Variant report

Variant	rs4652478
Chromosome Location	chr1:180120994-180120995
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:55)
CpG islands
(count:0)
Chromatin interactive
region (count:3)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:55 , 50 per page) page: 1 2

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	MAX	chr1:180120553-180121127	SK-N-SH	brain:	n/a	n/a
2	MAX	chr1:180120728-180121144	SK-N-SH	brain:	n/a	n/a
3	NFIC	chr1:180119959-180121269	SK-N-SH	brain:	n/a	n/a
4	POLR2A	chr1:180120425-180121250	HUVEC	blood vessel:	n/a	n/a
5	RCOR1	chr1:180120547-180121008	Hela-S3	cervix:	n/a	n/a
6	PBX3	chr1:180120077-180121120	SK-N-SH	brain:	n/a	n/a
7	MYC	chr1:180120674-180121026	MCF10A-Er-Src	breast:	n/a	n/a
8	TAF1	chr1:180120767-180121010	SK-N-SH	brain:	n/a	n/a
9	POLR2A	chr1:180120758-180121064	HUVEC	blood vessel:	n/a	n/a
10	NFIC	chr1:180120497-180121157	ECC-1	luminal epithelium:	n/a	n/a
11	JUND	chr1:180120495-180121071	Hela-S3	cervix:	n/a	n/a
12	POLR2A	chr1:180120544-180121058	SK-N-SH	brain:	n/a	n/a
13	FOS	chr1:180120534-180121063	MCF10A-Er-Src	breast:	n/a	n/a
14	JUN	chr1:180120550-180121042	Hela-S3	cervix:	n/a	n/a
15	JUND	chr1:180119969-180121393	SK-N-SH	brain:	n/a	n/a
16	TEAD4	chr1:180120498-180121138	SK-N-SH	brain:	n/a	n/a
17	GATA3	chr1:180120463-180121179	A549	lung:	n/a	n/a
18	POLR2A	chr1:180120528-180121130	HUVEC	blood vessel:	n/a	n/a
19	FOXA1	chr1:180120638-180121023	ECC-1	luminal epithelium:	n/a	n/a
20	GATA3	chr1:180120538-180121172	SK-N-SH	brain:	n/a	n/a
21	FOS	chr1:180120542-180121073	MCF10A-Er-Src	breast:	n/a	n/a
22	FOSL2	chr1:180120501-180121189	SK-N-SH	brain:	n/a	n/a
23	FOXP2	chr1:180120722-180121059	SK-N-MC	brain:	n/a	n/a
24	FOXA1	chr1:180120638-180121002	HepG2	liver:	n/a	n/a
25	FOSL2	chr1:180120440-180121234	SK-N-SH	brain:	n/a	n/a
26	MAX	chr1:180120648-180121184	Hela-S3	cervix:	n/a	n/a
27	TCF12	chr1:180119964-180121334	SK-N-SH	brain:	n/a	n/a
28	STAT3	chr1:180120654-180121026	MCF10A-Er-Src	breast:	n/a	n/a
29	POLR2A	chr1:180120635-180121310	SK-N-MC	brain:	n/a	n/a
30	FOXA1	chr1:180120762-180121028	ECC-1	luminal epithelium:	n/a	n/a
31	NFIC	chr1:180120542-180121111	SK-N-SH	brain:	n/a	n/a
32	JUND	chr1:180120410-180121212	SK-N-SH	brain:	n/a	n/a
33	FOXP2	chr1:180120823-180121050	SK-N-MC	brain:	n/a	n/a
34	POLR2A	chr1:180120960-180121039	HUVEC	blood vessel:	n/a	n/a
35	POLR2A	chr1:180120583-180121153	HUVEC	blood vessel:	n/a	n/a
36	FOSL2	chr1:180120790-180121060	HepG2	liver:	n/a	n/a
37	TEAD4	chr1:180120460-180121169	ECC-1	luminal epithelium:	n/a	n/a
38	FOS	chr1:180120541-180121078	MCF10A-Er-Src	breast:	n/a	n/a
39	FOS	chr1:180120567-180121013	Hela-S3	cervix:	n/a	n/a
40	MYC	chr1:180120733-180121060	MCF10A-Er-Src	breast:	n/a	n/a
41	FOSL2	chr1:180120539-180121124	A549	lung:	n/a	n/a
42	GATA3	chr1:180120470-180121272	SK-N-SH	brain:	n/a	n/a
43	FOS	chr1:180120393-180121096	HUVEC	blood vessel:	n/a	n/a
44	EP300	chr1:180120014-180121138	SK-N-SH	brain:	n/a	n/a
45	JUND	chr1:180120391-180121233	SK-N-SH	brain:	n/a	n/a
46	JUN	chr1:180120520-180121149	HUVEC	blood vessel:	n/a	n/a
47	EP300	chr1:180120440-180121140	ECC-1	luminal epithelium:	n/a	n/a
48	PBX3	chr1:180120040-180121176	SK-N-SH	brain:	n/a	n/a
49	TEAD4	chr1:180120620-180121115	ECC-1	luminal epithelium:	n/a	n/a
50	TCF12	chr1:180119998-180121307	SK-N-SH	brain:	n/a	n/a

No data

(count:3 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr1:179848997..179852603-chr1:180119148..180121667,3	K562	blood:
2	chr1:180103980..180105902-chr1:180120420..180121995,2	MCF-7	breast:
3	chr1:179849594..179851989-chr1:180117889..180121532,3	K562	blood:

No data

Variant related genes	Relation type
QSOX1	TF binding region
ENSG00000143337	Chromatin interaction
ENSG00000272906	Chromatin interaction

Extended variants
information (count: 60 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:52)

rs_ID	r²[population]
rs10798731	0.80[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs10798733	0.91[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs10913911	1.00[ASN][1000 genomes]
rs10913912	1.00[ASN][1000 genomes]
rs10913913	1.00[ASN][1000 genomes]
rs10913915	1.00[ASN][1000 genomes]
rs10913921	1.00[ASN][1000 genomes]
rs10913922	1.00[ASN][1000 genomes]
rs10913926	1.00[ASN][1000 genomes]
rs10913928	1.00[ASN][1000 genomes]
rs10913929	1.00[ASN][1000 genomes]
rs11579402	1.00[ASN][1000 genomes]
rs11589421	1.00[ASN][1000 genomes]
rs12117957	1.00[ASN][1000 genomes]
rs12119113	1.00[ASN][1000 genomes]
rs12120822	1.00[ASN][1000 genomes]
rs12124175	1.00[ASN][1000 genomes]
rs12124336	1.00[ASN][1000 genomes]
rs12127248	1.00[ASN][1000 genomes]
rs12129928	1.00[ASN][1000 genomes]
rs12131995	1.00[ASN][1000 genomes]
rs12135952	1.00[ASN][1000 genomes]
rs12138251	1.00[ASN][1000 genomes]
rs12141545	1.00[ASN][1000 genomes]
rs12144757	1.00[ASN][1000 genomes]
rs12743903	0.80[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs12744192	0.80[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs3845390	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4083553	0.89[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4652477	0.92[AFR][1000 genomes];0.90[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs55676403	1.00[ASN][1000 genomes]
rs55882713	1.00[ASN][1000 genomes]
rs56166206	1.00[ASN][1000 genomes]
rs58121876	1.00[ASN][1000 genomes]
rs59953116	1.00[ASN][1000 genomes]
rs61605706	1.00[ASN][1000 genomes]
rs6425605	1.00[ASN][1000 genomes]
rs6693288	1.00[ASN][1000 genomes]
rs6702845	0.88[AFR][1000 genomes];0.85[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs72710619	1.00[ASN][1000 genomes]
rs72710658	1.00[ASN][1000 genomes]
rs7521701	1.00[ASN][1000 genomes]
rs7521873	1.00[ASN][1000 genomes]
rs7522347	1.00[ASN][1000 genomes]
rs7533903	1.00[ASN][1000 genomes]
rs7538086	1.00[ASN][1000 genomes]
rs7539784	1.00[ASN][1000 genomes]
rs7550093	1.00[ASN][1000 genomes]
rs7555418	1.00[ASN][1000 genomes]
rs9425862	1.00[ASN][1000 genomes]
rs9425864	0.90[AFR][1000 genomes];0.85[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs9425869	0.93[AFR][1000 genomes];0.90[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][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	nsv429936	chr1:179790343-180214343	Active TSS Strong transcription Flanking Active TSS Weak transcription Enhancers Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	72 gene(s)	inside rSNPs	diseases
2	nsv1003739	chr1:180027760-180483292	Enhancers ZNF genes & repeats Weak transcription Flanking Bivalent TSS/Enh Strong transcription Flanking Active TSS Active TSS Genic enhancers Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	67 gene(s)	inside rSNPs	diseases
3	nsv535217	chr1:180027760-180483292	Enhancers Active TSS Flanking Active TSS Weak transcription ZNF genes & repeats Strong transcription Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	67 gene(s)	inside rSNPs	diseases
4	nsv1012558	chr1:180027960-180217613	Weak transcription Flanking Active TSS Flanking Bivalent TSS/Enh Enhancers Strong transcription Active TSS Bivalent/Poised TSS Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	33 gene(s)	inside rSNPs	diseases
5	nsv535218	chr1:180027960-180217613	Weak transcription Flanking Active TSS Strong transcription Bivalent Enhancer Bivalent/Poised TSS Enhancers Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	33 gene(s)	inside rSNPs	diseases
6	nsv497930	chr1:180031321-180220723	Flanking Bivalent TSS/Enh Weak transcription Bivalent/Poised TSS Flanking Active TSS Active TSS Genic enhancers Enhancers Bivalent Enhancer Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	33 gene(s)	inside rSNPs	diseases
7	nsv533073	chr1:180031328-180217612	Strong transcription Active TSS Enhancers Flanking Active TSS Genic enhancers Bivalent/Poised TSS Weak transcription Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	33 gene(s)	inside rSNPs	diseases
8	nsv916937	chr1:180031328-180220685	Strong transcription Weak transcription Flanking Bivalent TSS/Enh Enhancers Flanking Active TSS Bivalent Enhancer Genic enhancers Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	33 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:36 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:180118400-180123000	Weak transcription	Right Atrium	heart
2	chr1:180119400-180121400	Enhancers	NHEK	skin
3	chr1:180119600-180121200	Enhancers	HSMMtube	muscle
4	chr1:180119600-180121400	Enhancers	Primary monocytes fromperipheralblood	blood
5	chr1:180119600-180121400	Enhancers	Hela-S3	cervix
6	chr1:180119600-180122000	Enhancers	Foreskin Fibroblast Primary Cells skin02	Skin
7	chr1:180119600-180122800	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
8	chr1:180119600-180122800	Enhancers	Primary hematopoietic stem cells short term culture	blood
9	chr1:180119600-180123000	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
10	chr1:180119600-180123000	Enhancers	NHDF-Ad	bronchial
11	chr1:180119600-180123000	Enhancers	NHLF	lung
12	chr1:180119800-180121400	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
13	chr1:180119800-180121400	Enhancers	HSMM	muscle
14	chr1:180119800-180121800	Enhancers	Muscle Satellite Cultured Cells	--
15	chr1:180119800-180122200	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
16	chr1:180120000-180121200	Flanking Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
17	chr1:180120000-180121400	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
18	chr1:180120000-180121400	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
19	chr1:180120200-180121400	Enhancers	NH-A	brain
20	chr1:180120400-180121200	Enhancers	Primary hematopoietic stem cells	blood
21	chr1:180120400-180121200	Bivalent Enhancer	HepG2	liver
22	chr1:180120400-180121400	Flanking Active TSS	HUVEC	blood vessel
23	chr1:180120400-180121400	Flanking Active TSS	Osteobl	bone
24	chr1:180120400-180122200	Enhancers	HMEC	breast
25	chr1:180120400-180122800	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
26	chr1:180120400-180122800	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
27	chr1:180120400-180122800	Weak transcription	Fetal Lung	lung
28	chr1:180120400-180123000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
29	chr1:180120600-180121400	Enhancers	Primary neutrophils fromperipheralblood	blood
30	chr1:180120600-180121400	Flanking Active TSS	A549	lung
31	chr1:180120600-180121800	Weak transcription	Dnd41	blood
32	chr1:180120800-180121000	Enhancers	Primary B cells from cord blood	blood
33	chr1:180120800-180121200	Weak transcription	Pancreatic Islets	Pancreatic Islet
34	chr1:180120800-180121200	Weak transcription	Placenta	Placenta
35	chr1:180120800-180121400	Enhancers	Monocytes-CD14+_RO01746	blood
36	chr1:180120800-180122800	Weak transcription	Fetal Heart	heart

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