Variant report

Variant	rs2274878
Chromosome Location	chr10:91102098-91102099
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 54 )
Associated
traits (count: 8 )

rSNPs within LD-proxies of this variant (count:49)

rs_ID	r²[population]
rs10509571	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];0.94[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs10509572	0.86[CEU][hapmap];0.89[GIH][hapmap];0.91[TSI][hapmap];0.81[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs10788641	0.95[CHB][hapmap]
rs10887946	0.95[CHB][hapmap]
rs10887947	0.95[CHB][hapmap]
rs10887950	0.86[CEU][hapmap];0.84[GIH][hapmap]
rs10887953	0.81[CEU][hapmap]
rs10887959	0.81[LWK][hapmap]
rs11203063	0.81[CEU][hapmap];0.83[LWK][hapmap]
rs11203070	0.84[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs11203072	0.81[AFR][1000 genomes];0.86[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs11203078	0.95[CHB][hapmap]
rs11203090	0.81[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs11203099	0.86[CEU][hapmap];0.89[GIH][hapmap];0.81[LWK][hapmap];0.88[TSI][hapmap];0.82[EUR][1000 genomes]
rs11203109	0.81[CEU][hapmap]
rs11203115	0.81[LWK][hapmap]
rs11819073	0.81[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs12244233	0.86[CEU][hapmap];0.89[GIH][hapmap];0.88[TSI][hapmap]
rs12248331	0.81[AFR][1000 genomes];0.87[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs12255504	0.86[CEU][hapmap];0.81[AFR][1000 genomes];0.87[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs12766862	0.90[AFR][1000 genomes];0.98[AMR][1000 genomes];0.92[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs1332330	0.90[CEU][hapmap];0.81[AMR][1000 genomes]
rs1591051	0.86[CEU][hapmap];0.83[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs17096301	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17120001	0.81[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs17120004	0.81[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs17120325	0.85[CEU][hapmap]
rs305374	0.95[CHB][hapmap];0.83[YRI][hapmap]
rs34234196	0.81[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs34712773	0.81[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs35830608	0.81[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs3740027	0.81[MEX][hapmap];0.82[TSI][hapmap]
rs3780878	0.93[ASW][hapmap];0.86[CEU][hapmap];0.89[GIH][hapmap];0.85[LWK][hapmap];0.82[MEX][hapmap];0.88[TSI][hapmap];0.85[AFR][1000 genomes];0.87[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs4339948	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];0.94[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4630205	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.88[MEX][hapmap];0.89[TSI][hapmap];0.91[AMR][1000 genomes];0.90[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs627127	0.95[CHB][hapmap];0.83[YRI][hapmap]
rs6586182	0.81[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs6586183	0.86[ASW][hapmap];0.86[CEU][hapmap];0.91[TSI][hapmap];0.81[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs6586188	0.91[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.88[MEX][hapmap];0.81[TSI][hapmap];0.85[AMR][1000 genomes];0.92[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7073534	0.81[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs7085361	0.81[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs7088579	0.86[CEU][hapmap];0.89[GIH][hapmap];0.81[LWK][hapmap];0.88[TSI][hapmap];0.81[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs71479013	0.81[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs7897619	0.86[ASW][hapmap];0.86[CEU][hapmap];0.89[GIH][hapmap];0.85[TSI][hapmap];0.81[AMR][1000 genomes]
rs7897873	0.86[CEU][hapmap];0.81[AMR][1000 genomes]
rs7910389	0.82[AFR][1000 genomes];0.87[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs7916812	1.00[ASW][hapmap];0.95[CEU][hapmap];0.95[GIH][hapmap];0.95[LWK][hapmap];0.94[MEX][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.93[AFR][1000 genomes];0.95[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs812451	0.95[CHB][hapmap]
rs884407	0.81[AMR][1000 genomes];0.84[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:5 , 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
4	nsv1040375	chr10:91022218-91153074	Enhancers Active TSS Weak transcription Flanking Active TSS Transcr. at gene 5' and 3' Strong transcription Genic enhancers ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	16 gene(s)	inside rSNPs	diseases
5	esv34085	chr10:91065949-91174175	Enhancers Weak transcription Active TSS Strong transcription Genic enhancers Flanking Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	14 gene(s)	inside rSNPs	diseases

mRNA abundance (count:8)

SNP	Gene	Cis/trans	Tissue	Source
rs2274878	LDB3	cis	cerebellum	SCAN
rs2274878	IFIT5	Cis_1M	lymphoblastoid	RTeQTL
rs2274878	C10orf116	cis	cerebellum	SCAN
rs2274878	IFIT5	cis	multi-tissue	Pritchard
rs2274878	CH25H	cis	cerebellum	SCAN
rs2274878	IDE	cis	parietal	SCAN
rs2274878	IFIT5	cis	brain	seeQTL
rs2274878	IFIT5	cis	lymphoblastoid	seeQTL

Chromatin state (count:103 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr10:91090200-91107600	Weak transcription	Pancreas	Pancrea
2	chr10:91093800-91106000	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
3	chr10:91093800-91106400	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
4	chr10:91094000-91102200	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
5	chr10:91094000-91103400	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
6	chr10:91094000-91105400	Weak transcription	iPS-20b Cell Line	embryonic stem cell
7	chr10:91094000-91110200	Weak transcription	Colonic Mucosa	Colon
8	chr10:91094000-91112000	Weak transcription	Esophagus	oesophagus
9	chr10:91094200-91103400	Weak transcription	H9 Cell Line	embryonic stem cell
10	chr10:91094200-91106800	Weak transcription	Fetal Kidney	kidney
11	chr10:91094200-91108400	Weak transcription	Stomach Mucosa	stomach
12	chr10:91095200-91110400	Weak transcription	Colon Smooth Muscle	Colon
13	chr10:91095600-91105600	Weak transcription	Skeletal Muscle Female	skeletal muscle
14	chr10:91097400-91105600	Weak transcription	Sigmoid Colon	Sigmoid Colon
15	chr10:91097600-91102200	Weak transcription	ES-I3 Cell Line	embryonic stem cell
16	chr10:91097600-91102800	Strong transcription	GM12878-XiMat	blood
17	chr10:91097600-91106200	Weak transcription	H1 Cell Line	embryonic stem cell
18	chr10:91097600-91106200	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
19	chr10:91097600-91107400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
20	chr10:91097600-91107400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
21	chr10:91097800-91102200	Weak transcription	HMEC	breast
22	chr10:91098800-91106400	Weak transcription	Psoas Muscle	Psoas
23	chr10:91098800-91111200	Weak transcription	Aorta	Aorta
24	chr10:91099400-91102200	Weak transcription	HSMMtube	muscle
25	chr10:91099400-91102600	Weak transcription	Dnd41	blood
26	chr10:91099400-91106000	Weak transcription	Rectal Mucosa Donor 31	rectum
27	chr10:91099400-91106200	Weak transcription	HSMM	muscle
28	chr10:91099400-91107800	Weak transcription	Primary T helper cells PMA-I stimulated	--
29	chr10:91099400-91111000	Weak transcription	Rectal Smooth Muscle	rectum
30	chr10:91099600-91102200	Weak transcription	Hela-S3	cervix
31	chr10:91099600-91102800	Weak transcription	Primary T helper naive cells from peripheral blood	blood
32	chr10:91099600-91106400	Weak transcription	Primary hematopoietic stem cells	blood
33	chr10:91099600-91110400	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
34	chr10:91099600-91110800	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
35	chr10:91099800-91102200	Weak transcription	Muscle Satellite Cultured Cells	--
36	chr10:91099800-91102200	Weak transcription	Duodenum Smooth Muscle	Duodenum
37	chr10:91099800-91106400	Weak transcription	Primary hematopoietic stem cells short term culture	blood
38	chr10:91099800-91110400	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
39	chr10:91099800-91111000	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
40	chr10:91100000-91102200	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
41	chr10:91100000-91106000	Weak transcription	NHLF	lung
42	chr10:91100000-91106400	Weak transcription	Spleen	Spleen
43	chr10:91100000-91106600	Weak transcription	Primary B cells from cord blood	blood
44	chr10:91100000-91106800	Weak transcription	Primary B cells from peripheral blood	blood
45	chr10:91100000-91107400	Weak transcription	Breast Myoepithelial Primary Cells	Breast
46	chr10:91100000-91107600	Weak transcription	Fetal Thymus	thymus
47	chr10:91100000-91110400	Weak transcription	Stomach Smooth Muscle	stomach
48	chr10:91100000-91111000	Weak transcription	Primary T helper cells fromperipheralblood	blood
49	chr10:91100200-91106200	Weak transcription	Fetal Stomach	stomach
50	chr10:91100600-91102200	Weak transcription	Cortex derived primary cultured neurospheres	brain

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