Variant report

Variant	rs304500
Chromosome Location	chr10:91149563-91149564
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	CTCF	chr10:91148858-91149630	A549	lung:	n/a	chr10:91149207-91149225 chr10:91149202-91149223
2	CTCF	chr10:91148788-91149670	SK-N-SH	brain:	n/a	chr10:91149207-91149225 chr10:91149202-91149223
3	SPI1	chr10:91149486-91149689	GM12891	blood:	n/a	chr10:91149591-91149600
4	SMC3	chr10:91148561-91149574	SK-N-SH	brain:	n/a	n/a
5	RAD21	chr10:91148844-91149590	SK-N-SH	brain:	n/a	chr10:91149214-91149223

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr10:91052972..91053701-chr10:91148823..91149651,3	MCF-7	breast:
2	chr10:91019602..91020678-chr10:91148799..91149709,3	MCF-7	breast:

Variant related genes	Relation type
IFIT1	TF binding region

Extended variants
information (count: 39 )
Associated
traits (count: 14 )

rSNPs within LD-proxies of this variant (count:34)

rs_ID	r²[population]
rs10887946	0.83[MEX][hapmap]
rs11203078	0.83[MEX][hapmap]
rs184236	0.95[GIH][hapmap];0.93[TSI][hapmap];0.89[EUR][1000 genomes]
rs188589	0.95[GIH][hapmap];0.93[TSI][hapmap];0.89[EUR][1000 genomes]
rs188591	0.82[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2484046	0.86[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs2484047	0.83[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs303171	0.86[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs303173	0.82[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs303208	0.95[JPT][hapmap]
rs303209	0.92[CEU][hapmap];1.00[YRI][hapmap];0.87[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs303210	1.00[ASW][hapmap];0.94[CEU][hapmap];0.95[GIH][hapmap];0.82[JPT][hapmap];0.83[MEX][hapmap];0.93[TSI][hapmap];1.00[YRI][hapmap];0.87[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs303212	0.95[JPT][hapmap]
rs303213	0.89[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs303215	0.94[CEU][hapmap];0.82[JPT][hapmap];1.00[YRI][hapmap];0.89[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs303216	0.89[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs303218	0.82[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.98[CHD][hapmap];0.98[GIH][hapmap];0.95[JPT][hapmap];0.84[LWK][hapmap];0.83[MEX][hapmap];0.83[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.92[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs304411	1.00[ASW][hapmap];0.82[CEU][hapmap];0.95[GIH][hapmap];0.83[MEX][hapmap];0.93[TSI][hapmap];0.80[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs304434	0.86[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs304436	0.81[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs304437	1.00[ASW][hapmap];0.94[CEU][hapmap];0.95[GIH][hapmap];0.83[MEX][hapmap];0.96[TSI][hapmap];1.00[YRI][hapmap];0.84[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs304441	0.94[CEU][hapmap];1.00[YRI][hapmap];0.84[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs304442	0.84[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs304447	0.95[GIH][hapmap];0.93[TSI][hapmap];0.88[EUR][1000 genomes]
rs304450	0.86[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs304492	0.92[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs304493	0.94[CEU][hapmap];0.95[JPT][hapmap];0.82[TSI][hapmap];0.85[EUR][1000 genomes]
rs304497	0.89[AFR][1000 genomes];0.94[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs304498	1.00[CEU][hapmap];0.95[JPT][hapmap];0.85[EUR][1000 genomes]
rs304502	1.00[ASW][hapmap];0.94[CEU][hapmap];0.86[GIH][hapmap];0.82[JPT][hapmap];0.88[MEX][hapmap];0.96[TSI][hapmap];1.00[YRI][hapmap];0.89[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs304503	0.89[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs304505	1.00[ASW][hapmap];0.94[CEU][hapmap];0.98[GIH][hapmap];0.82[JPT][hapmap];0.83[MEX][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.90[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs304506	0.94[CEU][hapmap];0.82[JPT][hapmap];1.00[YRI][hapmap];0.90[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs781501	0.84[AMR][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:14)

SNP	Gene	Cis/trans	Tissue	Source
rs304500	RPP30	cis	parietal	SCAN
rs304500	IFIT5	cis	Artery Tibial	GTEx
rs304500	IFIT5	cis	lymphoblastoid	seeQTL
rs304500	IFIT5	Cis_1M	lymphoblastoid	RTeQTL
rs304500	IFIT5	cis	Esophagus Muscularis	GTEx
rs304500	IFIT5	cis	Esophagus Mucosa	GTEx
rs304500	IFIT5	cis	parietal	SCAN
rs304500	IFIT1	Cis_1M	lymphoblastoid	RTeQTL
rs304500	LIPA	cis	parietal	SCAN
rs304500	IFIT5	cis	cerebellum	SCAN
rs304500	IDE	cis	parietal	SCAN
rs304500	IFIT5	cis	Thyroid	GTEx
rs304500	IFIT1	cis	cerebellum	SCAN
rs304500	IFIT5	cis	Nerve Tibial	GTEx

Chromatin state (count:28 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr10:91135000-91150200	Weak transcription	Fetal Brain Male	brain
2	chr10:91141000-91150000	Weak transcription	Fetal Heart	heart
3	chr10:91145400-91151000	Weak transcription	GM12878-XiMat	blood
4	chr10:91145400-91151800	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
5	chr10:91145600-91151600	Weak transcription	Primary neutrophils fromperipheralblood	blood
6	chr10:91145800-91151600	Weak transcription	Monocytes-CD14+_RO01746	blood
7	chr10:91146000-91151400	Weak transcription	Primary monocytes fromperipheralblood	blood
8	chr10:91146200-91151400	Weak transcription	Primary hematopoietic stem cells	blood
9	chr10:91146200-91151800	Weak transcription	ES-I3 Cell Line	embryonic stem cell
10	chr10:91146200-91152400	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
11	chr10:91146400-91150200	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
12	chr10:91146400-91150600	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
13	chr10:91146400-91151600	Weak transcription	Primary hematopoietic stem cells short term culture	blood
14	chr10:91146600-91152000	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
15	chr10:91146800-91151800	Weak transcription	iPS-15b Cell Line	embryonic stem cell
16	chr10:91148000-91151600	Weak transcription	Primary T helper cells PMA-I stimulated	--
17	chr10:91148600-91151600	Weak transcription	A549	lung
18	chr10:91149000-91149600	Enhancers	Cortex derived primary cultured neurospheres	brain
19	chr10:91149200-91150200	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
20	chr10:91149200-91150200	Weak transcription	Brain Cingulate Gyrus	brain
21	chr10:91149200-91150400	Weak transcription	Brain Angular Gyrus	brain
22	chr10:91149200-91150400	Weak transcription	Brain Anterior Caudate	brain
23	chr10:91149200-91150400	Weak transcription	Brain Substantia Nigra	brain
24	chr10:91149200-91151000	Enhancers	Brain Hippocampus Middle	brain
25	chr10:91149200-91151600	Weak transcription	NHDF-Ad	bronchial
26	chr10:91149200-91151800	Weak transcription	HUES64 Cell Line	embryonic stem cell
27	chr10:91149200-91151800	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
28	chr10:91149400-91151800	Weak transcription	HUES6 Cell Line	embryonic stem cell

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