];0.89[EUR][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:13)

SNP	Gene	Cis/trans	Tissue	Source
rs304447	LIPA	cis	parietal	SCAN
rs304447	IFIT5	cis	Esophagus Mucosa	GTEx
rs304447	IFIT5	cis	Nerve Tibial	GTEx
rs304447	IFIT5	cis	cerebellum	SCAN
rs304447	IFIT5	cis	lymphoblastoid	seeQTL
rs304447	IFIT5	Cis_1M	lymphoblastoid	RTeQTL
rs304447	IFIT1	cis	cerebellum	SCAN
rs304447	IFIT5	cis	Artery Tibial	GTEx
rs304447	IDE	cis	parietal	SCAN
rs304447	IFIT5	cis	Esophagus Muscularis	GTEx
rs304447	IFIT5	cis	Thyroid	GTEx
rs304447	IFIT5	cis	parietal	SCAN
rs304447	IFIT1	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:113 , 50 per page) page: 1 2 3

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	chr10:91175600-91179600	Enhancers	Primary T killer naive cells fromperipheralblood	blood
4	chr10:91175600-91181200	Enhancers	Primary T helper naive cells fromperipheralblood	blood
5	chr10:91175600-91181200	Weak transcription	Placenta Amnion	Placenta Amnion
6	chr10:91175600-91183800	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
7	chr10:91175600-91188200	Weak transcription	Skeletal Muscle Male	skeletal muscle
8	chr10:91175600-91191800	Weak transcription	Psoas Muscle	Psoas
9	chr10:91175600-91191800	Weak transcription	Hela-S3	cervix
10	chr10:91175800-91179600	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
11	chr10:91175800-91182600	Weak transcription	Thymus	Thymus
12	chr10:91176000-91179600	Enhancers	Primary T helper naive cells from peripheral blood	blood
13	chr10:91176000-91180000	Weak transcription	Colonic Mucosa	Colon
14	chr10:91176200-91179000	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
15	chr10:91176200-91186400	Weak transcription	Skeletal Muscle Female	skeletal muscle
16	chr10:91176600-91179400	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
17	chr10:91176600-91182800	Weak transcription	Esophagus	oesophagus
18	chr10:91177000-91179200	Genic enhancers	Primary T helper cells PMA-I stimulated	--
19	chr10:91177000-91181400	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
20	chr10:91177200-91181600	Strong transcription	Fetal Intestine Large	intestine
21	chr10:91177200-91181800	Strong transcription	Monocytes-CD14+_RO01746	blood
22	chr10:91177400-91179800	Enhancers	iPS-15b Cell Line	embryonic stem cell
23	chr10:91177400-91182000	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
24	chr10:91177600-91179200	Enhancers	Pancreatic Islets	Pancreatic Islet
25	chr10:91177600-91184000	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
26	chr10:91177800-91179400	Enhancers	HUES48 Cell Line	embryonic stem cell
27	chr10:91178000-91179400	Enhancers	HUES64 Cell Line	embryonic stem cell
28	chr10:91178000-91179400	Enhancers	Brain Substantia Nigra	brain
29	chr10:91178000-91183600	Weak transcription	Primary hematopoietic stem cells	blood
30	chr10:91178000-91186000	Weak transcription	HMEC	breast
31	chr10:91178000-91186200	Weak transcription	HSMMtube	muscle
32	chr10:91178000-91186400	Weak transcription	Fetal Stomach	stomach
33	chr10:91178000-91187800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
34	chr10:91178200-91179200	Weak transcription	Liver	Liver
35	chr10:91178200-91179400	Enhancers	ES-I3 Cell Line	embryonic stem cell
36	chr10:91178200-91179400	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
37	chr10:91178200-91179600	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
38	chr10:91178200-91179600	Enhancers	Brain Cingulate Gyrus	brain
39	chr10:91178200-91179800	Weak transcription	Primary hematopoietic stem cells short term culture	blood
40	chr10:91178200-91180200	Weak transcription	Breast Myoepithelial Primary Cells	Breast
41	chr10:91178200-91180200	Weak transcription	Placenta	Placenta
42	chr10:91178200-91180200	Weak transcription	NHEK	skin
43	chr10:91178200-91180600	Weak transcription	Fetal Heart	heart
44	chr10:91178200-91182200	Weak transcription	Rectal Mucosa Donor 31	rectum
45	chr10:91178200-91183800	Weak transcription	HepG2	liver
46	chr10:91178200-91184800	Weak transcription	Duodenum Smooth Muscle	Duodenum
47	chr10:91178200-91186400	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
48	chr10:91178200-91191800	Weak transcription	Aorta	Aorta
49	chr10:91178200-91197600	Weak transcription	Pancreas	Pancrea
50	chr10:91178400-91179000	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--

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