Variant report

Variant	rs530118
Chromosome Location	chr15:43478511-43478512
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:43)
CpG islands
(count:0)
Chromatin interactive
region (count:13)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:43 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	POLR2A	chr15:43477291-43478513	GM12892	blood:	n/a	n/a
2	SPI1	chr15:43477938-43478554	HL-60	blood:	n/a	n/a
3	GABPA	chr15:43477474-43478513	HL-60	blood:	n/a	n/a
4	ZBTB7A	chr15:43477550-43478521	ECC-1	luminal epithelium:	n/a	n/a
5	POLR2A	chr15:43477242-43478527	HL-60	blood:	n/a	n/a
6	POLR2A	chr15:43477239-43478695	GM12878	blood:	n/a	n/a
7	MYC	chr15:43477220-43478627	NB4	blood:	n/a	n/a
8	CTCF	chr15:43477143-43478704	SK-N-SH	brain:	n/a	chr15:43478084-43478097 chr15:43478084-43478097
9	POLR2A	chr15:43477199-43478537	K562	blood:	n/a	n/a
10	ELF1	chr15:43477247-43478573	GM12878	blood:	n/a	chr15:43477613-43477622 chr15:43477612-43477623
11	TEAD4	chr15:43477914-43478551	K562	blood:	n/a	n/a
12	POLR2A	chr15:43477337-43478599	GM12878	blood:	n/a	n/a
13	CTBP2	chr15:43477159-43478520	H1-hESC	embryonic stem cell:	n/a	n/a
14	POLR2A	chr15:43477139-43478637	GM12878	blood:	n/a	n/a
15	POLR2A	chr15:43477328-43478523	GM19099	blood:	n/a	n/a
16	UBTF	chr15:43477210-43478586	K562	blood:	n/a	n/a
17	GABPA	chr15:43477916-43478569	HL-60	blood:	n/a	n/a
18	MAZ	chr15:43477178-43478644	GM12878	blood:	n/a	n/a
19	MXI1	chr15:43476643-43479389	SK-N-SH	brain:	n/a	n/a
20	MAX	chr15:43477226-43478551	HepG2	liver:	n/a	n/a
21	MAX	chr15:43477221-43478520	K562	blood:	n/a	n/a
22	MXI1	chr15:43477135-43478758	IMR90	lung:	n/a	n/a
23	POLR2A	chr15:43477199-43478607	GM12892	blood:	n/a	n/a
24	POLR2A	chr15:43477402-43478602	GM12878	blood:	n/a	n/a
25	RCOR1	chr15:43477251-43478514	K562	blood:	n/a	n/a
26	POLR2A	chr15:43477334-43478530	Hela-S3	cervix:	n/a	n/a
27	USF2	chr15:43478314-43478532	H1-hESC	embryonic stem cell:	n/a	n/a
28	POLR2A	chr15:43477217-43478546	HepG2	liver:	n/a	n/a
29	CTCF	chr15:43478420-43478570	HBMEC	blood vessel:	n/a	n/a
30	HCFC1	chr15:43476740-43478838	Hela-S3	cervix:	n/a	n/a
31	POLR2A	chr15:43477166-43478521	H1-neurons	neurons:	n/a	n/a
32	POLR2A	chr15:43477894-43478530	GM12891	blood:	n/a	n/a
33	MAX	chr15:43477125-43478523	HCT-116	colon:	n/a	n/a
34	MTA3	chr15:43476972-43478561	GM12878	blood:	n/a	n/a
35	MAZ	chr15:43477111-43478739	K562	blood:	n/a	n/a
36	RCOR1	chr15:43477098-43478898	IMR90	lung:	n/a	n/a
37	POLR2A	chr15:43476955-43478621	PBDE	blood:	n/a	n/a
38	POLR2A	chr15:43477033-43478579	GM12891	blood:	n/a	n/a
39	REST	chr15:43476986-43478627	H1-neurons	neurons:	n/a	chr15:43478209-43478223 chr15:43477604-43477611 chr15:43478209-43478229
40	MAX	chr15:43477259-43478575	ECC-1	luminal epithelium:	n/a	n/a
41	RELA	chr15:43477431-43478545	GM15510	blood:	n/a	n/a
42	POLR2A	chr15:43477155-43478548	HepG2	liver:	n/a	n/a
43	RELA	chr15:43477544-43478560	GM19099	blood:	n/a	n/a

No data

(count:13 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr15:43478456..43479959-chr15:43502893..43504984,2	K562	blood:
2	chr15:43476285..43479868-chr15:43558571..43560739,3	K562	blood:
3	chr15:43476272..43478901-chr15:43620777..43622927,4	K562	blood:
4	chr15:43478112..43478717-chr17:42401330..42402214,2	Hela-S3	cervix:
5	chr15:43414543..43416437-chr15:43476770..43479731,2	K562	blood:
6	chr15:43477582..43480144-chr15:43497635..43499944,2	K562	blood:
7	chr15:43460424..43462230-chr15:43476704..43478906,2	MCF-7	breast:
8	chr15:43413837..43416869-chr15:43476770..43480897,4	K562	blood:
9	chr15:43471322..43474436-chr15:43477554..43479456,3	K562	blood:
10	chr15:43212538..43214244-chr15:43477789..43479955,2	K562	blood:
11	chr15:43478113..43480240-chr15:43513375..43516202,2	K562	blood:
12	chr15:43368519..43371458-chr15:43478469..43480102,2	K562	blood:
13	chr15:43477046..43479733-chr15:43513135..43515650,2	MCF-7	breast:

No data

Variant related genes	Relation type
ENSG00000261687	TF binding region
CCNDBP1	TF binding region
ENSG00000013306	Chromatin interaction
ENSG00000261679	Chromatin interaction
ENSG00000168803	Chromatin interaction
ENSG00000166947	Chromatin interaction
ENSG00000168806	Chromatin interaction
ENSG00000104055	Chromatin interaction
ENSG00000128881	Chromatin interaction
ENSG00000137842	Chromatin interaction

Extended variants
information (count: 30 )
Associated
traits (count: 5 )

rSNPs within LD-proxies of this variant (count:22)

rs_ID	r²[population]
rs10851414	0.87[AFR][1000 genomes];0.92[EUR][1000 genomes]
rs11070389	1.00[ASW][hapmap];0.82[CHD][hapmap];0.82[MKK][hapmap]
rs11070390	0.82[EUR][1000 genomes]
rs11632120	0.88[CEU][hapmap];0.83[JPT][hapmap]
rs12442190	0.88[CEU][hapmap];0.89[GIH][hapmap];0.87[JPT][hapmap];0.83[TSI][hapmap];0.84[EUR][1000 genomes]
rs1814323	1.00[ASW][hapmap]
rs2056346	1.00[YRI][hapmap]
rs2139651	0.88[CEU][hapmap];0.82[CHD][hapmap];0.89[GIH][hapmap];0.83[JPT][hapmap];0.86[TSI][hapmap];0.81[EUR][1000 genomes]
rs2139652	0.91[AFR][1000 genomes];0.93[EUR][1000 genomes]
rs2438149	1.00[AFR][1000 genomes]
rs476342	0.96[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs489964	1.00[ASW][hapmap];1.00[CEU][hapmap];0.82[CHD][hapmap];1.00[GIH][hapmap];0.83[JPT][hapmap];1.00[LWK][hapmap];0.80[MKK][hapmap];0.97[TSI][hapmap];0.87[AFR][1000 genomes];0.88[EUR][1000 genomes]
rs4923956	0.80[CHD][hapmap]
rs502157	1.00[ASW][hapmap];1.00[CEU][hapmap];0.82[CHD][hapmap];0.85[GIH][hapmap];0.83[JPT][hapmap];1.00[LWK][hapmap];1.00[MKK][hapmap];0.97[TSI][hapmap];0.87[AFR][1000 genomes];0.88[EUR][1000 genomes]
rs504417	1.00[ASW][hapmap]
rs513970	1.00[ASW][hapmap]
rs525403	0.88[CEU][hapmap]
rs531598	0.87[EUR][1000 genomes]
rs574531	0.87[AFR][1000 genomes];0.88[EUR][1000 genomes]
rs574856	0.98[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs7165861	0.82[EUR][1000 genomes]
rs7166467	0.96[CEU][hapmap];0.80[CHD][hapmap];0.98[GIH][hapmap];0.83[JPT][hapmap];0.97[TSI][hapmap];0.93[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:8 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv525461	chr15:43062548-43482127	Enhancers Flanking Active TSS Weak transcription Strong transcription ZNF genes & repeats Flanking Bivalent TSS/Enh Genic enhancers Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	32 gene(s)	inside rSNPs	diseases
2	nsv1044522	chr15:43115348-43658417	Strong transcription Weak transcription Flanking Active TSS Transcr. at gene 5' and 3' Enhancers Active TSS Genic enhancers Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	47 gene(s)	inside rSNPs	diseases
3	nsv569241	chr15:43201109-43522922	Active TSS Weak transcription ZNF genes & repeats Strong transcription Enhancers Flanking Active TSS Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	32 gene(s)	inside rSNPs	diseases
4	nsv904136	chr15:43257475-43482127	Weak transcription Enhancers Strong transcription Active TSS Flanking Active TSS Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	29 gene(s)	inside rSNPs	diseases
5	nsv904139	chr15:43268970-43482127	Weak transcription Strong transcription Active TSS Flanking Active TSS Genic enhancers Enhancers Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	28 gene(s)	inside rSNPs	diseases
6	nsv1044508	chr15:43270637-43658417	Weak transcription Genic enhancers Strong transcription Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Active TSS Active TSS Enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	43 gene(s)	inside rSNPs	diseases
7	nsv904144	chr15:43276345-43482127	Bivalent/Poised TSS Strong transcription Weak transcription Enhancers Active TSS Flanking Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	28 gene(s)	inside rSNPs	diseases
8	esv1802035	chr15:43370916-43487742	Weak transcription Active TSS Strong transcription Enhancers Flanking Active TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	28 gene(s)	inside rSNPs	diseases

mRNA abundance (count:5)

SNP	Gene	Cis/trans	Tissue	Source
rs530118	TGM5	cis	lymphoblastoid	seeQTL
rs530118	TYRO3	cis	parietal	SCAN
rs530118	VPS39	cis	cerebellum	SCAN
rs530118	SNAP23	cis	cerebellum	SCAN
rs530118	WDR76	cis	parietal	SCAN

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:43476800-43478800	Active TSS	Foreskin Fibroblast Primary Cells skin02	Skin
2	chr15:43477000-43478800	Active TSS	H9 Cell Line	embryonic stem cell
3	chr15:43477000-43479000	Active TSS	Brain Hippocampus Middle	brain
4	chr15:43477000-43479200	Active TSS	Brain Dorsolateral Prefrontal Cortex	brain
5	chr15:43477200-43478600	Active TSS	H1 Cell Line	embryonic stem cell
6	chr15:43477200-43478600	Active TSS	iPS DF 6.9 Cell Line	embryonic stem cell
7	chr15:43477200-43478600	Active TSS	Foreskin Keratinocyte Primary Cells skin02	Skin
8	chr15:43477200-43478600	Active TSS	Brain Anterior Caudate	brain
9	chr15:43477200-43478600	Active TSS	Colon Smooth Muscle	Colon
10	chr15:43477200-43478600	Active TSS	Fetal Kidney	kidney
11	chr15:43477200-43478800	Active TSS	ES-I3 Cell Line	embryonic stem cell
12	chr15:43477200-43478800	Active TSS	IMR90 fetal lung fibroblasts Cell Line	lung
13	chr15:43477200-43478800	Active TSS	iPS-15b Cell Line	embryonic stem cell
14	chr15:43477200-43478800	Active TSS	iPS DF 19.11 Cell Line	embryonic stem cell
15	chr15:43477200-43478800	Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
16	chr15:43477200-43478800	Active TSS	Right Ventricle	heart
17	chr15:43477200-43479000	Active TSS	iPS-20b Cell Line	embryonic stem cell
18	chr15:43477200-43479000	Active TSS	Foreskin Melanocyte Primary Cells skin03	Skin
19	chr15:43477200-43479000	Active TSS	Duodenum Smooth Muscle	Duodenum
20	chr15:43477200-43479000	Active TSS	NHDF-Ad	bronchial
21	chr15:43477200-43479200	Flanking Active TSS	Primary T helper cells fromperipheralblood	blood
22	chr15:43477200-43479600	Flanking Active TSS	Primary T regulatory cells fromperipheralblood	blood
23	chr15:43477400-43478600	Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
24	chr15:43477400-43478600	Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
25	chr15:43477400-43478600	Active TSS	Duodenum Mucosa	Duodenum
26	chr15:43477400-43478600	Active TSS	Esophagus	oesophagus
27	chr15:43477400-43478600	Active TSS	Fetal Intestine Small	intestine
28	chr15:43477400-43478600	Active TSS	Gastric	stomach
29	chr15:43477400-43478600	Active TSS	Lung	lung
30	chr15:43477400-43478600	Active TSS	Ovary	ovary
31	chr15:43477400-43478600	Active TSS	Pancreas	Pancrea
32	chr15:43477400-43478600	Active TSS	Placenta Amnion	Placenta Amnion
33	chr15:43477400-43478600	Active TSS	Rectal Mucosa Donor 31	rectum
34	chr15:43477400-43478600	Active TSS	HSMMtube	muscle
35	chr15:43477400-43478800	Active TSS	HUES48 Cell Line	embryonic stem cell
36	chr15:43477400-43478800	Active TSS	HUES6 Cell Line	embryonic stem cell
37	chr15:43477400-43478800	Active TSS	HUES64 Cell Line	embryonic stem cell
38	chr15:43477400-43478800	Active TSS	iPS-18 Cell Line	embryonic stem cell
39	chr15:43477400-43478800	Active TSS	Fetal Intestine Large	intestine
40	chr15:43477400-43478800	Active TSS	Pancreatic Islets	Pancreatic Islet
41	chr15:43477400-43478800	Active TSS	Left Ventricle	heart
42	chr15:43477400-43478800	Active TSS	A549	lung
43	chr15:43477400-43479000	Active TSS	K562	blood
44	chr15:43477400-43479200	Active TSS	Brain Angular Gyrus	brain
45	chr15:43477400-43479200	Active TSS	Colonic Mucosa	Colon
46	chr15:43477400-43479200	Active TSS	Placenta	Placenta
47	chr15:43477400-43479200	Active TSS	Stomach Mucosa	stomach
48	chr15:43477400-43479200	Active TSS	NHLF	lung
49	chr15:43477600-43478600	Active TSS	H1 Derived Mesenchymal Stem Cells	ES cell derived
50	chr15:43477600-43478600	Active TSS	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived

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