Variant report

Variant	rs304450
Chromosome Location	chr10:91175412-91175413
allele	A/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	CHD1	chr10:91174007-91175505	GM12878	blood:	n/a	chr10:91174671-91174681
2	MAX	chr10:91174177-91175556	GM12878	blood:	n/a	chr10:91175372-91175379 chr10:91175372-91175381 chr10:91175371-91175380
3	MAX	chr10:91174139-91175590	HepG2	liver:	n/a	chr10:91175372-91175379 chr10:91175372-91175381 chr10:91175371-91175380
4	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
5	GATA1	chr10:91173874-91175539	PBDE	blood:	n/a	chr10:91175287-91175297 chr10:91174172-91174181
6	POLR2A	chr10:91173633-91175510	MCF10A-Er-Src	breast:	n/a	n/a
7	TBP	chr10:91175121-91175573	GM12878	blood:	n/a	n/a
8	TBL1XR1	chr10:91173990-91175486	GM12878	blood:	n/a	n/a
9	USF2	chr10:91174870-91175545	GM12878	blood:	n/a	chr10:91174992-91175008
10	MAX	chr10:91173961-91175539	HepG2	liver:	n/a	chr10:91175372-91175379 chr10:91175372-91175381 chr10:91175371-91175380
11	RELA	chr10:91173972-91175518	GM15510	blood:	n/a	n/a
12	MAX	chr10:91174231-91175521	H1-hESC	embryonic stem cell:	n/a	chr10:91175372-91175379 chr10:91175372-91175381 chr10:91175371-91175380
13	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
14	POLR2A	chr10:91174094-91175417	GM12878	blood:	n/a	n/a
15	KAP1	chr10:91173807-91175476	HEK293	kidney:	n/a	n/a
16	E2F6	chr10:91174252-91175612	H1-hESC	embryonic stem cell:	n/a	chr10:91174446-91174455 chr10:91175046-91175056 chr10:91174452-91174461
17	MAZ	chr10:91174864-91175504	GM12878	blood:	n/a	chr10:91175372-91175379 chr10:91175372-91175381 chr10:91175371-91175380
18	POLR2A	chr10:91173805-91175564	GM12878	blood:	n/a	n/a
19	RUNX3	chr10:91174004-91175532	GM12878	blood:	n/a	chr10:91175121-91175138
20	MAX	chr10:91174250-91175575	H1-hESC	embryonic stem cell:	n/a	chr10:91175372-91175379 chr10:91175372-91175381 chr10:91175371-91175380
21	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
22	EBF1	chr10:91175131-91175525	GM12878	blood:	n/a	chr10:91175345-91175356
23	TBP	chr10:91174094-91175428	H1-hESC	embryonic stem cell:	n/a	n/a
24	RUNX3	chr10:91174018-91175541	GM12878	blood:	n/a	chr10:91175121-91175138
25	POLR2A	chr10:91173147-91175624	GM12891	blood:	n/a	n/a
26	MAX	chr10:91174848-91175547	A549	lung:	n/a	chr10:91175372-91175379 chr10:91175372-91175381 chr10:91175371-91175380
27	GATA3	chr10:91175099-91175419	SH-SY5Y	brain:	n/a	chr10:91175287-91175297
28	USF1	chr10:91175246-91175524	H1-hESC	embryonic stem cell:	n/a	n/a
29	USF1	chr10:91175202-91175499	A549	lung:	n/a	n/a
30	SIN3A	chr10:91174043-91175508	GM12878	blood:	n/a	chr10:91175017-91175026 chr10:91174537-91174548 chr10:91175046-91175059 chr10:91175034-91175043 chr10:91174485-91174499
31	MAX	chr10:91174219-91175517	MCF-7	breast:	n/a	chr10:91175372-91175379 chr10:91175372-91175381 chr10:91175371-91175380
32	POLR2A	chr10:91174241-91175481	IMR90	lung:	n/a	n/a
33	POLR2A	chr10:91173811-91175472	MCF10A-Er-Src	breast:	n/a	n/a
34	POLR2A	chr10:91174999-91175479	SK-N-SH	brain:	n/a	n/a
35	GATA3	chr10:91174878-91175452	T-47D	breast:	n/a	chr10:91175287-91175297
36	SETDB1	chr10:91175085-91175581	U2OS	brain:	n/a	n/a
37	E2F6	chr10:91174151-91175632	A549	lung:	n/a	chr10:91174446-91174455 chr10:91175046-91175056 chr10:91174452-91174461
38	MYC	chr10:91175196-91175544	MCF10A-Er-Src	breast:	n/a	chr10:91175372-91175379 chr10:91175372-91175381 chr10:91175371-91175380
39	ZNF263	chr10:91173906-91175558	HEK293-T-REx	kidney:	n/a	chr10:91174826-91174835 chr10:91174827-91174848
40	MXI1	chr10:91174005-91175561	GM12878	blood:	n/a	chr10:91175372-91175381
41	MAX	chr10:91174104-91175619	SK-N-SH	brain:	n/a	chr10:91175372-91175379 chr10:91175372-91175381 chr10:91175371-91175380
42	STAT5A	chr10:91175025-91175425	GM12878	blood:	n/a	chr10:91175208-91175220
43	TCF12	chr10:91174099-91175533	A549	lung:	n/a	chr10:91174280-91174287 chr10:91175049-91175059
44	MXI1	chr10:91173550-91175625	SK-N-SH	brain:	n/a	chr10:91175372-91175381
45	MAX	chr10:91174694-91175448	MCF-7	breast:	n/a	chr10:91175372-91175379 chr10:91175372-91175381 chr10:91175371-91175380
46	GATA3	chr10:91174787-91175456	MCF-7	breast:	n/a	chr10:91175287-91175297
47	SIN3AK20	chr10:91173933-91175544	MCF-7	breast:	n/a	n/a
48	GATA3	chr10:91173879-91175437	T-47D	breast:	n/a	chr10:91175287-91175297 chr10:91174172-91174181
49	MAX	chr10:91174210-91175569	SK-N-SH	brain:	n/a	chr10:91175372-91175379 chr10:91175372-91175381 chr10:91175371-91175380
50	YY1	chr10:91174063-91175486	GM12878	blood:	n/a	chr10:91174993-91175007 chr10:91174994-91175008 chr10:91174982-91174996 chr10:91174376-91174387 chr10:91174800-91174811 chr10:91174993-91175002

No.	Chromosome Location	Cell Line	Cell type	Cell Stage
1	chr10:91175366-91175416	AG10803	skin:	n/a
2	chr10:91175366-91175416	AoSMC	blood vessel:	n/a
3	chr10:91175366-91175416	HAEpiC	amniotic membrane:	n/a
4	chr10:91175366-91175416	HCF	heart:	n/a
5	chr10:91175366-91175416	HPAEpiC	pulmonary alveolar:	n/a
6	chr10:91175366-91175416	NHDF-neo	bronchial:	n/a
7	chr10:91175366-91175416	GM12878	blood:	n/a
8	chr10:91175366-91175416	HEEpiC	esophagus:	n/a
9	chr10:91175366-91175416	NB4	blood:	n/a
10	chr10:91175366-91175416	AG09319	gingival:	n/a
11	chr10:91175366-91175416	CMK	blood:	n/a
12	chr10:91175366-91175416	Caco-2	colon:	n/a
13	chr10:91175366-91175416	MCF10A-Er-Src	breast:	n/a
14	chr10:91175366-91175416	SK-N-MC	brain:	n/a
15	chr10:91175366-91175416	HCM	heart:	n/a
16	chr10:91175366-91175416	A549	lung:	n/a
17	chr10:91175366-91175416	IMR90	lung:	fetal
18	chr10:91175366-91175416	HMEC	breast:	n/a
19	chr10:91175366-91175416	BE2_C	brain:	n/a
20	chr10:91175366-91175416	GM06990	blood:	n/a
21	chr10:91175366-91175416	T-47D	breast:	n/a
22	chr10:91175366-91175416	HNPCEpiC	eye:	n/a
23	chr10:91175366-91175416	NT2-D1	testis:	n/a
24	chr10:91175366-91175416	HepG2	liver:	n/a
25	chr10:91175366-91175416	U87	brain:	n/a
26	chr10:91175366-91175416	GM19239	blood:	n/a
27	chr10:91175366-91175416	HRE	kidney:	n/a
28	chr10:91175366-91175416	SK-N-SH_RA	brain:	n/a
29	chr10:91175366-91175416	ProgFib	skin:	n/a
30	chr10:91175366-91175416	PFSK-1	brain:	n/a
31	chr10:91175366-91175416	AG04450	lung:	fetal
32	chr10:91175366-91175416	MCF-7	breast:	n/a
33	chr10:91175366-91175416	HCPEpiC	choroid plexus:	n/a
34	chr10:91175366-91175416	HUVEC	blood vessel:	n/a
35	chr10:91175366-91175416	RPTEC	kidney:	n/a
36	chr10:91175366-91175416	HL-60	blood:	n/a
37	chr10:91175366-91175416	NH-A	brain:	n/a
38	chr10:91175366-91175416	HCT-116	colon:	n/a
39	chr10:91175366-91175416	GM12892	blood:	n/a
40	chr10:91175366-91175416	PrEC	prostate:	n/a
41	chr10:91175366-91175416	SK-N-SH	brain:	n/a
42	chr10:91175366-91175416	LNCaP	prostate:	n/a
43	chr10:91175366-91175416	HIPEpiC	eye:	n/a
44	chr10:91175366-91175416	ovcar-3	ovarian:	n/a
45	chr10:91175366-91175416	GM12891	blood:	n/a
46	chr10:91175366-91175416	PANC-1	pancreas:	n/a
47	chr10:91175366-91175416	HEK293	kidney:	embryo
48	chr10:91175366-91175416	Hepatocyte	liver:	n/a
49	chr10:91175366-91175416	Jurkat	blood:	n/a
50	chr10:91175366-91175416	K562	blood:	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
LIPA	CpG island
ENSG00000107798	Chromatin interaction
ENSG00000152782	Chromatin interaction
ENSG00000185745	Chromatin interaction
ENSG00000249962	Chromatin interaction
ENSG00000232936	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];0.90[ASN][1000 genomes]
rs188589	0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs188591	0.82[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs2484046	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2484047	0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs303171	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs303173	1.00[AFR][1000 genomes];0.95[AMR][1000 genomes];0.90[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs303209	1.00[AFR][1000 genomes];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs303210	0.94[AFR][1000 genomes];0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs303213	0.94[AFR][1000 genomes];0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs303215	0.94[AFR][1000 genomes];0.94[AMR][1000 genomes];0.94[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs303216	0.83[AFR][1000 genomes];0.94[AMR][1000 genomes];0.94[EUR][1000 genomes];0.90[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];0.86[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];0.96[ASN][1000 genomes]
rs304436	0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs304437	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs304441	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs304442	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs304447	0.94[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs304492	0.94[AFR][1000 genomes];0.87[AMR][1000 genomes];0.93[EUR][1000 genomes];0.87[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];0.88[ASN][1000 genomes]
rs304503	1.00[AFR][1000 genomes];0.84[AMR][1000 genomes];0.93[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs304505	0.94[AFR][1000 genomes];0.86[AMR][1000 genomes];0.93[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs304506	0.94[AFR][1000 genomes];0.86[AMR][1000 genomes];0.93[EUR][1000 genomes];0.87[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
rs304450	IFIT5	cis	Esophagus Muscularis	GTEx
rs304450	IFIT5	Cis_1M	lymphoblastoid	RTeQTL
rs304450	IFIT5	cis	Thyroid	GTEx
rs304450	IFIT5	cis	Nerve Tibial	GTEx
rs304450	IFIT5	cis	Esophagus Mucosa	GTEx
rs304450	IFIT1	Cis_1M	lymphoblastoid	RTeQTL
rs304450	IFIT5	cis	Artery Tibial	GTEx

Chromatin state (count:119 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr10:91173400-91175600	Active TSS	H9 Derived Neuron Cultured Cells	ES cell derived
2	chr10:91173400-91175600	Active TSS	NHDF-Ad	bronchial
3	chr10:91173600-91175600	Bivalent/Poised TSS	HUES64 Cell Line	embryonic stem cell
4	chr10:91173600-91175600	Bivalent/Poised TSS	iPS-20b Cell Line	embryonic stem cell
5	chr10:91173600-91175600	Active TSS	Foreskin Fibroblast Primary Cells skin02	Skin
6	chr10:91173600-91175600	Active TSS	Aorta	Aorta
7	chr10:91173600-91175600	Active TSS	Fetal Kidney	kidney
8	chr10:91173600-91176000	Active TSS	GM12878-XiMat	blood
9	chr10:91173600-91176200	Active TSS	Right Atrium	heart
10	chr10:91173600-91176200	Active TSS	HSMM	muscle
11	chr10:91173800-91175600	Active TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
12	chr10:91173800-91175600	Active TSS	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
13	chr10:91173800-91175600	Active TSS	Primary T cells effector/memory enriched fromperipheralblood	blood
14	chr10:91173800-91175600	Active TSS	Foreskin Melanocyte Primary Cells skin01	Skin
15	chr10:91173800-91175600	Flanking Active TSS	Primary mononuclear cells fromperipheralblood	Blood
16	chr10:91173800-91175600	Active TSS	Brain Dorsolateral Prefrontal Cortex	brain
17	chr10:91173800-91175600	Active TSS	Brain Substantia Nigra	brain
18	chr10:91173800-91175600	Active TSS	Colonic Mucosa	Colon
19	chr10:91173800-91175600	Active TSS	Colon Smooth Muscle	Colon
20	chr10:91173800-91175600	Active TSS	Left Ventricle	heart
21	chr10:91173800-91175600	Active TSS	Ovary	ovary
22	chr10:91173800-91175600	Active TSS	Psoas Muscle	Psoas
23	chr10:91173800-91175800	Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
24	chr10:91173800-91175800	Active TSS	Right Ventricle	heart
25	chr10:91173800-91175800	Active TSS	NHLF	lung
26	chr10:91173800-91176200	Active TSS	Duodenum Smooth Muscle	Duodenum
27	chr10:91174000-91175600	Active TSS	Breast Myoepithelial Primary Cells	Breast
28	chr10:91174000-91175600	Active TSS	Brain Angular Gyrus	brain
29	chr10:91174000-91175600	Active TSS	Brain Inferior Temporal Lobe	brain
30	chr10:91174000-91175600	Active TSS	Lung	lung
31	chr10:91174000-91175600	Active TSS	Rectal Smooth Muscle	rectum
32	chr10:91174000-91175800	Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
33	chr10:91174000-91175800	Active TSS	Muscle Satellite Cultured Cells	--
34	chr10:91174000-91176000	Active TSS	Brain Anterior Caudate	brain
35	chr10:91174000-91176000	Active TSS	Brain Cingulate Gyrus	brain
36	chr10:91174000-91176200	Active TSS	Stomach Smooth Muscle	stomach
37	chr10:91174600-91175600	Bivalent/Poised TSS	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
38	chr10:91174600-91175600	Flanking Active TSS	Skeletal Muscle Female	skeletal muscle
39	chr10:91174600-91175800	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
40	chr10:91174600-91177000	Weak transcription	K562	blood
41	chr10:91174800-91175600	Bivalent/Poised TSS	iPS-18 Cell Line	embryonic stem cell
42	chr10:91174800-91175600	Flanking Active TSS	Adipose Nuclei	Adipose
43	chr10:91174800-91175600	Flanking Active TSS	HMEC	breast
44	chr10:91174800-91175800	Flanking Active TSS	Primary B cells from cord blood	blood
45	chr10:91175000-91175600	Flanking Active TSS	IMR90 fetal lung fibroblasts Cell Line	lung
46	chr10:91175000-91175600	Flanking Active TSS	Primary monocytes fromperipheralblood	blood
47	chr10:91175000-91175600	Flanking Active TSS	Primary Natural Killer cells fromperipheralblood	blood
48	chr10:91175000-91175600	Flanking Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
49	chr10:91175000-91175600	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Female	--
50	chr10:91175000-91175600	Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links