Variant report

Variant	rs8058144
Chromosome Location	chr16:47007985-47007986
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	MAX	chr16:47007224-47008192	HCT-116	colon:	n/a	n/a
2	POLR2A	chr16:47006279-47008925	GM12878	blood:	n/a	n/a
3	RFX5	chr16:47007420-47007989	HepG2	liver:	n/a	n/a
4	MAX	chr16:47006177-47008159	K562	blood:	n/a	chr16:47006377-47006384 chr16:47006376-47006385
5	POLR2A	chr16:47007387-47008553	HCT-116	colon:	n/a	n/a
6	EBF1	chr16:47007443-47008593	GM12878	blood:	n/a	n/a
7	FOXA1	chr16:47006873-47008093	HepG2	liver:	n/a	n/a
8	TAF1	chr16:47007293-47008043	ECC-1	luminal epithelium:	n/a	n/a
9	TEAD4	chr16:47007399-47008085	K562	blood:	n/a	n/a
10	E2F6	chr16:47007350-47008285	A549	lung:	n/a	chr16:47007654-47007663 chr16:47007361-47007371 chr16:47007597-47007606
11	POLR2A	chr16:47006360-47008038	H1-hESC	embryonic stem cell:	n/a	n/a
12	CHD1	chr16:47007397-47008431	H1-hESC	embryonic stem cell:	n/a	n/a
13	POLR2A	chr16:47007281-47008042	SK-N-MC	brain:	n/a	n/a
14	POLR2A	chr16:47006406-47008908	Raji	blood:	n/a	n/a
15	POLR2A	chr16:47006774-47008042	MCF-7	breast:	n/a	n/a
16	MAX	chr16:47007405-47008669	GM12878	blood:	n/a	chr16:47008457-47008468 chr16:47008377-47008387
17	SP1	chr16:47007267-47008033	A549	lung:	n/a	chr16:47007596-47007608 chr16:47007654-47007663 chr16:47007598-47007607 chr16:47007597-47007607 chr16:47007652-47007663 chr16:47007598-47007607 chr16:47007596-47007607 chr16:47007652-47007664 chr16:47007596-47007608 chr16:47007597-47007606 chr16:47007653-47007662 chr16:47007597-47007607 chr16:47007652-47007664
18	E2F6	chr16:47007350-47008019	H1-hESC	embryonic stem cell:	n/a	chr16:47007654-47007663 chr16:47007361-47007371 chr16:47007597-47007606
19	TAF1	chr16:47006696-47008031	HepG2	liver:	n/a	n/a
20	POLR2A	chr16:47006263-47008909	GM18505	blood:	n/a	n/a
21	POLR2A	chr16:47006349-47008106	H1-neurons	neurons:	n/a	n/a
22	POLR2A	chr16:47007152-47008096	HUVEC	blood vessel:	n/a	n/a
23	MAX	chr16:47006133-47008675	HepG2	liver:	n/a	chr16:47006377-47006384 chr16:47006376-47006385 chr16:47008457-47008468 chr16:47008377-47008387
24	YY1	chr16:47007305-47008056	ECC-1	luminal epithelium:	n/a	chr16:47007668-47007682 chr16:47007552-47007566 chr16:47007597-47007606 chr16:47007352-47007366 chr16:47007739-47007750 chr16:47007355-47007369 chr16:47007908-47007922
25	MAZ	chr16:47006661-47008190	IMR90	lung:	n/a	n/a
26	POLR2A	chr16:47007285-47008103	U87	brain:	n/a	n/a
27	POLR2A	chr16:47007236-47008000	GM12891	blood:	n/a	n/a
28	PML	chr16:47007335-47008004	K562	blood:	n/a	n/a
29	MAX	chr16:47006955-47008660	A549	lung:	n/a	chr16:47008457-47008468 chr16:47008377-47008387
30	POLR2A	chr16:47007355-47008640	K562	blood:	n/a	n/a
31	ELF1	chr16:47007390-47007999	HepG2	liver:	n/a	chr16:47007649-47007661 chr16:47007595-47007607
32	MAX	chr16:47007274-47008769	HCT-116	colon:	n/a	chr16:47008457-47008468 chr16:47008377-47008387
33	POLR2A	chr16:47006578-47008985	MCF10A-Er-Src	breast:	n/a	n/a
34	POLR2A	chr16:47006765-47008750	K562	blood:	n/a	n/a
35	YY1	chr16:47006719-47008034	K562	blood:	n/a	chr16:47007261-47007270 chr16:47007668-47007682 chr16:47007552-47007566 chr16:47007261-47007272 chr16:47007253-47007267 chr16:47007597-47007606 chr16:47007259-47007273 chr16:47006982-47006991 chr16:47007264-47007273 chr16:47007352-47007366 chr16:47007739-47007750 chr16:47007355-47007369 chr16:47007908-47007922 chr16:47007298-47007312 chr16:47007265-47007279
36	STAT5A	chr16:47007340-47008162	GM12878	blood:	n/a	n/a
37	REST	chr16:47007347-47008116	HL-60	blood:	n/a	chr16:47007385-47007398
38	SMARCB1	chr16:47006657-47008095	Hela-S3	cervix:	n/a	n/a
39	HDAC2	chr16:47007371-47007998	HepG2	liver:	n/a	n/a
40	TAF1	chr16:47006442-47008108	H1-hESC	embryonic stem cell:	n/a	n/a
41	YY1	chr16:47007314-47008106	H1-hESC	embryonic stem cell:	n/a	chr16:47007668-47007682 chr16:47007552-47007566 chr16:47007597-47007606 chr16:47007352-47007366 chr16:47007739-47007750 chr16:47007355-47007369 chr16:47007908-47007922
42	PML	chr16:47006247-47008765	GM12878	blood:	n/a	n/a
43	POLR2A	chr16:47006560-47008696	K562	blood:	n/a	n/a
44	POLR2A	chr16:47006105-47008953	GM12878	blood:	n/a	n/a
45	MYC	chr16:47007331-47008538	MCF10A-Er-Src	breast:	n/a	chr16:47008457-47008468 chr16:47008377-47008387
46	MYC	chr16:47007092-47008576	K562	blood:	n/a	chr16:47008457-47008468 chr16:47008377-47008387
47	MYBL2	chr16:47007317-47008080	HepG2	liver:	n/a	n/a
48	CHD2	chr16:47007411-47008053	HepG2	liver:	n/a	n/a
49	POLR2A	chr16:47006739-47008051	K562	blood:	n/a	n/a
50	POLR2A	chr16:47006129-47008902	HepG2	liver:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr16:47005665..47009288-chr16:47176479..47179650,5	K562	blood:
2	chr16:47007838..47011337-chr16:47047601..47050592,3	MCF-7	breast:
3	chr16:47007686..47008500-chr19:41196000..41196982,2	Hela-S3	cervix:
4	chr16:47005815..47008447-chr16:47177298..47179122,2	K562	blood:

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-GPT2-1	chr16:47007717-47008036	XLOC_011704
2	lnc-GPT2-1	chr16:47007900-47008036	ENSG00000261173.1
3	lnc-GPT2-1	chr16:47007627-47010136	NONHSAT142273

Variant related genes	Relation type
DNAJA2	TF binding region
ENSG00000171208	Chromatin interaction
ENSG00000259983	Chromatin interaction
ENSG00000260281	Chromatin interaction
ENSG00000105245	Chromatin interaction

Extended variants
information (count: 50 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:45)

rs_ID	r²[population]
rs10459877	0.88[AFR][1000 genomes];0.88[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11247542	0.90[EUR][1000 genomes]
rs11859515	0.92[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12445492	0.87[EUR][1000 genomes]
rs12447719	0.90[EUR][1000 genomes]
rs12596824	0.92[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12719759	0.89[AFR][1000 genomes]
rs12925296	0.90[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs1362406	1.00[CEU][hapmap];1.00[CHB][hapmap];0.93[YRI][hapmap];0.96[AFR][1000 genomes];0.92[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1376734	1.00[CEU][hapmap];1.00[CHB][hapmap];0.82[YRI][hapmap];0.81[AFR][1000 genomes];0.88[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1551188	0.88[AFR][1000 genomes];0.80[AMR][1000 genomes];0.90[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs1894886	0.80[AMR][1000 genomes];0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1978336	0.90[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs2058673	1.00[CEU][hapmap];1.00[CHB][hapmap];0.96[YRI][hapmap];0.94[AFR][1000 genomes];0.88[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2341648	0.84[AMR][1000 genomes];0.90[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs35405784	0.95[AFR][1000 genomes];0.88[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4246393	1.00[CEU][hapmap];1.00[CHB][hapmap];0.97[YRI][hapmap]
rs4577108	0.90[EUR][1000 genomes]
rs4625742	0.82[EUR][1000 genomes]
rs4966781	0.94[AFR][1000 genomes];0.92[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4966794	0.92[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs4966795	0.92[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs4966800	0.90[EUR][1000 genomes]
rs4967664	0.93[AFR][1000 genomes];0.92[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4967696	1.00[CEU][hapmap];1.00[CHB][hapmap];0.96[YRI][hapmap];1.00[AFR][1000 genomes];0.92[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4967724	0.81[AFR][1000 genomes]
rs4967726	1.00[CEU][hapmap];1.00[CHB][hapmap]
rs4967739	0.87[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs62059134	0.83[ASN][1000 genomes]
rs7189628	1.00[CEU][hapmap];1.00[CHB][hapmap];0.93[YRI][hapmap];0.96[AFR][1000 genomes];0.92[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7199379	0.90[EUR][1000 genomes]
rs7199772	0.92[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs7202325	0.92[AFR][1000 genomes];0.92[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7203206	0.92[AFR][1000 genomes];0.92[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs8046142	0.88[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs8047353	0.90[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs8052160	1.00[CEU][hapmap];1.00[CHB][hapmap];0.88[AMR][1000 genomes];0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs8054039	1.00[CEU][hapmap];1.00[CHB][hapmap];0.93[YRI][hapmap];0.96[AFR][1000 genomes];0.92[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs8060193	1.00[CEU][hapmap];1.00[CHB][hapmap];0.87[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs9745921	0.88[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9923192	1.00[ASN][1000 genomes]
rs9925290	0.94[AFR][1000 genomes];0.88[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9925525	0.88[AMR][1000 genomes];0.83[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs9927843	0.90[AFR][1000 genomes];0.88[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9939872	1.00[CEU][hapmap];1.00[CHB][hapmap];0.97[YRI][hapmap]

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	nsv1059456	chr16:46463770-47307580	Flanking Active TSS Bivalent/Poised TSS Enhancers Weak transcription Active TSS Strong transcription ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	65 gene(s)	inside rSNPs	diseases
2	nsv1066115	chr16:46463770-47318415	Enhancers Flanking Active TSS Weak transcription Active TSS Strong transcription Bivalent/Poised TSS Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	65 gene(s)	inside rSNPs	diseases
3	nsv1059147	chr16:46500740-47010960	Flanking Active TSS Active TSS Weak transcription Strong transcription Enhancers ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	54 gene(s)	inside rSNPs	diseases
4	nsv542909	chr16:46500740-47010960	Weak transcription Strong transcription Enhancers Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' Active TSS Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	54 gene(s)	inside rSNPs	diseases
5	esv3439120	chr16:47006276-47008824	Enhancers Flanking Active TSS Weak transcription Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases

No data

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr16:47004400-47008600	Active TSS	GM12878-XiMat	blood
2	chr16:47005600-47008000	Active TSS	A549	lung
3	chr16:47005600-47008200	Active TSS	Breast Myoepithelial Primary Cells	Breast
4	chr16:47005800-47008200	Active TSS	H1 Cell Line	embryonic stem cell
5	chr16:47005800-47008400	Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
6	chr16:47006000-47008000	Active TSS	iPS-18 Cell Line	embryonic stem cell
7	chr16:47006000-47008000	Active TSS	Foreskin Fibroblast Primary Cells skin02	Skin
8	chr16:47006000-47008200	Active TSS	Foreskin Melanocyte Primary Cells skin01	Skin
9	chr16:47006000-47008200	Active TSS	Fetal Intestine Small	intestine
10	chr16:47006000-47008200	Active TSS	Fetal Thymus	thymus
11	chr16:47006000-47008200	Active TSS	HSMMtube	muscle
12	chr16:47006000-47008400	Active TSS	ES-I3 Cell Line	embryonic stem cell
13	chr16:47006000-47008400	Active TSS	ES-WA7 Cell Line	embryonic stem cell
14	chr16:47006000-47008400	Active TSS	H9 Cell Line	embryonic stem cell
15	chr16:47006000-47008400	Flanking Active TSS	Primary B cells from cord blood	blood
16	chr16:47006000-47008400	Active TSS	Right Ventricle	heart
17	chr16:47006200-47008000	Active TSS	Gastric	stomach
18	chr16:47006200-47008000	Active TSS	Lung	lung
19	chr16:47006200-47008200	Active TSS	iPS-15b Cell Line	embryonic stem cell
20	chr16:47006200-47008200	Active TSS	iPS DF 6.9 Cell Line	embryonic stem cell
21	chr16:47006200-47008200	Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
22	chr16:47006200-47008200	Flanking Active TSS	Primary mononuclear cells fromperipheralblood	Blood
23	chr16:47006200-47008200	Active TSS	Ovary	ovary
24	chr16:47006200-47008400	Active TSS	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
25	chr16:47006200-47008400	Active TSS	Fetal Muscle Trunk	muscle
26	chr16:47006200-47008600	Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
27	chr16:47006400-47008000	Active TSS	H1 Derived Mesenchymal Stem Cells	ES cell derived
28	chr16:47006400-47008000	Active TSS	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
29	chr16:47006400-47008000	Active TSS	Primary T helper memory cells from peripheral blood 2	blood
30	chr16:47006400-47008000	Active TSS	Muscle Satellite Cultured Cells	--
31	chr16:47006400-47008000	Active TSS	NHDF-Ad	bronchial
32	chr16:47006400-47008200	Active TSS	HUES48 Cell Line	embryonic stem cell
33	chr16:47006400-47008200	Active TSS	iPS-20b Cell Line	embryonic stem cell
34	chr16:47006400-47008200	Active TSS	Primary T helper naive cells from peripheral blood	blood
35	chr16:47006400-47008200	Active TSS	Foreskin Melanocyte Primary Cells skin03	Skin
36	chr16:47006400-47008200	Active TSS	Brain Dorsolateral Prefrontal Cortex	brain
37	chr16:47006400-47008200	Active TSS	Esophagus	oesophagus
38	chr16:47006400-47008200	Active TSS	Fetal Intestine Large	intestine
39	chr16:47006400-47008200	Active TSS	Fetal Kidney	kidney
40	chr16:47006400-47008200	Active TSS	Sigmoid Colon	Sigmoid Colon
41	chr16:47006400-47008200	Active TSS	Small Intestine	intestine
42	chr16:47006400-47008200	Active TSS	HSMM	muscle
43	chr16:47006400-47008200	Active TSS	NHLF	lung
44	chr16:47006400-47008400	Active TSS	Pancreatic Islets	Pancreatic Islet
45	chr16:47006400-47008400	Active TSS	Psoas Muscle	Psoas
46	chr16:47006400-47008600	Active TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
47	chr16:47006400-47008600	Active TSS	Left Ventricle	heart
48	chr16:47006600-47008000	Active TSS	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
49	chr16:47006600-47008000	Active TSS	HUES6 Cell Line	embryonic stem cell
50	chr16:47006600-47008000	Active TSS	HUES64 Cell Line	embryonic stem cell

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