Variant report

Variant	rs1513830
Chromosome Location	chr2:20252014-20252015
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	PBX3	chr2:20251044-20252225	A549	lung:	n/a	chr2:20251483-20251492
2	YY1	chr2:20251021-20252049	K562	blood:	n/a	chr2:20251849-20251858 chr2:20251846-20251860
3	RCOR1	chr2:20251504-20252097	K562	blood:	n/a	n/a
4	POLR2A	chr2:20251145-20252201	HUVEC	blood vessel:	n/a	n/a
5	YY1	chr2:20251126-20252395	SK-N-SH	brain:	n/a	chr2:20251849-20251858 chr2:20251846-20251860
6	SP1	chr2:20251147-20252051	GM12878	blood:	n/a	chr2:20251845-20251859 chr2:20251849-20251859 chr2:20251481-20251502 chr2:20251848-20251860 chr2:20251850-20251859 chr2:20251849-20251859 chr2:20251848-20251860 chr2:20251850-20251859 chr2:20251391-20251401 chr2:20251849-20251858
7	CEBPB	chr2:20251554-20252136	MCF-7	breast:	n/a	n/a
8	POLR2A	chr2:20251041-20252121	HL-60	blood:	n/a	n/a
9	POLR2A	chr2:20251056-20252093	GM12891	blood:	n/a	n/a
10	CEBPB	chr2:20251336-20252051	HepG2	liver:	n/a	n/a
11	TAF1	chr2:20250346-20252400	H1-hESC	embryonic stem cell:	n/a	n/a
12	CHD2	chr2:20251151-20252072	Hela-S3	cervix:	n/a	n/a
13	MAX	chr2:20251080-20252413	SK-N-SH	brain:	n/a	n/a
14	NFYA	chr2:20251190-20252076	Hela-S3	cervix:	n/a	chr2:20251513-20251531
15	POLR2A	chr2:20251120-20252378	HepG2	liver:	n/a	n/a
16	NRF1	chr2:20251258-20252025	K562	blood:	n/a	chr2:20251849-20251858 chr2:20251426-20251437 chr2:20251428-20251437 chr2:20251426-20251437 chr2:20251423-20251437 chr2:20251426-20251440
17	POLR2A	chr2:20251097-20252132	GM18505	blood:	n/a	n/a
18	STAT1	chr2:20251163-20252033	GM12878	blood:	n/a	n/a
19	BHLHE40	chr2:20251197-20252116	A549	lung:	n/a	chr2:20251401-20251417
20	RELA	chr2:20251191-20252101	GM19099	blood:	n/a	n/a
21	REST	chr2:20251595-20252077	PFSK-1	brain:	n/a	chr2:20251846-20251859 chr2:20251871-20251880
22	MYC	chr2:20251153-20252081	K562	blood:	n/a	n/a
23	TAF1	chr2:20251148-20252037	MCF-7	breast:	n/a	n/a
24	PML	chr2:20250934-20252246	GM12878	blood:	n/a	n/a
25	JUND	chr2:20251198-20252059	A549	lung:	n/a	chr2:20251519-20251528
26	CEBPB	chr2:20251632-20252083	H1-hESC	embryonic stem cell:	n/a	n/a
27	POLR2A	chr2:20251118-20252137	GM15510	blood:	n/a	n/a
28	NFIC	chr2:20251405-20252074	GM12878	blood:	n/a	n/a
29	POLR2A	chr2:20251102-20252058	HepG2	liver:	n/a	n/a
30	CEBPD	chr2:20251212-20252051	K562	blood:	n/a	n/a
31	MXI1	chr2:20249818-20253177	Hela-S3	cervix:	n/a	n/a
32	IRF1	chr2:20251222-20252033	K562	blood:	n/a	chr2:20251848-20251862
33	MAX	chr2:20251064-20252042	K562	blood:	n/a	n/a
34	TBL1XR1	chr2:20251207-20252069	K562	blood:	n/a	n/a
35	POLR2A	chr2:20251471-20252037	H1-hESC	embryonic stem cell:	n/a	n/a
36	REST	chr2:20249044-20253112	H1-neurons	neurons:	n/a	chr2:20250974-20250987 chr2:20251116-20251129 chr2:20251113-20251126 chr2:20252708-20252728 chr2:20251846-20251859 chr2:20251871-20251880
37	HNF4G	chr2:20251116-20252059	HepG2	liver:	n/a	chr2:20251814-20251826 chr2:20251809-20251831 chr2:20251813-20251826
38	EP300	chr2:20251344-20252171	A549	lung:	n/a	chr2:20251394-20251410
39	EGR1	chr2:20251047-20253113	HCT-116	colon:	n/a	chr2:20252760-20252771 chr2:20252758-20252773 chr2:20252760-20252770 chr2:20251427-20251436 chr2:20252760-20252769 chr2:20252758-20252772 chr2:20252759-20252772 chr2:20251844-20251857 chr2:20251393-20251406 chr2:20251849-20251859 chr2:20252760-20252770 chr2:20252759-20252772 chr2:20252759-20252772 chr2:20252756-20252770 chr2:20252759-20252772 chr2:20252760-20252771 chr2:20251390-20251404
40	YY1	chr2:20251586-20252060	GM12892	blood:	n/a	chr2:20251849-20251858 chr2:20251846-20251860
41	POLR2A	chr2:20250996-20252117	A549	lung:	n/a	n/a
42	POLR2A	chr2:20251056-20252058	GM12878	blood:	n/a	n/a
43	CEBPB	chr2:20251503-20252417	A549	lung:	n/a	n/a
44	STAT3	chr2:20251358-20253018	MCF10A-Er-Src	breast:	n/a	chr2:20252736-20252747
45	POLR2A	chr2:20251173-20252270	H1-hESC	embryonic stem cell:	n/a	n/a
46	TAF1	chr2:20251083-20252096	MCF-7	breast:	n/a	n/a
47	SIN3AK20	chr2:20251050-20252151	SK-N-SH	brain:	n/a	n/a
48	POLR2A	chr2:20251058-20252044	A549	lung:	n/a	n/a
49	CTCF	chr2:20251920-20252070	HCPEpiC	choroid plexus:	n/a	n/a
50	TAF1	chr2:20251151-20252100	Hela-S3	cervix:	n/a	n/a

No.	Chromosome Location	Cell Line	Cell type	Cell Stage
1	chr2:20251973-20252023	PFSK-1	brain:	n/a
2	chr2:20251973-20252023	HPAEpiC	pulmonary alveolar:	n/a
3	chr2:20251973-20252023	H1-hESC	embryonic stem cell:	embryo
4	chr2:20251993-20252043	NT2-D1	testis:	n/a
5	chr2:20251993-20252043	T-47D	breast:	n/a
6	chr2:20251973-20252023	AG10803	skin:	n/a
7	chr2:20251993-20252043	ECC-1	luminal epithelium:	n/a
8	chr2:20251993-20252043	SK-N-MC	brain:	n/a
9	chr2:20251973-20252023	HL-60	blood:	n/a
10	chr2:20251993-20252043	HEEpiC	esophagus:	n/a
11	chr2:20251993-20252043	HCF	heart:	n/a
12	chr2:20251973-20252023	T-47D	breast:	n/a
13	chr2:20251973-20252023	CMK	blood:	n/a
14	chr2:20251993-20252043	ProgFib	skin:	n/a
15	chr2:20251993-20252043	RPTEC	kidney:	n/a
16	chr2:20251993-20252043	HMEC	breast:	n/a
17	chr2:20251993-20252043	HEK293	kidney:	embryo
18	chr2:20251973-20252023	SK-N-MC	brain:	n/a
19	chr2:20251973-20252023	IMR90	lung:	fetal
20	chr2:20251973-20252023	U87	brain:	n/a
21	chr2:20251993-20252043	HPAEpiC	pulmonary alveolar:	n/a
22	chr2:20251973-20252023	HRE	kidney:	n/a
23	chr2:20251993-20252043	HL-60	blood:	n/a
24	chr2:20251993-20252043	SKMC	muscle:	n/a
25	chr2:20251993-20252043	ovcar-3	ovarian:	n/a
26	chr2:20251993-20252043	H1-hESC	embryonic stem cell:	embryo
27	chr2:20251993-20252043	HAEpiC	amniotic membrane:	n/a
28	chr2:20251973-20252023	HAEpiC	amniotic membrane:	n/a
29	chr2:20251993-20252043	HCM	heart:	n/a
30	chr2:20251993-20252043	AG04450	lung:	fetal
31	chr2:20251993-20252043	BJ	skin:	n/a
32	chr2:20251993-20252043	HCPEpiC	choroid plexus:	n/a
33	chr2:20251973-20252023	HUVEC	blood vessel:	n/a
34	chr2:20251993-20252043	Hela-S3	cervix:	n/a
35	chr2:20251993-20252043	SK-N-SH_RA	brain:	n/a
36	chr2:20251973-20252023	HNPCEpiC	eye:	n/a
37	chr2:20251973-20252023	Jurkat	blood:	n/a
38	chr2:20251973-20252023	NB4	blood:	n/a
39	chr2:20251993-20252043	PFSK-1	brain:	n/a
40	chr2:20251993-20252043	HRE	kidney:	n/a
41	chr2:20251993-20252043	GM12892	blood:	n/a
42	chr2:20251993-20252043	MCF10A-Er-Src	breast:	n/a
43	chr2:20251993-20252043	CMK	blood:	n/a
44	chr2:20251993-20252043	LNCaP	prostate:	n/a
45	chr2:20251973-20252023	LNCaP	prostate:	n/a
46	chr2:20251973-20252023	HRPEpiC	eye:	n/a
47	chr2:20251973-20252023	Hela-S3	cervix:	n/a
48	chr2:20251973-20252023	K562	blood:	n/a
49	chr2:20251993-20252043	A549	lung:	n/a
50	chr2:20251993-20252043	GM12891	blood:	n/a

No.	Distal block	Cell Line	Cell type
1	chr2:20249888..20254017-chr2:20419396..20423263,3	MCF-7	breast:
2	chr2:20208645..20229804-chr2:20247969..20254330,37	MCF-7	breast:
3	chr2:20100261..20103746-chr2:20249026..20255152,7	K562	blood:
4	chr2:20233333..20235780-chr2:20251551..20254111,2	K562	blood:
5	chr2:20209928..20212604-chr2:20250418..20252144,2	MCF-7	breast:
6	chr1:28974783..28975713-chr2:20251159..20252070,2	Hela-S3	cervix:
7	chr2:20251925..20253878-chr2:20548760..20551591,2	K562	blood:
8	chr2:20251385..20252181-chr6:74230268..74230794,2	Hela-S3	cervix:
9	chr16:27279568..27280111-chr2:20251412..20252038,2	Hela-S3	cervix:
10	chr14:24701099..24702081-chr2:20251545..20252199,2	Hela-S3	cervix:
11	chr2:20249637..20253449-chr2:20421472..20424385,3	MCF-7	breast:
12	chr2:20154730..20157342-chr2:20251930..20254193,3	MCF-7	breast:
13	chr2:20249233..20252415-chr2:20424056..20425890,4	MCF-7	breast:

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-RHOB-2	chr2:20251914-20252255	NONHSAT069423
2	lnc-RHOB-2	chr2:20251895-20252255	ENSG00000223734.2

Variant related genes	Relation type
LAPTM4A	TF binding region
LAPTM4A	CpG island
ENSG00000055917	Chromatin interaction
ENSG00000270103	Chromatin interaction
ENSG00000132031	Chromatin interaction
ENSG00000115884	Chromatin interaction
ENSG00000068697	Chromatin interaction
ENSG00000100938	Chromatin interaction
ENSG00000129559	Chromatin interaction
ENSG00000183891	Chromatin interaction
ENSG00000169189	Chromatin interaction
ENSG00000156508	Chromatin interaction
ENSG00000271991	Chromatin interaction
ENSG00000255526	Chromatin interaction

Extended variants
information (count: 29 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:29)

rs_ID	r²[population]
rs1016316	1.00[CEU][hapmap];0.81[CHD][hapmap];0.81[GIH][hapmap];1.00[TSI][hapmap];0.92[EUR][1000 genomes]
rs11674251	1.00[ASW][hapmap];0.87[CEU][hapmap];0.89[CHD][hapmap];0.92[JPT][hapmap];1.00[MKK][hapmap];0.85[ASN][1000 genomes]
rs11679737	0.86[ASW][hapmap]
rs11689320	0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs11689431	1.00[ASW][hapmap];0.82[CEU][hapmap];0.84[JPT][hapmap]
rs11694170	1.00[ASW][hapmap];1.00[CEU][hapmap];0.83[CHB][hapmap];0.92[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[TSI][hapmap];0.97[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs11695154	0.91[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs1191805	0.83[EUR][1000 genomes]
rs1191817	0.84[EUR][1000 genomes]
rs12988954	0.94[CEU][hapmap];0.89[CHB][hapmap];0.92[JPT][hapmap];0.86[ASN][1000 genomes]
rs1473890	0.91[EUR][1000 genomes]
rs1513831	1.00[ASW][hapmap];1.00[CEU][hapmap];0.83[CHB][hapmap];0.92[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[TSI][hapmap];0.97[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs16987338	0.94[CEU][hapmap];0.83[CHB][hapmap];1.00[JPT][hapmap];0.95[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs34539547	1.00[CEU][hapmap];0.94[CHB][hapmap];0.92[CHD][hapmap];0.90[GIH][hapmap];0.92[JPT][hapmap];0.93[MEX][hapmap];1.00[TSI][hapmap];0.88[AMR][1000 genomes];0.97[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs35030383	0.81[ASN][1000 genomes]
rs36071721	0.90[EUR][1000 genomes]
rs3731673	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.89[MKK][hapmap];1.00[TSI][hapmap];0.86[AFR][1000 genomes];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3769759	0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs3769760	1.00[CEU][hapmap];1.00[CHB][hapmap];0.94[CHD][hapmap];1.00[GIH][hapmap];0.86[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs3769762	1.00[CEU][hapmap];1.00[CHB][hapmap];0.86[JPT][hapmap];0.88[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs62109431	0.96[AMR][1000 genomes];0.95[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs6706375	1.00[CEU][hapmap];1.00[CHB][hapmap];0.86[JPT][hapmap];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6709349	0.86[ASW][hapmap]
rs6720508	0.97[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs7558777	0.89[EUR][1000 genomes]
rs7558988	0.87[EUR][1000 genomes]
rs7570360	0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs7587612	0.95[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs878983	0.86[ASW][hapmap];1.00[MKK][hapmap]

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs1513830	AC098828.2	cis	Skin Sun Exposed Lower leg	GTEx

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:20247400-20252600	Active TSS	Ovary	ovary
2	chr2:20248400-20252800	Active TSS	IMR90 fetal lung fibroblasts Cell Line	lung
3	chr2:20248400-20252800	Active TSS	Aorta	Aorta
4	chr2:20248600-20252800	Active TSS	Fetal Muscle Leg	muscle
5	chr2:20248600-20252800	Active TSS	Psoas Muscle	Psoas
6	chr2:20248600-20252800	Active TSS	Right Ventricle	heart
7	chr2:20248800-20252400	Active TSS	Fetal Intestine Large	intestine
8	chr2:20248800-20252400	Active TSS	Stomach Smooth Muscle	stomach
9	chr2:20248800-20252800	Active TSS	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
10	chr2:20248800-20252800	Active TSS	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
11	chr2:20248800-20252800	Active TSS	Foreskin Melanocyte Primary Cells skin01	Skin
12	chr2:20248800-20253000	Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
13	chr2:20249000-20252200	Active TSS	Fetal Thymus	thymus
14	chr2:20249000-20252200	Active TSS	GM12878-XiMat	blood
15	chr2:20249000-20252400	Active TSS	Colon Smooth Muscle	Colon
16	chr2:20249000-20252400	Active TSS	Fetal Lung	lung
17	chr2:20249000-20252400	Active TSS	HSMM	muscle
18	chr2:20249000-20252600	Active TSS	H9 Cell Line	embryonic stem cell
19	chr2:20249000-20252600	Active TSS	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
20	chr2:20249000-20252800	Active TSS	ES-WA7 Cell Line	embryonic stem cell
21	chr2:20249000-20252800	Active TSS	H1 Cell Line	embryonic stem cell
22	chr2:20249000-20252800	Active TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
23	chr2:20249000-20252800	Active TSS	Fetal Kidney	kidney
24	chr2:20249000-20252800	Active TSS	NHDF-Ad	bronchial
25	chr2:20249000-20252800	Active TSS	NHLF	lung
26	chr2:20249000-20253200	Active TSS	Foreskin Fibroblast Primary Cells skin02	Skin
27	chr2:20249200-20252200	Active TSS	Fetal Stomach	stomach
28	chr2:20249200-20252600	Active TSS	Breast Myoepithelial Primary Cells	Breast
29	chr2:20249200-20252600	Active TSS	Colonic Mucosa	Colon
30	chr2:20249200-20252800	Active TSS	ES-I3 Cell Line	embryonic stem cell
31	chr2:20249200-20252800	Active TSS	H9 Derived Neuron Cultured Cells	ES cell derived
32	chr2:20249200-20252800	Active TSS	iPS-15b Cell Line	embryonic stem cell
33	chr2:20249200-20252800	Active TSS	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
34	chr2:20249200-20252800	Active TSS	Brain Dorsolateral Prefrontal Cortex	brain
35	chr2:20249200-20252800	Active TSS	Fetal Muscle Trunk	muscle
36	chr2:20249200-20253000	Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
37	chr2:20249200-20253000	Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
38	chr2:20249200-20253000	Active TSS	HSMMtube	muscle
39	chr2:20249200-20253200	Active TSS	HUES6 Cell Line	embryonic stem cell
40	chr2:20249400-20252200	Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
41	chr2:20249400-20252200	Active TSS	Muscle Satellite Cultured Cells	--
42	chr2:20249400-20252200	Active TSS	Left Ventricle	heart
43	chr2:20249400-20252200	Active TSS	HMEC	breast
44	chr2:20249400-20252400	Active TSS	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
45	chr2:20249400-20252400	Active TSS	Duodenum Smooth Muscle	Duodenum
46	chr2:20249400-20252400	Active TSS	Esophagus	oesophagus
47	chr2:20249400-20252400	Active TSS	Pancreas	Pancrea
48	chr2:20249400-20252600	Active TSS	iPS DF 6.9 Cell Line	embryonic stem cell
49	chr2:20249400-20252600	Active TSS	ES-UCSF4 Cell Line	embryonic stem cell
50	chr2:20249400-20252600	Active TSS	Foreskin Keratinocyte Primary Cells skin02	Skin

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