Variant report

Variant	rs303199
Chromosome Location	chr10:91238486-91238487
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 27 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:24)

rs_ID	r²[population]
rs160053	0.89[ASN][1000 genomes]
rs160054	0.92[CEU][hapmap];1.00[GIH][hapmap];0.82[JPT][hapmap];0.88[TSI][hapmap];0.84[EUR][1000 genomes]
rs303162	0.88[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.91[ASN][1000 genomes]
rs303175	0.88[ASW][hapmap];1.00[CEU][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.87[MKK][hapmap];0.95[TSI][hapmap];0.91[AMR][1000 genomes];0.94[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs303177	0.95[CEU][hapmap];0.81[EUR][1000 genomes]
rs303178	0.96[CEU][hapmap];1.00[GIH][hapmap];0.82[JPT][hapmap];0.87[MEX][hapmap];0.90[TSI][hapmap];0.81[EUR][1000 genomes]
rs303179	0.80[EUR][1000 genomes]
rs303181	0.96[CEU][hapmap];1.00[GIH][hapmap];0.82[JPT][hapmap];0.87[MEX][hapmap];0.90[TSI][hapmap];0.80[EUR][1000 genomes]
rs303183	0.90[CEU][hapmap];0.81[AMR][1000 genomes];0.90[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs303184	0.96[CEU][hapmap];1.00[JPT][hapmap];0.81[AMR][1000 genomes];0.86[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs303188	0.91[CEU][hapmap]
rs303190	0.84[EUR][1000 genomes]
rs303192	0.92[CEU][hapmap];1.00[GIH][hapmap];0.83[TSI][hapmap]
rs303195	1.00[CEU][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.95[TSI][hapmap];0.89[AMR][1000 genomes];0.95[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs303196	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.83[LWK][hapmap];1.00[MEX][hapmap];0.90[MKK][hapmap];0.95[TSI][hapmap];0.89[YRI][hapmap];0.86[AFR][1000 genomes];0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs303197	1.00[CEU][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.86[AFR][1000 genomes];0.97[AMR][1000 genomes];0.95[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs303202	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.80[YRI][hapmap];0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs303204	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.90[TSI][hapmap];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs304416	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs304429	1.00[CEU][hapmap];0.88[CHB][hapmap];1.00[JPT][hapmap];0.97[AMR][1000 genomes];0.93[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs304430	1.00[ASW][hapmap];1.00[CEU][hapmap];0.88[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.85[MKK][hapmap];0.90[TSI][hapmap];0.80[YRI][hapmap];0.97[AMR][1000 genomes];0.93[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs497191	0.91[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs7903979	0.88[CEU][hapmap]
rs7924208	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:4)

SNP	Gene	Cis/trans	Tissue	Source
rs303199	IFIT5	cis	lymphoblastoid	seeQTL
rs303199	STAMBPL1	cis	cerebellum	SCAN
rs303199	IFIT1	cis	parietal	SCAN
rs303199	NUDT9P1	cis	parietal	SCAN

Chromatin state (count:71 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr10:91234600-91238800	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
2	chr10:91234600-91240400	Enhancers	Breast Myoepithelial Primary Cells	Breast
3	chr10:91234600-91242400	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
4	chr10:91234600-91242600	Enhancers	Muscle Satellite Cultured Cells	--
5	chr10:91235200-91240400	Enhancers	NH-A	brain
6	chr10:91235600-91238800	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
7	chr10:91235600-91239200	Enhancers	HMEC	breast
8	chr10:91235600-91239800	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
9	chr10:91235600-91243400	Enhancers	HSMM	muscle
10	chr10:91235800-91239000	Enhancers	Left Ventricle	heart
11	chr10:91236800-91238600	Weak transcription	Brain Anterior Caudate	brain
12	chr10:91237000-91240800	Weak transcription	A549	lung
13	chr10:91237600-91238800	Enhancers	iPS-18 Cell Line	embryonic stem cell
14	chr10:91237600-91239400	Enhancers	HUES64 Cell Line	embryonic stem cell
15	chr10:91237600-91239400	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
16	chr10:91237600-91240200	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
17	chr10:91237600-91240200	Enhancers	Colon Smooth Muscle	Colon
18	chr10:91237600-91241000	Enhancers	Fetal Lung	lung
19	chr10:91237800-91238600	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
20	chr10:91237800-91238800	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
21	chr10:91237800-91239000	Enhancers	HUES48 Cell Line	embryonic stem cell
22	chr10:91237800-91239000	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
23	chr10:91237800-91239000	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
24	chr10:91237800-91239000	Enhancers	Primary B cells from cord blood	blood
25	chr10:91237800-91239000	Enhancers	Placenta	Placenta
26	chr10:91237800-91239000	Enhancers	Pancreas	Pancrea
27	chr10:91237800-91239000	Enhancers	Placenta Amnion	Placenta Amnion
28	chr10:91237800-91239000	Enhancers	NHEK	skin
29	chr10:91237800-91239200	Enhancers	HUES6 Cell Line	embryonic stem cell
30	chr10:91237800-91239200	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
31	chr10:91237800-91239200	Enhancers	Right Atrium	heart
32	chr10:91237800-91239400	Enhancers	iPS-15b Cell Line	embryonic stem cell
33	chr10:91237800-91239400	Enhancers	Primary B cells from peripheral blood	blood
34	chr10:91237800-91239400	Enhancers	Stomach Smooth Muscle	stomach
35	chr10:91237800-91239800	Enhancers	Skeletal Muscle Male	skeletal muscle
36	chr10:91237800-91240000	Enhancers	Foreskin Fibroblast Primary Cells skin02	Skin
37	chr10:91237800-91240000	Enhancers	Fetal Intestine Large	intestine
38	chr10:91237800-91240000	Enhancers	Fetal Intestine Small	intestine
39	chr10:91237800-91240200	Enhancers	Skeletal Muscle Female	skeletal muscle
40	chr10:91237800-91241000	Enhancers	Duodenum Smooth Muscle	Duodenum
41	chr10:91237800-91241400	Enhancers	HSMMtube	muscle
42	chr10:91237800-91242000	Enhancers	Pancreatic Islets	Pancreatic Islet
43	chr10:91237800-91242200	Enhancers	Adipose Nuclei	Adipose
44	chr10:91237800-91242200	Enhancers	Rectal Smooth Muscle	rectum
45	chr10:91237800-91242400	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
46	chr10:91237800-91242400	Enhancers	NHDF-Ad	bronchial
47	chr10:91237800-91242400	Enhancers	Osteobl	bone
48	chr10:91238000-91238800	Enhancers	ES-I3 Cell Line	embryonic stem cell
49	chr10:91238000-91238800	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
50	chr10:91238000-91238800	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived

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