Variant report

Variant	rs2484046
Chromosome Location	chr10:91174919-91174920
allele	C/T
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	POLR2A	chr10:91173608-91175392	GM12878	blood:	n/a	n/a
2	CHD1	chr10:91174007-91175505	GM12878	blood:	n/a	chr10:91174671-91174681
3	MAX	chr10:91174177-91175556	GM12878	blood:	n/a	chr10:91175372-91175379 chr10:91175372-91175381 chr10:91175371-91175380
4	MAX	chr10:91174139-91175590	HepG2	liver:	n/a	chr10:91175372-91175379 chr10:91175372-91175381 chr10:91175371-91175380
5	ELF1	chr10:91174373-91175168	MCF-7	breast:	n/a	chr10:91174989-91175001 chr10:91174999-91175008 chr10:91174995-91175007
6	YY1	chr10:91174877-91175242	H1-hESC	embryonic stem cell:	n/a	chr10:91174993-91175007 chr10:91174994-91175008 chr10:91174982-91174996 chr10:91174993-91175002
7	SIN3A	chr10:91173739-91175457	H1-hESC	embryonic stem cell:	n/a	chr10:91175017-91175026 chr10:91174537-91174548 chr10:91175046-91175059 chr10:91175034-91175043 chr10:91174485-91174499
8	CTBP2	chr10:91174066-91175091	H1-hESC	embryonic stem cell:	n/a	n/a
9	GATA1	chr10:91173874-91175539	PBDE	blood:	n/a	chr10:91175287-91175297 chr10:91174172-91174181
10	MXI1	chr10:91174074-91175142	HepG2	liver:	n/a	n/a
11	TAF1	chr10:91173944-91175228	H1-hESC	embryonic stem cell:	n/a	n/a
12	POLR2A	chr10:91173633-91175510	MCF10A-Er-Src	breast:	n/a	n/a
13	TBL1XR1	chr10:91173990-91175486	GM12878	blood:	n/a	n/a
14	YY1	chr10:91174211-91175387	H1-hESC	embryonic stem cell:	n/a	chr10:91174993-91175007 chr10:91174994-91175008 chr10:91174982-91174996 chr10:91174376-91174387 chr10:91174800-91174811 chr10:91174993-91175002
15	USF2	chr10:91174870-91175545	GM12878	blood:	n/a	chr10:91174992-91175008
16	MAX	chr10:91173961-91175539	HepG2	liver:	n/a	chr10:91175372-91175379 chr10:91175372-91175381 chr10:91175371-91175380
17	SMC3	chr10:91173906-91174988	GM12878	blood:	n/a	n/a
18	RELA	chr10:91173972-91175518	GM15510	blood:	n/a	n/a
19	MAX	chr10:91174231-91175521	H1-hESC	embryonic stem cell:	n/a	chr10:91175372-91175379 chr10:91175372-91175381 chr10:91175371-91175380
20	REST	chr10:91174900-91175096	H1-hESC	embryonic stem cell:	n/a	chr10:91175046-91175059
21	POLR2A	chr10:91174283-91175238	MCF-7	breast:	n/a	n/a
22	YY1	chr10:91174120-91175497	GM12891	blood:	n/a	chr10:91174993-91175007 chr10:91174994-91175008 chr10:91174982-91174996 chr10:91174376-91174387 chr10:91174800-91174811 chr10:91174993-91175002
23	POLR2A	chr10:91174094-91175417	GM12878	blood:	n/a	n/a
24	KAP1	chr10:91173807-91175476	HEK293	kidney:	n/a	n/a
25	E2F6	chr10:91174252-91175612	H1-hESC	embryonic stem cell:	n/a	chr10:91174446-91174455 chr10:91175046-91175056 chr10:91174452-91174461
26	MAZ	chr10:91174864-91175504	GM12878	blood:	n/a	chr10:91175372-91175379 chr10:91175372-91175381 chr10:91175371-91175380
27	POLR2A	chr10:91174173-91174970	HepG2	liver:	n/a	n/a
28	TCF3	chr10:91174585-91175269	GM12878	blood:	n/a	chr10:91175046-91175059
29	POLR2A	chr10:91173805-91175564	GM12878	blood:	n/a	n/a
30	POLR2A	chr10:91174324-91175149	A549	lung:	n/a	n/a
31	RUNX3	chr10:91174004-91175532	GM12878	blood:	n/a	chr10:91175121-91175138
32	E2F6	chr10:91174778-91175305	A549	lung:	n/a	chr10:91175046-91175056
33	MAX	chr10:91174250-91175575	H1-hESC	embryonic stem cell:	n/a	chr10:91175372-91175379 chr10:91175372-91175381 chr10:91175371-91175380
34	MYC	chr10:91174794-91175256	MCF-7	breast:	n/a	n/a
35	CTCF	chr10:91174860-91175130	HMEC	breast:	n/a	n/a
36	YY1	chr10:91174277-91175536	GM12892	blood:	n/a	chr10:91174993-91175007 chr10:91174994-91175008 chr10:91174982-91174996 chr10:91174376-91174387 chr10:91174800-91174811 chr10:91174993-91175002
37	CTCF	chr10:91174800-91174950	HCM	heart:	n/a	n/a
38	TBP	chr10:91174094-91175428	H1-hESC	embryonic stem cell:	n/a	n/a
39	TAF1	chr10:91174119-91175031	A549	lung:	n/a	n/a
40	POLR2A	chr10:91173681-91175322	GM18951	blood:	n/a	n/a
41	STAT2	chr10:91173841-91174961	K562	blood:	n/a	chr10:91174316-91174331 chr10:91174304-91174315 chr10:91174319-91174330 chr10:91174278-91174289 chr10:91174356-91174371 chr10:91174275-91174290 chr10:91174301-91174316
42	RUNX3	chr10:91174018-91175541	GM12878	blood:	n/a	chr10:91175121-91175138
43	POLR2A	chr10:91173147-91175624	GM12891	blood:	n/a	n/a
44	MAX	chr10:91174879-91175248	HepG2	liver:	n/a	n/a
45	MAX	chr10:91174848-91175547	A549	lung:	n/a	chr10:91175372-91175379 chr10:91175372-91175381 chr10:91175371-91175380
46	FOXM1	chr10:91174137-91174924	GM12878	blood:	n/a	n/a
47	POLR2A	chr10:91174300-91175266	GM12878	blood:	n/a	n/a
48	MYC	chr10:91174881-91175322	MCF-7	breast:	n/a	n/a
49	POLR2A	chr10:91174057-91175361	HCT-116	colon:	n/a	n/a
50	CTCF	chr10:91174780-91174930	AG04449	skin:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr10:91009631..91012227-chr10:91174311..91176643,2	MCF-7	breast:
2	chr10:91157615..91160495-chr10:91173578..91176122,3	MCF-7	breast:
3	chr10:91174610..91176445-chr10:91403039..91405498,2	MCF-7	breast:

Variant related genes	Relation type
LIPA	TF binding region
ENSG00000185745	Chromatin interaction
ENSG00000232936	Chromatin interaction
ENSG00000249962	Chromatin interaction
ENSG00000152782	Chromatin interaction
ENSG00000107798	Chromatin interaction

Extended variants
information (count: 33 )
Associated
traits (count: 7 )

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

rs_ID	r²[population]
rs184236	0.95[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs188589	0.95[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs188591	0.82[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs2484047	0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs303171	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs303173	1.00[AFR][1000 genomes];0.95[AMR][1000 genomes];0.90[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs303209	1.00[AFR][1000 genomes];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs303210	0.94[AFR][1000 genomes];0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs303213	0.94[AFR][1000 genomes];0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs303215	0.94[AFR][1000 genomes];0.94[AMR][1000 genomes];0.94[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs303216	0.83[AFR][1000 genomes];0.94[AMR][1000 genomes];0.94[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs303218	0.84[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs304411	1.00[AFR][1000 genomes];0.94[AMR][1000 genomes];0.93[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs304412	0.87[AMR][1000 genomes]
rs304413	0.84[AMR][1000 genomes]
rs304434	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs304436	0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs304437	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs304441	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs304442	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs304447	0.94[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs304450	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs304492	0.94[AFR][1000 genomes];0.87[AMR][1000 genomes];0.93[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs304497	0.83[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs304500	0.86[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs304502	1.00[AFR][1000 genomes];0.84[AMR][1000 genomes];0.92[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs304503	1.00[AFR][1000 genomes];0.84[AMR][1000 genomes];0.93[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs304505	0.94[AFR][1000 genomes];0.86[AMR][1000 genomes];0.93[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs304506	0.94[AFR][1000 genomes];0.86[AMR][1000 genomes];0.93[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs781501	0.80[AMR][1000 genomes]

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:7)

SNP	Gene	Cis/trans	Tissue	Source
rs2484046	IFIT5	cis	Esophagus Muscularis	GTEx
rs2484046	IFIT5	cis	Thyroid	GTEx
rs2484046	IFIT5	cis	Esophagus Mucosa	GTEx
rs2484046	IFIT5	Cis_1M	lymphoblastoid	RTeQTL
rs2484046	IFIT5	cis	Artery Tibial	GTEx
rs2484046	IFIT5	cis	Nerve Tibial	GTEx
rs2484046	IFIT1	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:127 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr10:91173400-91175400	Active TSS	Fetal Lung	lung
2	chr10:91173400-91175600	Active TSS	H9 Derived Neuron Cultured Cells	ES cell derived
3	chr10:91173400-91175600	Active TSS	NHDF-Ad	bronchial
4	chr10:91173600-91175000	Bivalent/Poised TSS	H1 Cell Line	embryonic stem cell
5	chr10:91173600-91175000	Active TSS	Primary T cells fromperipheralblood	blood
6	chr10:91173600-91175000	Active TSS	Primary Natural Killer cells fromperipheralblood	blood
7	chr10:91173600-91175000	Active TSS	Fetal Thymus	thymus
8	chr10:91173600-91175200	Bivalent/Poised TSS	HUES6 Cell Line	embryonic stem cell
9	chr10:91173600-91175200	Active TSS	Fetal Muscle Leg	muscle
10	chr10:91173600-91175400	Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
11	chr10:91173600-91175400	Active TSS	Fetal Brain Female	brain
12	chr10:91173600-91175400	Active TSS	Fetal Muscle Trunk	muscle
13	chr10:91173600-91175600	Bivalent/Poised TSS	HUES64 Cell Line	embryonic stem cell
14	chr10:91173600-91175600	Bivalent/Poised TSS	iPS-20b Cell Line	embryonic stem cell
15	chr10:91173600-91175600	Active TSS	Foreskin Fibroblast Primary Cells skin02	Skin
16	chr10:91173600-91175600	Active TSS	Aorta	Aorta
17	chr10:91173600-91175600	Active TSS	Fetal Kidney	kidney
18	chr10:91173600-91176000	Active TSS	GM12878-XiMat	blood
19	chr10:91173600-91176200	Active TSS	Right Atrium	heart
20	chr10:91173600-91176200	Active TSS	HSMM	muscle
21	chr10:91173800-91175000	Active TSS	IMR90 fetal lung fibroblasts Cell Line	lung
22	chr10:91173800-91175000	Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Female	--
23	chr10:91173800-91175000	Active TSS	Dnd41	blood
24	chr10:91173800-91175200	Active TSS	ES-WA7 Cell Line	embryonic stem cell
25	chr10:91173800-91175200	Active TSS	Primary T helper memory cells from peripheral blood 2	blood
26	chr10:91173800-91175200	Active TSS	Fetal Intestine Small	intestine
27	chr10:91173800-91175200	Active TSS	Placenta Amnion	Placenta Amnion
28	chr10:91173800-91175400	Bivalent/Poised TSS	ES-I3 Cell Line	embryonic stem cell
29	chr10:91173800-91175400	Active TSS	H9 Cell Line	embryonic stem cell
30	chr10:91173800-91175400	Bivalent/Poised TSS	HUES48 Cell Line	embryonic stem cell
31	chr10:91173800-91175400	Active TSS	Foreskin Melanocyte Primary Cells skin03	Skin
32	chr10:91173800-91175400	Active TSS	Pancreatic Islets	Pancreatic Islet
33	chr10:91173800-91175400	Active TSS	Skeletal Muscle Male	skeletal muscle
34	chr10:91173800-91175400	Active TSS	Small Intestine	intestine
35	chr10:91173800-91175400	Active TSS	Thymus	Thymus
36	chr10:91173800-91175600	Active TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
37	chr10:91173800-91175600	Active TSS	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
38	chr10:91173800-91175600	Active TSS	Primary T cells effector/memory enriched fromperipheralblood	blood
39	chr10:91173800-91175600	Active TSS	Foreskin Melanocyte Primary Cells skin01	Skin
40	chr10:91173800-91175600	Flanking Active TSS	Primary mononuclear cells fromperipheralblood	Blood
41	chr10:91173800-91175600	Active TSS	Brain Dorsolateral Prefrontal Cortex	brain
42	chr10:91173800-91175600	Active TSS	Brain Substantia Nigra	brain
43	chr10:91173800-91175600	Active TSS	Colonic Mucosa	Colon
44	chr10:91173800-91175600	Active TSS	Colon Smooth Muscle	Colon
45	chr10:91173800-91175600	Active TSS	Left Ventricle	heart
46	chr10:91173800-91175600	Active TSS	Ovary	ovary
47	chr10:91173800-91175600	Active TSS	Psoas Muscle	Psoas
48	chr10:91173800-91175800	Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
49	chr10:91173800-91175800	Active TSS	Right Ventricle	heart
50	chr10:91173800-91175800	Active TSS	NHLF	lung

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