Variant report

Variant	rs304508
Chromosome Location	chr10:91134555-91134556
allele	C/G
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	ZNF384	chr10:91134520-91134906	K562	blood:	n/a	n/a
2	GATA1	chr10:91133912-91135158	K562	blood:	n/a	chr10:91134818-91134834 chr10:91134707-91134720 chr10:91134823-91134830 chr10:91134709-91134717 chr10:91134489-91134496 chr10:91134821-91134831 chr10:91134819-91134832 chr10:91134519-91134529 chr10:91134821-91134830
3	POLR2A	chr10:91134532-91134926	K562	blood:	n/a	n/a
4	TBL1XR1	chr10:91133999-91134903	K562	blood:	n/a	n/a
5	ATF1	chr10:91134093-91134950	K562	blood:	n/a	n/a
6	MYC	chr10:91133992-91134996	K562	blood:	n/a	chr10:91134266-91134277
7	ZNF274	chr10:91134216-91134930	K562	blood:	n/a	n/a
8	CCNT2	chr10:91134089-91134932	K562	blood:	n/a	n/a
9	TEAD4	chr10:91134458-91135017	K562	blood:	n/a	n/a
10	TEAD4	chr10:91134473-91134991	K562	blood:	n/a	n/a
11	RCOR1	chr10:91133954-91135017	K562	blood:	n/a	n/a
12	HDAC2	chr10:91134523-91134852	K562	blood:	n/a	chr10:91134822-91134831
13	GATA2	chr10:91134526-91134973	K562	blood:	n/a	chr10:91134818-91134834 chr10:91134707-91134720 chr10:91134823-91134830 chr10:91134709-91134717 chr10:91134821-91134831 chr10:91134819-91134832 chr10:91134821-91134830
14	TRIM28	chr10:91134553-91134968	K562	blood:	n/a	n/a
15	MAX	chr10:91134555-91134892	K562	blood:	n/a	n/a
16	EP300	chr10:91133986-91135058	K562	blood:	n/a	chr10:91134517-91134531
17	STAT5A	chr10:91134441-91134943	K562	blood:	n/a	n/a
18	TAL1	chr10:91133962-91135096	K562	blood:	n/a	n/a
19	GATA1	chr10:91133688-91135118	PBDE	blood:	n/a	chr10:91134818-91134834 chr10:91134707-91134720 chr10:91134823-91134830 chr10:91134709-91134717 chr10:91134489-91134496 chr10:91134821-91134831 chr10:91134819-91134832 chr10:91134519-91134529 chr10:91134821-91134830
20	CUX1	chr10:91133988-91134670	K562	blood:	n/a	n/a
21	JUND	chr10:91133981-91135085	K562	blood:	n/a	n/a
22	GATA2	chr10:91134169-91135012	SH-SY5Y	brain:	n/a	chr10:91134818-91134834 chr10:91134707-91134720 chr10:91134823-91134830 chr10:91134709-91134717 chr10:91134489-91134496 chr10:91134821-91134831 chr10:91134819-91134832 chr10:91134519-91134529 chr10:91134821-91134830
23	PML	chr10:91134534-91134855	K562	blood:	n/a	n/a
24	ZMIZ1	chr10:91134487-91134906	K562	blood:	n/a	n/a
25	NFIC	chr10:91133757-91134608	ECC-1	luminal epithelium:	n/a	chr10:91134243-91134260
26	GATA3	chr10:91134484-91134903	SH-SY5Y	brain:	n/a	chr10:91134818-91134834 chr10:91134707-91134720 chr10:91134823-91134830 chr10:91134709-91134717 chr10:91134489-91134496 chr10:91134821-91134831 chr10:91134819-91134832 chr10:91134519-91134529 chr10:91134821-91134830
27	PML	chr10:91134519-91134954	K562	blood:	n/a	n/a
28	CEBPD	chr10:91134488-91134957	K562	blood:	n/a	n/a
29	BHLHE40	chr10:91134544-91134952	K562	blood:	n/a	n/a
30	TBL1XR1	chr10:91134102-91134862	K562	blood:	n/a	n/a
31	NR2F2	chr10:91134515-91134900	K562	blood:	n/a	n/a
32	GATA2	chr10:91134082-91134972	K562	blood:	n/a	chr10:91134818-91134834 chr10:91134707-91134720 chr10:91134823-91134830 chr10:91134709-91134717 chr10:91134489-91134496 chr10:91134821-91134831 chr10:91134819-91134832 chr10:91134519-91134529 chr10:91134821-91134830
33	NFIC	chr10:91133808-91134597	SK-N-SH	brain:	n/a	chr10:91134243-91134260
34	HCFC1	chr10:91134452-91134785	K562	blood:	n/a	n/a
35	IRF1	chr10:91134543-91135005	K562	blood:	n/a	n/a
36	CEBPD	chr10:91134515-91134989	K562	blood:	n/a	n/a

Variant related genes	Relation type
IFIT1B	TF binding region

Extended variants
information (count: 35 )
Associated
traits (count: 8 )

rSNPs within LD-proxies of this variant (count:30)

rs_ID	r²[population]
rs10788641	0.94[CEU][hapmap];0.95[GIH][hapmap];1.00[MEX][hapmap];0.97[TSI][hapmap];0.89[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs10887942	0.82[EUR][1000 genomes]
rs10887945	0.84[EUR][1000 genomes]
rs10887946	0.94[CEU][hapmap];0.84[MEX][hapmap];0.91[TSI][hapmap];0.84[EUR][1000 genomes]
rs10887947	0.94[CEU][hapmap];0.86[EUR][1000 genomes]
rs10887948	0.86[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs11203064	0.82[EUR][1000 genomes]
rs11203065	0.83[EUR][1000 genomes]
rs11203078	0.94[CEU][hapmap];0.91[GIH][hapmap];0.84[MEX][hapmap];0.97[TSI][hapmap];0.88[EUR][1000 genomes]
rs1141862	0.86[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs12220939	0.84[EUR][1000 genomes]
rs188589	0.81[JPT][hapmap]
rs191027	0.95[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs303210	0.81[JPT][hapmap];0.84[MEX][hapmap]
rs303212	0.85[MEX][hapmap]
rs303215	0.81[JPT][hapmap]
rs303218	0.84[MEX][hapmap]
rs304411	0.84[MEX][hapmap]
rs304437	0.86[JPT][hapmap];0.84[MEX][hapmap]
rs304493	0.89[GIH][hapmap];0.94[MEX][hapmap];0.80[AMR][1000 genomes]
rs304501	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs304502	0.81[JPT][hapmap]
rs304505	0.81[JPT][hapmap];0.84[MEX][hapmap]
rs304506	0.81[JPT][hapmap]
rs305374	0.94[CEU][hapmap];0.92[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs4934472	0.82[EUR][1000 genomes]
rs627127	0.94[CEU][hapmap];1.00[GIH][hapmap];0.95[MEX][hapmap];0.84[TSI][hapmap];0.92[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs627496	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs781501	0.89[EUR][1000 genomes]
rs812451	0.94[CEU][hapmap];0.86[AMR][1000 genomes];0.95[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
rs304508	IFIT5	cis	Artery Tibial	GTEx
rs304508	IFIT5	cis	parietal	SCAN
rs304508	IFIT5	cis	Esophagus Mucosa	GTEx
rs304508	IFIT5	cis	lymphoblastoid	seeQTL
rs304508	IFIT1	cis	cerebellum	SCAN
rs304508	IFIT5	cis	cerebellum	SCAN
rs304508	LIPA	cis	parietal	SCAN
rs304508	IFIT5	cis	Nerve Tibial	GTEx

Chromatin state (count:81 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr10:91129400-91138000	Weak transcription	HUES6 Cell Line	embryonic stem cell
2	chr10:91130600-91134800	Enhancers	Primary hematopoietic stem cells	blood
3	chr10:91130600-91135800	Enhancers	Liver	Liver
4	chr10:91130800-91135800	Enhancers	Fetal Heart	heart
5	chr10:91131000-91135400	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
6	chr10:91131200-91135200	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
7	chr10:91132400-91135000	Enhancers	Stomach Mucosa	stomach
8	chr10:91133000-91134600	Weak transcription	Fetal Brain Male	brain
9	chr10:91133000-91135000	Enhancers	Hela-S3	cervix
10	chr10:91133000-91135200	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
11	chr10:91133000-91135400	Enhancers	Fetal Adrenal Gland	Adrenal Gland
12	chr10:91133000-91135400	Enhancers	Fetal Intestine Small	intestine
13	chr10:91133200-91134600	Enhancers	Brain Angular Gyrus	brain
14	chr10:91133200-91134800	Enhancers	Fetal Stomach	stomach
15	chr10:91133200-91134800	Enhancers	HSMM	muscle
16	chr10:91133200-91135000	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
17	chr10:91133200-91135000	Enhancers	Muscle Satellite Cultured Cells	--
18	chr10:91133200-91135000	Enhancers	Colonic Mucosa	Colon
19	chr10:91133200-91135000	Enhancers	Duodenum Mucosa	Duodenum
20	chr10:91133200-91135000	Enhancers	Duodenum Smooth Muscle	Duodenum
21	chr10:91133200-91135200	Enhancers	Breast Myoepithelial Primary Cells	Breast
22	chr10:91133200-91135200	Enhancers	Cortex derived primary cultured neurospheres	brain
23	chr10:91133200-91135200	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
24	chr10:91133200-91135200	Enhancers	Pancreatic Islets	Pancreatic Islet
25	chr10:91133200-91135200	Enhancers	Fetal Muscle Leg	muscle
26	chr10:91133200-91135200	Enhancers	Sigmoid Colon	Sigmoid Colon
27	chr10:91133200-91135200	Enhancers	NHDF-Ad	bronchial
28	chr10:91133200-91135200	Enhancers	NHLF	lung
29	chr10:91133200-91135400	Enhancers	Foreskin Fibroblast Primary Cells skin02	Skin
30	chr10:91133200-91135400	Enhancers	Brain Dorsolateral Prefrontal Cortex	brain
31	chr10:91133200-91135600	Enhancers	Fetal Intestine Large	intestine
32	chr10:91133200-91135800	Enhancers	Brain Substantia Nigra	brain
33	chr10:91133400-91134800	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
34	chr10:91133400-91135000	Enhancers	Fetal Kidney	kidney
35	chr10:91133400-91135200	Enhancers	Skeletal Muscle Male	skeletal muscle
36	chr10:91133600-91134800	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
37	chr10:91133600-91135000	Flanking Active TSS	Rectal Smooth Muscle	rectum
38	chr10:91133600-91135000	Enhancers	Right Ventricle	heart
39	chr10:91133600-91135000	Enhancers	HMEC	breast
40	chr10:91133800-91134600	Flanking Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
41	chr10:91133800-91134600	Enhancers	Primary monocytes fromperipheralblood	blood
42	chr10:91133800-91134600	Flanking Active TSS	Colon Smooth Muscle	Colon
43	chr10:91133800-91134800	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
44	chr10:91133800-91134800	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
45	chr10:91133800-91134800	Flanking Active TSS	Brain Hippocampus Middle	brain
46	chr10:91133800-91134800	Enhancers	NHEK	skin
47	chr10:91133800-91135000	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
48	chr10:91133800-91135000	Enhancers	Psoas Muscle	Psoas
49	chr10:91133800-91135000	Flanking Active TSS	Rectal Mucosa Donor 31	rectum
50	chr10:91133800-91135000	Enhancers	Small Intestine	intestine

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