Variant report

Variant	rs491082
Chromosome Location	chr5:89822992-89822993
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:4)
CpG islands
(count:61)
Chromatin interactive
region (count:11)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:4 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	POLR2A	chr5:89821851-89826472	K562	blood:	n/a	n/a
2	POLR2A	chr5:89821783-89823769	GM12878	blood:	n/a	n/a
3	POLR2A	chr5:89822095-89826185	IMR90	lung:	n/a	n/a
4	POLR2A	chr5:89822834-89823305	MCF10A-Er-Src	breast:	n/a	n/a

(count:61 , 50 per page) page: 1 2

No.	Chromosome Location	Cell Line	Cell type	Cell Stage
1	chr5:89822945-89822995	SK-N-SH	brain:	n/a
2	chr5:89822945-89822995	MCF10A-Er-Src	breast:	n/a
3	chr5:89822945-89822995	HEK293	kidney:	embryo
4	chr5:89822945-89822995	AoSMC	blood vessel:	n/a
5	chr5:89822945-89822995	H1-hESC	embryonic stem cell:	embryo
6	chr5:89822945-89822995	HCPEpiC	choroid plexus:	n/a
7	chr5:89822945-89822995	GM19239	blood:	n/a
8	chr5:89822945-89822995	GM06990	blood:	n/a
9	chr5:89822945-89822995	HCT-116	colon:	n/a
10	chr5:89822945-89822995	HNPCEpiC	eye:	n/a
11	chr5:89822945-89822995	RPTEC	kidney:	n/a
12	chr5:89822945-89822995	HUVEC	blood vessel:	n/a
13	chr5:89822945-89822995	BE2_C	brain:	n/a
14	chr5:89822945-89822995	HepG2	liver:	n/a
15	chr5:89822945-89822995	HPAEpiC	pulmonary alveolar:	n/a
16	chr5:89822945-89822995	SK-N-MC	brain:	n/a
17	chr5:89822945-89822995	ProgFib	skin:	n/a
18	chr5:89822945-89822995	NT2-D1	testis:	n/a
19	chr5:89822945-89822995	HMEC	breast:	n/a
20	chr5:89822945-89822995	BJ	skin:	n/a
21	chr5:89822945-89822995	ovcar-3	ovarian:	n/a
22	chr5:89822945-89822995	NB4	blood:	n/a
23	chr5:89822945-89822995	HAEpiC	amniotic membrane:	n/a
24	chr5:89822945-89822995	NH-A	brain:	n/a
25	chr5:89822945-89822995	AG04450	lung:	fetal
26	chr5:89822945-89822995	MCF-7	breast:	n/a
27	chr5:89822945-89822995	HEEpiC	esophagus:	n/a
28	chr5:89822945-89822995	Hela-S3	cervix:	n/a
29	chr5:89822945-89822995	AG04449	skin:	fetal
30	chr5:89822945-89822995	HRE	kidney:	n/a
31	chr5:89822945-89822995	CMK	blood:	n/a
32	chr5:89822945-89822995	Hepatocyte	liver:	n/a
33	chr5:89822945-89822995	GM12878	blood:	n/a
34	chr5:89822945-89822995	AG09319	gingival:	n/a
35	chr5:89822945-89822995	HL-60	blood:	n/a
36	chr5:89822945-89822995	Caco-2	colon:	n/a
37	chr5:89822945-89822995	HRPEpiC	eye:	n/a
38	chr5:89822945-89822995	PANC-1	pancreas:	n/a
39	chr5:89822945-89822995	HRCEpiC	kidney:	n/a
40	chr5:89822945-89822995	Jurkat	blood:	n/a
41	chr5:89822945-89822995	NHBE	bronchial:	n/a
42	chr5:89822945-89822995	AG09309	skin:	n/a
43	chr5:89822945-89822995	HIPEpiC	eye:	n/a
44	chr5:89822945-89822995	U87	brain:	n/a
45	chr5:89822945-89822995	T-47D	breast:	n/a
46	chr5:89822945-89822995	PFSK-1	brain:	n/a
47	chr5:89822945-89822995	SAEC	small airway:	n/a
48	chr5:89822945-89822995	PrEC	prostate:	n/a
49	chr5:89822945-89822995	GM12891	blood:	n/a
50	chr5:89822945-89822995	LNCaP	prostate:	n/a

(count:11 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr5:89777835..89781277-chr5:89821033..89823702,3	K562	blood:
2	chr5:89822248..89824854-chr5:89913620..89915921,2	K562	blood:
3	chr5:89821102..89822996-chr5:89857418..89859041,2	K562	blood:
4	chr5:89822684..89827061-chr5:89851623..89857043,7	MCF-7	breast:
5	chr5:89821999..89823611-chr5:89823888..89826662,2	MCF-7	breast:
6	chr5:89768855..89773751-chr5:89822671..89829297,12	K562	blood:
7	chr5:89768691..89773005-chr5:89822332..89827140,9	MCF-7	breast:
8	chr5:89703407..89707223-chr5:89822965..89826833,10	K562	blood:
9	chr5:89822535..89824744-chr5:89842428..89844021,2	K562	blood:
10	chr5:89821919..89824561-chr5:89840686..89844146,3	MCF-7	breast:
11	chr5:89818873..89823263-chr5:89823614..89827101,4	MCF-7	breast:

No data

Variant related genes	Relation type
GPR98	TF binding region
GPR98	CpG island
ENSG00000176018	Chromatin interaction
ENSG00000164199	Chromatin interaction
ENSG00000113356	Chromatin interaction
ENSG00000153140	Chromatin interaction
ENSG00000255647	Chromatin interaction
ENSG00000176055	Chromatin interaction

Extended variants
information (count: 34 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:27)

rs_ID	r²[population]
rs10069050	0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs154568	0.89[EUR][1000 genomes]
rs154569	0.89[EUR][1000 genomes]
rs154570	0.90[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs154572	0.84[EUR][1000 genomes]
rs154573	0.85[EUR][1000 genomes]
rs1553545	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs171790	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs250377	0.82[AMR][1000 genomes];0.95[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs257850	0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs257851	0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2656957	0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs27201	0.91[EUR][1000 genomes]
rs37238	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs37239	0.83[EUR][1000 genomes]
rs37240	0.83[EUR][1000 genomes]
rs42467	0.81[AMR][1000 genomes];0.91[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs43149	0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs511393	0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs526806	0.85[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs556894	0.92[AMR][1000 genomes];0.99[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs59159252	0.84[ASN][1000 genomes]
rs594990	0.82[AMR][1000 genomes];0.95[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs599432	0.87[EUR][1000 genomes]
rs679568	0.96[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs6884154	0.81[EUR][1000 genomes]
rs810974	0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:7 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1021142	chr5:89102893-89897826	Active TSS Weak transcription Enhancers Bivalent Enhancer Strong transcription Flanking Active TSS Genic enhancers Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	55 gene(s)	inside rSNPs	diseases
2	nsv537804	chr5:89102893-89897826	Enhancers Weak transcription Active TSS Flanking Active TSS Strong transcription Genic enhancers ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	55 gene(s)	inside rSNPs	diseases
3	nsv917025	chr5:89208994-89855436	Enhancers Active TSS Strong transcription Bivalent Enhancer Weak transcription Flanking Bivalent TSS/Enh Flanking Active TSS ZNF genes & repeats Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	52 gene(s)	inside rSNPs	diseases
4	nsv432750	chr5:89410113-90137144	Enhancers Weak transcription Strong transcription Active TSS Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Genic enhancers Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	50 gene(s)	inside rSNPs	diseases
5	nsv432751	chr5:89457044-90090444	Weak transcription Enhancers Active TSS Flanking Bivalent TSS/Enh Strong transcription Flanking Active TSS ZNF genes & repeats Bivalent Enhancer Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	50 gene(s)	inside rSNPs	diseases
6	nsv529544	chr5:89523963-90412409	Weak transcription Enhancers Active TSS Strong transcription Flanking Bivalent TSS/Enh Flanking Active TSS ZNF genes & repeats Genic enhancers Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	58 gene(s)	inside rSNPs	diseases
7	nsv882365	chr5:89770768-89882618	Flanking Active TSS Genic enhancers Enhancers Weak transcription Strong transcription Flanking Bivalent TSS/Enh Active TSS Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region miRNA target site	13 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs491082	LYSMD3	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:124 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:89773800-89824400	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
2	chr5:89793800-89823400	Weak transcription	Hela-S3	cervix
3	chr5:89797600-89824200	Weak transcription	Brain Angular Gyrus	brain
4	chr5:89802600-89824600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
5	chr5:89805600-89823200	Weak transcription	Brain Inferior Temporal Lobe	brain
6	chr5:89809000-89824000	Weak transcription	Right Ventricle	heart
7	chr5:89809000-89824400	Weak transcription	Psoas Muscle	Psoas
8	chr5:89809200-89824600	Weak transcription	Spleen	Spleen
9	chr5:89810600-89824400	Weak transcription	Lung	lung
10	chr5:89810800-89824400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
11	chr5:89810800-89824400	Weak transcription	Esophagus	oesophagus
12	chr5:89811000-89824000	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
13	chr5:89811000-89824400	Weak transcription	Pancreas	Pancrea
14	chr5:89813000-89823400	Weak transcription	Placenta Amnion	Placenta Amnion
15	chr5:89813400-89824200	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
16	chr5:89813400-89824400	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
17	chr5:89813600-89823400	Weak transcription	Brain Cingulate Gyrus	brain
18	chr5:89814800-89824000	Weak transcription	HSMMtube	muscle
19	chr5:89814800-89824200	Weak transcription	Brain Germinal Matrix	brain
20	chr5:89815000-89823800	Weak transcription	ES-I3 Cell Line	embryonic stem cell
21	chr5:89815000-89824400	Weak transcription	Gastric	stomach
22	chr5:89815200-89823000	Weak transcription	A549	lung
23	chr5:89815200-89823800	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
24	chr5:89815200-89824400	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
25	chr5:89815200-89824400	Weak transcription	H9 Cell Line	embryonic stem cell
26	chr5:89815200-89824400	Weak transcription	Brain Substantia Nigra	brain
27	chr5:89816400-89824200	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
28	chr5:89816600-89824000	Weak transcription	Aorta	Aorta
29	chr5:89816600-89824200	Weak transcription	Fetal Brain Male	brain
30	chr5:89816600-89824200	Weak transcription	Ovary	ovary
31	chr5:89817400-89824000	Weak transcription	Fetal Kidney	kidney
32	chr5:89817600-89824200	Weak transcription	Fetal Muscle Leg	muscle
33	chr5:89818000-89824200	Weak transcription	Brain Hippocampus Middle	brain
34	chr5:89818200-89823200	Weak transcription	NHLF	lung
35	chr5:89818200-89824200	Weak transcription	Fetal Muscle Trunk	muscle
36	chr5:89818200-89824200	Weak transcription	Fetal Stomach	stomach
37	chr5:89818200-89824400	Weak transcription	Left Ventricle	heart
38	chr5:89818600-89823400	Weak transcription	Skeletal Muscle Male	skeletal muscle
39	chr5:89818600-89824000	Weak transcription	Cortex derived primary cultured neurospheres	brain
40	chr5:89819000-89823400	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
41	chr5:89820000-89823600	Weak transcription	Primary hematopoietic stem cells	blood
42	chr5:89820000-89824000	Weak transcription	Colonic Mucosa	Colon
43	chr5:89820000-89824200	Weak transcription	Stomach Smooth Muscle	stomach
44	chr5:89820400-89824400	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
45	chr5:89820600-89823200	Weak transcription	NH-A	brain
46	chr5:89820800-89824600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
47	chr5:89821000-89823200	Weak transcription	HUES64 Cell Line	embryonic stem cell
48	chr5:89821000-89823600	Weak transcription	Duodenum Smooth Muscle	Duodenum
49	chr5:89821000-89824200	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
50	chr5:89821200-89823000	Weak transcription	Primary neutrophils fromperipheralblood	blood

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