Variant report

Variant	rs13136055
Chromosome Location	chr4:16228538-16228539
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	ETS1	chr4:16227820-16228550	K562	blood:	n/a	chr4:16228102-16228113
2	POLR2A	chr4:16227517-16229201	MCF-7	breast:	n/a	n/a
3	POLR2A	chr4:16227518-16229442	HepG2	liver:	n/a	n/a
4	POLR2A	chr4:16227404-16229475	GM18526	blood:	n/a	n/a
5	POLR2A	chr4:16227539-16228863	HEK293	kidney:	n/a	n/a
6	UBTF	chr4:16227470-16229465	K562	blood:	n/a	n/a
7	HEY1	chr4:16227474-16228546	HepG2	liver:	n/a	n/a
8	RFX5	chr4:16228209-16228574	Hela-S3	cervix:	n/a	n/a
9	YY1	chr4:16227737-16228600	H1-hESC	embryonic stem cell:	n/a	chr4:16228102-16228111 chr4:16227813-16227824 chr4:16228071-16228088 chr4:16227813-16227822 chr4:16228133-16228147 chr4:16227816-16227825
10	TCF7L2	chr4:16227633-16228990	HCT-116	colon:	n/a	n/a
11	POLR2A	chr4:16227556-16229064	GM10847	blood:	n/a	n/a
12	MAZ	chr4:16227273-16229432	K562	blood:	n/a	chr4:16228103-16228113
13	POLR2A	chr4:16227561-16228748	HUVEC	blood vessel:	n/a	n/a
14	POLR2A	chr4:16227474-16229038	HUVEC	blood vessel:	n/a	n/a
15	YY1	chr4:16227807-16228604	ECC-1	luminal epithelium:	n/a	chr4:16228102-16228111 chr4:16227813-16227824 chr4:16228071-16228088 chr4:16227813-16227822 chr4:16228133-16228147 chr4:16227816-16227825
16	POLR2A	chr4:16227473-16229161	NB4	blood:	n/a	n/a
17	TAF1	chr4:16227800-16228897	H1-hESC	embryonic stem cell:	n/a	n/a
18	POLR2A	chr4:16227467-16228542	H1-neurons	neurons:	n/a	n/a
19	MAZ	chr4:16227203-16229671	IMR90	lung:	n/a	chr4:16228103-16228113
20	MXI1	chr4:16227193-16229611	IMR90	lung:	n/a	n/a
21	RCOR1	chr4:16228139-16229043	K562	blood:	n/a	n/a
22	MAX	chr4:16227353-16228572	ECC-1	luminal epithelium:	n/a	chr4:16228103-16228113
23	POLR2A	chr4:16226799-16229901	GM12891	blood:	n/a	n/a
24	POLR2A	chr4:16228140-16228544	A549	lung:	n/a	n/a
25	TAF1	chr4:16227527-16228560	K562	blood:	n/a	n/a
26	MAZ	chr4:16227978-16229217	HepG2	liver:	n/a	chr4:16228103-16228113
27	MAX	chr4:16227571-16229498	K562	blood:	n/a	chr4:16228103-16228113
28	POLR2A	chr4:16227458-16229614	H1-hESC	embryonic stem cell:	n/a	n/a
29	POLR2A	chr4:16228431-16229169	H1-hESC	embryonic stem cell:	n/a	n/a
30	TBP	chr4:16227326-16229601	K562	blood:	n/a	n/a
31	CREB1	chr4:16227828-16228594	HepG2	liver:	n/a	n/a
32	MAX	chr4:16227397-16229058	HepG2	liver:	n/a	chr4:16228103-16228113
33	POLR2A	chr4:16228529-16229938	GM12892	blood:	n/a	n/a
34	POLR2A	chr4:16227816-16228701	A549	lung:	n/a	n/a
35	POLR2A	chr4:16227284-16229859	MCF10A-Er-Src	breast:	n/a	n/a
36	MAX	chr4:16227318-16228854	NB4	blood:	n/a	chr4:16228103-16228113
37	MAX	chr4:16227465-16229097	K562	blood:	n/a	chr4:16228103-16228113
38	MXI1	chr4:16227474-16229045	HepG2	liver:	n/a	n/a
39	TBP	chr4:16227543-16229131	H1-hESC	embryonic stem cell:	n/a	n/a
40	YY1	chr4:16227485-16229140	HepG2	liver:	n/a	chr4:16228102-16228111 chr4:16227813-16227824 chr4:16228816-16228830 chr4:16228071-16228088 chr4:16227813-16227822 chr4:16228133-16228147 chr4:16227816-16227825
41	YY1	chr4:16227524-16228697	SK-N-SH_RA	brain:	n/a	chr4:16228102-16228111 chr4:16227813-16227824 chr4:16228071-16228088 chr4:16227813-16227822 chr4:16228133-16228147 chr4:16227816-16227825
42	YY1	chr4:16227604-16228758	SK-N-SH	brain:	n/a	chr4:16228102-16228111 chr4:16227813-16227824 chr4:16228071-16228088 chr4:16227813-16227822 chr4:16228133-16228147 chr4:16227816-16227825
43	POLR2A	chr4:16226421-16229959	MCF10A-Er-Src	breast:	n/a	n/a
44	POLR2A	chr4:16227346-16229569	Hela-S3	cervix:	n/a	n/a
45	YY1	chr4:16227607-16228849	GM12878	blood:	n/a	chr4:16228102-16228111 chr4:16227813-16227824 chr4:16228816-16228830 chr4:16228071-16228088 chr4:16227813-16227822 chr4:16228133-16228147 chr4:16227816-16227825
46	POLR2A	chr4:16227550-16229081	ECC-1	luminal epithelium:	n/a	n/a
47	CREB1	chr4:16227904-16228545	GM12878	blood:	n/a	n/a
48	YY1	chr4:16227536-16228989	GM12878	blood:	n/a	chr4:16228102-16228111 chr4:16227813-16227824 chr4:16228816-16228830 chr4:16228071-16228088 chr4:16227813-16227822 chr4:16228133-16228147 chr4:16227816-16227825
49	HCFC1	chr4:16226663-16228826	Hela-S3	cervix:	n/a	n/a
50	POLR2A	chr4:16227368-16229531	GM12892	blood:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr4:16212529..16219737-chr4:16225844..16229602,8	MCF-7	breast:
2	chr4:16216932..16218804-chr4:16227245..16229857,2	MCF-7	breast:
3	chr4:16227890..16229761-chr4:17577650..17579806,2	MCF-7	breast:
4	chr4:15002785..15006911-chr4:16226901..16230678,5	K562	blood:
5	chr4:15681714..15684664-chr4:16226494..16229781,3	K562	blood:
6	chr17:59476916..59479068-chr4:16227271..16228837,2	MCF-7	breast:

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-CD38-2	chr4:16228286-16228800	ENSG00000225917
2	lnc-CD38-2	chr4:16228308-16228800	ENSG00000263327.1
3	lnc-CD38-2	chr4:16228286-16230207	ENSG00000263327.2
4	lnc-CD38-2	chr4:16228286-16228800	NONHSAT095674

Variant related genes	Relation type
TAPT1	TF binding region
TAPT1-AS1	TF binding region
ENSG00000267280	Chromatin interaction
ENSG00000237765	Chromatin interaction
ENSG00000137449	Chromatin interaction
ENSG00000121068	Chromatin interaction
ENSG00000002549	Chromatin interaction
ENSG00000267131	Chromatin interaction
ENSG00000169762	Chromatin interaction
ENSG00000247624	Chromatin interaction
ENSG00000118564	Chromatin interaction

Extended variants
information (count: 28 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:19)

rs_ID	r²[population]
rs10516297	0.81[ASN][1000 genomes]
rs11730922	0.82[ASN][1000 genomes]
rs13120908	0.85[AMR][1000 genomes];0.93[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs13132678	0.85[AMR][1000 genomes];0.94[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs13136172	0.85[AMR][1000 genomes];0.94[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs34129131	0.86[AMR][1000 genomes];0.89[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs34496855	0.85[AMR][1000 genomes];0.93[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs34592687	0.86[AMR][1000 genomes];0.91[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs34663238	0.86[AMR][1000 genomes];0.91[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs34837883	0.89[EUR][1000 genomes]
rs35475888	0.84[AMR][1000 genomes];0.93[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs35517826	0.84[AMR][1000 genomes];0.88[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs35804424	0.86[AMR][1000 genomes];0.91[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs35806798	0.84[ASN][1000 genomes]
rs35899968	0.86[AMR][1000 genomes];0.91[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs3749544	0.86[AMR][1000 genomes]
rs56353092	0.85[AMR][1000 genomes];0.94[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs6810390	0.94[AMR][1000 genomes];0.95[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs6852432	0.94[AMR][1000 genomes];0.95[EUR][1000 genomes];0.85[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:9 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1004821	chr4:16055996-16830629	Enhancers Flanking Active TSS Weak transcription Strong transcription Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Active TSS Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	22 gene(s)	inside rSNPs	diseases
2	nsv537046	chr4:16055996-16830629	Enhancers Flanking Active TSS ZNF genes & repeats Strong transcription Weak transcription Genic enhancers Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	22 gene(s)	inside rSNPs	diseases
3	nsv537047	chr4:16182060-16375787	Strong transcription Weak transcription Active TSS Enhancers Flanking Active TSS 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	17 gene(s)	inside rSNPs	diseases
4	nsv878720	chr4:16222046-16242215	Weak transcription Active TSS Enhancers Flanking Active TSS Strong transcription Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	12 gene(s)	inside rSNPs	diseases
5	nsv537048	chr4:16226406-16375787	Enhancers Flanking Active TSS Weak transcription Active TSS ZNF genes & repeats Strong transcription Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	17 gene(s)	inside rSNPs	diseases
6	esv3405372	chr4:16226679-16229727	Enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' Active TSS Flanking Active TSS Weak transcription Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	12 gene(s)	inside rSNPs	diseases
7	esv3489117	chr4:16226904-16229802	Weak transcription Flanking Active TSS Active TSS Bivalent/Poised TSS Enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	12 gene(s)	inside rSNPs	diseases
8	esv3489118	chr4:16226904-16229802	Active TSS Flanking Active TSS Weak transcription Enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	12 gene(s)	inside rSNPs	diseases
9	nsv593778	chr4:16227851-16233787	Enhancers Active TSS Flanking Active TSS Weak transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	12 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs13136055	TAPT1	Cis_1M	lymphoblastoid	RTeQTL

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:16225600-16230800	Active TSS	A549	lung
2	chr4:16225800-16230000	Active TSS	Foreskin Melanocyte Primary Cells skin01	Skin
3	chr4:16226200-16229600	Active TSS	Right Atrium	heart
4	chr4:16226400-16228800	Active TSS	Primary T cells fromperipheralblood	blood
5	chr4:16226400-16228800	Active TSS	Primary Natural Killer cells fromperipheralblood	blood
6	chr4:16226400-16228800	Active TSS	Fetal Thymus	thymus
7	chr4:16226400-16228800	Active TSS	Thymus	Thymus
8	chr4:16226400-16229000	Active TSS	Brain Inferior Temporal Lobe	brain
9	chr4:16226400-16229200	Active TSS	Fetal Stomach	stomach
10	chr4:16226400-16229400	Active TSS	Aorta	Aorta
11	chr4:16226400-16229400	Active TSS	HepG2	liver
12	chr4:16226400-16229600	Active TSS	Left Ventricle	heart
13	chr4:16226400-16229600	Active TSS	Psoas Muscle	Psoas
14	chr4:16226400-16229800	Active TSS	Foreskin Melanocyte Primary Cells skin03	Skin
15	chr4:16226400-16229800	Active TSS	Right Ventricle	heart
16	chr4:16226400-16229800	Active TSS	Stomach Smooth Muscle	stomach
17	chr4:16226400-16230600	Active TSS	GM12878-XiMat	blood
18	chr4:16226600-16228600	Active TSS	Fetal Muscle Leg	muscle
19	chr4:16226600-16228800	Active TSS	Breast Myoepithelial Primary Cells	Breast
20	chr4:16226600-16228800	Active TSS	NH-A	brain
21	chr4:16226600-16229000	Active TSS	Skeletal Muscle Female	skeletal muscle
22	chr4:16226600-16229200	Active TSS	Ganglion Eminence derived primary cultured neurospheres	brain
23	chr4:16226600-16229200	Active TSS	Fetal Intestine Small	intestine
24	chr4:16226600-16229400	Active TSS	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
25	chr4:16226600-16229400	Active TSS	iPS-20b Cell Line	embryonic stem cell
26	chr4:16226600-16229400	Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
27	chr4:16226600-16229400	Active TSS	Rectal Mucosa Donor 31	rectum
28	chr4:16226600-16229600	Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
29	chr4:16226600-16229600	Active TSS	HMEC	breast
30	chr4:16226600-16229800	Active TSS	H1 Cell Line	embryonic stem cell
31	chr4:16226600-16229800	Active TSS	NHDF-Ad	bronchial
32	chr4:16226600-16230000	Active TSS	Pancreatic Islets	Pancreatic Islet
33	chr4:16226600-16230800	Active TSS	K562	blood
34	chr4:16226800-16228600	Active TSS	Foreskin Fibroblast Primary Cells skin02	Skin
35	chr4:16226800-16228800	Active TSS	Fetal Muscle Trunk	muscle
36	chr4:16226800-16229000	Active TSS	HSMM	muscle
37	chr4:16226800-16229200	Active TSS	NHLF	lung
38	chr4:16226800-16229400	Active TSS	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
39	chr4:16226800-16229400	Active TSS	Foreskin Keratinocyte Primary Cells skin03	Skin
40	chr4:16226800-16229600	Active TSS	ES-WA7 Cell Line	embryonic stem cell
41	chr4:16226800-16229600	Active TSS	HUES48 Cell Line	embryonic stem cell
42	chr4:16226800-16229600	Active TSS	HUES64 Cell Line	embryonic stem cell
43	chr4:16226800-16229600	Active TSS	Ovary	ovary
44	chr4:16226800-16229800	Active TSS	Primary T helper naive cells fromperipheralblood	blood
45	chr4:16226800-16230000	Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
46	chr4:16226800-16230600	Active TSS	Brain Anterior Caudate	brain
47	chr4:16227000-16228800	Active TSS	Skeletal Muscle Male	skeletal muscle
48	chr4:16227000-16228800	Active TSS	Dnd41	blood
49	chr4:16227000-16229000	Active TSS	IMR90 fetal lung fibroblasts Cell Line	lung
50	chr4:16227000-16229000	Active TSS	Duodenum Mucosa	Duodenum

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