Variant report

Variant	rs9726525
Chromosome Location	chr1:78354585-78354586
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:69)
CpG islands
(count:0)
Chromatin interactive
region (count:1)
LncRNA
region (count:1)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:69 , 50 per page) page: 1 2

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	ZNF263	chr1:78353847-78354901	HEK293-T-REx	kidney:	n/a	n/a
2	YY1	chr1:78354476-78354655	K562	blood:	n/a	n/a
3	TBP	chr1:78353785-78354857	H1-hESC	embryonic stem cell:	n/a	n/a
4	TCF12	chr1:78353994-78354986	ECC-1	luminal epithelium:	n/a	n/a
5	POLR2A	chr1:78354091-78355697	MCF10A-Er-Src	breast:	n/a	n/a
6	EGR1	chr1:78354311-78354631	K562	blood:	n/a	n/a
7	MAX	chr1:78353771-78354881	H1-hESC	embryonic stem cell:	n/a	n/a
8	ZNF143	chr1:78353800-78354881	H1-hESC	embryonic stem cell:	n/a	n/a
9	POLR2A	chr1:78353839-78354712	HepG2	liver:	n/a	n/a
10	POLR2A	chr1:78353729-78354692	HUVEC	blood vessel:	n/a	n/a
11	POLR2A	chr1:78353686-78354848	PFSK-1	brain:	n/a	n/a
12	POLR2A	chr1:78353771-78354894	HepG2	liver:	n/a	n/a
13	TEAD4	chr1:78353793-78354820	SK-N-SH	brain:	n/a	n/a
14	YY1	chr1:78353673-78354873	H1-hESC	embryonic stem cell:	n/a	n/a
15	POLR2A	chr1:78354117-78354610	PANC-1	pancreas:	n/a	n/a
16	TAF7	chr1:78353761-78354829	H1-hESC	embryonic stem cell:	n/a	n/a
17	MAX	chr1:78353738-78354725	SK-N-SH	brain:	n/a	n/a
18	PAX5	chr1:78354384-78354763	GM12892	blood:	n/a	n/a
19	UBTF	chr1:78354098-78354885	K562	blood:	n/a	n/a
20	POLR2A	chr1:78353710-78354944	H1-hESC	embryonic stem cell:	n/a	n/a
21	POLR2A	chr1:78354032-78354878	HUVEC	blood vessel:	n/a	n/a
22	SIN3A	chr1:78353805-78355436	H1-hESC	embryonic stem cell:	n/a	chr1:78355401-78355411
23	YY1	chr1:78354406-78354832	H1-hESC	embryonic stem cell:	n/a	n/a
24	MAX	chr1:78353770-78354889	H1-hESC	embryonic stem cell:	n/a	n/a
25	POLR2A	chr1:78353793-78354871	H1-hESC	embryonic stem cell:	n/a	n/a
26	EBF1	chr1:78354552-78354774	GM12878	blood:	n/a	n/a
27	POLR2A	chr1:78353649-78354668	PFSK-1	brain:	n/a	n/a
28	CHD2	chr1:78354479-78354764	H1-hESC	embryonic stem cell:	n/a	n/a
29	YY1	chr1:78354322-78354669	SK-N-SH_RA	brain:	n/a	n/a
30	YY1	chr1:78354434-78354737	GM12892	blood:	n/a	n/a
31	POLR2A	chr1:78353687-78354724	HUVEC	blood vessel:	n/a	n/a
32	ZBTB7A	chr1:78353821-78355219	ECC-1	luminal epithelium:	n/a	n/a
33	TAF1	chr1:78354048-78354825	ECC-1	luminal epithelium:	n/a	n/a
34	EP300	chr1:78353711-78354797	SK-N-SH	brain:	n/a	n/a
35	EP300	chr1:78353900-78354699	ECC-1	luminal epithelium:	n/a	n/a
36	JUND	chr1:78354477-78354677	H1-hESC	embryonic stem cell:	n/a	n/a
37	RUNX3	chr1:78354454-78354795	GM12878	blood:	n/a	n/a
38	ZBTB7A	chr1:78354252-78354608	K562	blood:	n/a	n/a
39	POLR2A	chr1:78354584-78354861	Gliobla	brain:	n/a	n/a
40	HMGN3	chr1:78354048-78354926	K562	blood:	n/a	n/a
41	YY1	chr1:78354328-78354856	HepG2	liver:	n/a	n/a
42	POLR2A	chr1:78353767-78355862	IMR90	lung:	n/a	n/a
43	POLR2A	chr1:78353683-78355811	HUVEC	blood vessel:	n/a	n/a
44	ZBTB7A	chr1:78354078-78354652	HepG2	liver:	n/a	n/a
45	UBTF	chr1:78353811-78354912	K562	blood:	n/a	n/a
46	POLR2A	chr1:78354529-78354812	ECC-1	luminal epithelium:	n/a	n/a
47	MAX	chr1:78353950-78354642	A549	lung:	n/a	n/a
48	MAX	chr1:78353877-78354770	ECC-1	luminal epithelium:	n/a	n/a
49	TAF1	chr1:78353848-78354867	H1-hESC	embryonic stem cell:	n/a	n/a
50	ZBTB7A	chr1:78353816-78354949	K562	blood:	n/a	n/a

No data

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

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr1:78354412..78357543-chr1:78468778..78471529,4	K562	blood:

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

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-FUBP1-1	chr1:78353285-78354953	ENSG00000235927

No data

Variant related genes	Relation type
NEXN-AS1	TF binding region
ENSG00000162616	Chromatin interaction
ENSG00000273338	Chromatin interaction

Extended variants
information (count: 10 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:6)

rs_ID	r²[population]
rs1166698	0.86[CHB][hapmap];1.00[JPT][hapmap]
rs28735417	0.89[CHB][hapmap]
rs6424659	0.85[CHB][hapmap];0.90[JPT][hapmap]
rs6699769	0.86[CHB][hapmap];0.90[JPT][hapmap]
rs6702939	0.86[CHB][hapmap];0.90[JPT][hapmap]
rs7537908	0.86[CHB][hapmap];0.91[JPT][hapmap]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv1794082	chr1:78102426-78492221	Weak transcription Flanking Active TSS Active TSS Enhancers Genic enhancers Strong transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	108 gene(s)	inside rSNPs	diseases
2	esv3434340	chr1:78153780-78607103	Weak transcription Enhancers Strong transcription Flanking Active TSS Genic enhancers Active TSS Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	98 gene(s)	inside rSNPs	diseases
3	nsv1006600	chr1:78222312-78384009	Weak transcription Strong transcription Transcr. at gene 5' and 3' Flanking Active TSS Enhancers Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	24 gene(s)	inside rSNPs	diseases
4	nsv535011	chr1:78222312-78384009	Weak transcription Strong transcription Flanking Bivalent TSS/Enh Active TSS Enhancers Flanking Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats Genic enhancers Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	24 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs9726525	DNAJB4	Cis_1M	lymphoblastoid	RTeQTL
rs9726525	NEXN	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:122 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:78352400-78359800	Active TSS	Right Ventricle	heart
2	chr1:78353200-78355600	Active TSS	Left Ventricle	heart
3	chr1:78353200-78355800	Active TSS	Psoas Muscle	Psoas
4	chr1:78353200-78357200	Active TSS	Duodenum Smooth Muscle	Duodenum
5	chr1:78353200-78359200	Active TSS	Right Atrium	heart
6	chr1:78353400-78356000	Active TSS	iPS-20b Cell Line	embryonic stem cell
7	chr1:78353400-78356400	Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
8	chr1:78353400-78356400	Active TSS	HSMM	muscle
9	chr1:78353400-78357000	Active TSS	IMR90 fetal lung fibroblasts Cell Line	lung
10	chr1:78353400-78357000	Active TSS	NHLF	lung
11	chr1:78353600-78355000	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
12	chr1:78353600-78355200	Active TSS	H9 Derived Neuron Cultured Cells	ES cell derived
13	chr1:78353600-78355200	Active TSS	HUES48 Cell Line	embryonic stem cell
14	chr1:78353600-78355400	Active TSS	H9 Cell Line	embryonic stem cell
15	chr1:78353600-78355600	Active TSS	Pancreatic Islets	Pancreatic Islet
16	chr1:78353600-78355600	Active TSS	Ovary	ovary
17	chr1:78353600-78355800	Active TSS	HUES6 Cell Line	embryonic stem cell
18	chr1:78353600-78356000	Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
19	chr1:78353600-78357000	Active TSS	Breast Myoepithelial Primary Cells	Breast
20	chr1:78353800-78354600	Bivalent/Poised TSS	Fetal Brain Female	brain
21	chr1:78353800-78354800	Active TSS	H1 Derived Mesenchymal Stem Cells	ES cell derived
22	chr1:78353800-78354800	Flanking Active TSS	Foreskin Fibroblast Primary Cells skin02	Skin
23	chr1:78353800-78355000	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Female	--
24	chr1:78353800-78355200	Active TSS	HUES64 Cell Line	embryonic stem cell
25	chr1:78353800-78355200	Active TSS	iPS-15b Cell Line	embryonic stem cell
26	chr1:78353800-78355200	Active TSS	iPS DF 19.11 Cell Line	embryonic stem cell
27	chr1:78353800-78355200	Flanking Active TSS	Primary hematopoietic stem cells short term culture	blood
28	chr1:78353800-78355200	Active TSS	Brain Dorsolateral Prefrontal Cortex	brain
29	chr1:78353800-78355200	Active TSS	Pancreas	Pancrea
30	chr1:78353800-78355400	Active TSS	iPS DF 6.9 Cell Line	embryonic stem cell
31	chr1:78353800-78355400	Active TSS	Primary hematopoietic stem cells	blood
32	chr1:78353800-78355400	Active TSS	Brain Angular Gyrus	brain
33	chr1:78353800-78355400	Active TSS	Brain Cingulate Gyrus	brain
34	chr1:78353800-78355400	Active TSS	Fetal Kidney	kidney
35	chr1:78353800-78355400	Active TSS	HepG2	liver
36	chr1:78353800-78355600	Active TSS	ES-WA7 Cell Line	embryonic stem cell
37	chr1:78353800-78355600	Active TSS	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
38	chr1:78353800-78355600	Active TSS	A549	lung
39	chr1:78353800-78355800	Active TSS	ES-I3 Cell Line	embryonic stem cell
40	chr1:78353800-78355800	Active TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
41	chr1:78353800-78355800	Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
42	chr1:78353800-78355800	Active TSS	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
43	chr1:78353800-78355800	Active TSS	Rectal Mucosa Donor 29	rectum
44	chr1:78353800-78356000	Active TSS	Fetal Intestine Large	intestine
45	chr1:78353800-78356400	Active TSS	Muscle Satellite Cultured Cells	--
46	chr1:78353800-78356600	Active TSS	Colon Smooth Muscle	Colon
47	chr1:78353800-78358400	Active TSS	Aorta	Aorta
48	chr1:78354000-78354600	Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
49	chr1:78354000-78354600	Bivalent Enhancer	Fetal Brain Male	brain
50	chr1:78354000-78354800	Active TSS	Brain Germinal Matrix	brain

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