Variant report

Variant	rs10887946
Chromosome Location	chr10:91090086-91090087
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	EP300	chr10:91089969-91090119	GM12878	blood:	n/a	n/a
2	POLR2A	chr10:91089849-91090388	GM12878	blood:	n/a	n/a
3	POLR2A	chr10:91089798-91091263	GM12891	blood:	n/a	n/a
4	BHLHE40	chr10:91089827-91090170	GM12878	blood:	n/a	n/a
5	POLR2A	chr10:91089771-91090389	GM12878	blood:	n/a	n/a
6	POLR2A	chr10:91089877-91091493	GM19099	blood:	n/a	n/a

Variant related genes	Relation type
IFIT3	TF binding region

Extended variants
information (count: 43 )
Associated
traits (count: 6 )

rSNPs within LD-proxies of this variant (count:38)

rs_ID	r²[population]
rs10509571	0.95[CHB][hapmap]
rs10788641	1.00[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];0.82[GIH][hapmap];1.00[JPT][hapmap];0.85[MEX][hapmap];0.94[TSI][hapmap];0.93[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs10887942	0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs10887945	0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs10887947	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs10887948	0.82[AMR][1000 genomes];0.93[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs11203064	0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs11203065	0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs11203078	1.00[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];0.87[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.94[TSI][hapmap];0.84[AMR][1000 genomes];0.96[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs1141862	0.82[AMR][1000 genomes];0.93[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs12220939	0.92[AMR][1000 genomes];0.99[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs191027	0.85[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2274878	0.95[CHB][hapmap]
rs303208	0.85[MEX][hapmap]
rs303210	0.82[CEU][hapmap];1.00[MEX][hapmap]
rs303215	0.82[CEU][hapmap]
rs303218	1.00[MEX][hapmap]
rs304411	1.00[MEX][hapmap]
rs304437	0.82[CEU][hapmap];1.00[MEX][hapmap]
rs304441	0.82[CEU][hapmap]
rs304492	0.83[AMR][1000 genomes]
rs304497	0.81[AMR][1000 genomes]
rs304500	0.83[MEX][hapmap]
rs304501	0.94[CEU][hapmap];0.85[MEX][hapmap];0.91[TSI][hapmap];0.84[EUR][1000 genomes]
rs304502	0.82[CEU][hapmap];0.94[MEX][hapmap];0.83[AMR][1000 genomes]
rs304503	0.83[AMR][1000 genomes]
rs304505	0.82[CEU][hapmap];1.00[MEX][hapmap];0.84[AMR][1000 genomes]
rs304506	0.82[CEU][hapmap];0.84[AMR][1000 genomes]
rs304508	0.94[CEU][hapmap];0.84[MEX][hapmap];0.91[TSI][hapmap];0.84[EUR][1000 genomes]
rs305374	0.89[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.82[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs4339948	0.95[CHB][hapmap]
rs4630205	0.95[CHB][hapmap]
rs4934472	0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs627127	0.89[CEU][hapmap];1.00[CHB][hapmap];0.92[CHD][hapmap];0.95[JPT][hapmap];0.80[MEX][hapmap];0.82[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs627496	0.88[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs6586188	0.95[CHB][hapmap]
rs781501	0.94[AMR][1000 genomes];0.87[ASN][1000 genomes]
rs812451	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.84[AMR][1000 genomes];0.88[EUR][1000 genomes];0.88[ASN][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:6)

SNP	Gene	Cis/trans	Tissue	Source
rs10887946	C10orf116	cis	cerebellum	SCAN
rs10887946	IFIT5	cis	cerebellum	SCAN
rs10887946	IFIT1	cis	cerebellum	SCAN
rs10887946	IFIT5	cis	lymphoblastoid	seeQTL
rs10887946	IFIT5	cis	parietal	SCAN
rs10887946	IFIT5	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:122 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr10:91087200-91093600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
2	chr10:91088000-91090200	Weak transcription	Sigmoid Colon	Sigmoid Colon
3	chr10:91088000-91091000	Enhancers	ES-I3 Cell Line	embryonic stem cell
4	chr10:91088000-91091200	Enhancers	HUES6 Cell Line	embryonic stem cell
5	chr10:91088000-91099800	Weak transcription	Gastric	stomach
6	chr10:91088200-91090200	Enhancers	Primary T killer naive cells fromperipheralblood	blood
7	chr10:91088200-91090600	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
8	chr10:91088200-91090600	Bivalent Enhancer	Primary Natural Killer cells fromperipheralblood	blood
9	chr10:91088200-91090600	Weak transcription	Stomach Mucosa	stomach
10	chr10:91088200-91091800	Enhancers	Primary B cells from peripheral blood	blood
11	chr10:91088200-91091800	Weak transcription	Fetal Muscle Trunk	muscle
12	chr10:91088200-91092000	Enhancers	Primary T helper 17 cells PMA-I stimulated	--
13	chr10:91088200-91092000	Weak transcription	Aorta	Aorta
14	chr10:91088200-91092400	Weak transcription	H1 Cell Line	embryonic stem cell
15	chr10:91088200-91093200	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
16	chr10:91088200-91093400	Weak transcription	Esophagus	oesophagus
17	chr10:91088400-91090400	Enhancers	HUVEC	blood vessel
18	chr10:91088400-91090800	Enhancers	Cortex derived primary cultured neurospheres	brain
19	chr10:91088400-91091000	Enhancers	Breast Myoepithelial Primary Cells	Breast
20	chr10:91088400-91091800	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
21	chr10:91088400-91091800	Enhancers	Primary T helper naive cells from peripheral blood	blood
22	chr10:91088400-91091800	Enhancers	Primary T helper cells fromperipheralblood	blood
23	chr10:91088400-91092000	Enhancers	Fetal Intestine Large	intestine
24	chr10:91088400-91092200	Weak transcription	HMEC	breast
25	chr10:91088600-91090400	Enhancers	Psoas Muscle	Psoas
26	chr10:91088600-91090400	Weak transcription	HepG2	liver
27	chr10:91088600-91090800	Enhancers	Skeletal Muscle Female	skeletal muscle
28	chr10:91088600-91091200	Weak transcription	Fetal Brain Male	brain
29	chr10:91088600-91091600	Enhancers	Primary T helper cells PMA-I stimulated	--
30	chr10:91088600-91091800	Weak transcription	K562	blood
31	chr10:91088600-91092200	Weak transcription	HUES64 Cell Line	embryonic stem cell
32	chr10:91088800-91090400	Enhancers	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
33	chr10:91088800-91090600	Enhancers	Primary hematopoietic stem cells short term culture	blood
34	chr10:91088800-91091400	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
35	chr10:91088800-91091400	Weak transcription	Primary B cells from cord blood	blood
36	chr10:91088800-91091800	Enhancers	Dnd41	blood
37	chr10:91088800-91092000	Weak transcription	A549	lung
38	chr10:91088800-91092200	Weak transcription	iPS-15b Cell Line	embryonic stem cell
39	chr10:91088800-91092200	Enhancers	Left Ventricle	heart
40	chr10:91088800-91092600	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
41	chr10:91089000-91090200	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
42	chr10:91089000-91090200	Enhancers	Brain Dorsolateral Prefrontal Cortex	brain
43	chr10:91089000-91090400	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
44	chr10:91089000-91090400	Enhancers	Lung	lung
45	chr10:91089000-91091200	Enhancers	Colon Smooth Muscle	Colon
46	chr10:91089000-91091800	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
47	chr10:91089000-91091800	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
48	chr10:91089000-91091800	Enhancers	Fetal Intestine Small	intestine
49	chr10:91089000-91091800	Weak transcription	Pancreatic Islets	Pancreatic Islet
50	chr10:91089000-91091800	Weak transcription	Rectal Mucosa Donor 29	rectum

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