Variant report

Variant	rs4845407
Chromosome Location	chr1:155024309-155024310
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:40)
CpG islands
(count:61)
Chromatin interactive
region (count:34)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:40 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	MAX	chr1:155022783-155024806	Hela-S3	cervix:	n/a	chr1:155024142-155024152
2	CTCF	chr1:155024160-155024310	SK-N-SH_RA	brain:	n/a	n/a
3	POLR2A	chr1:155024305-155024322	HepG2	liver:	n/a	n/a
4	MAX	chr1:155022281-155024472	HepG2	liver:	n/a	chr1:155024142-155024152
5	POLR2A	chr1:155024249-155024637	Hela-S3	cervix:	n/a	n/a
6	POLR2A	chr1:155022492-155024748	Hela-S3	cervix:	n/a	n/a
7	EBF1	chr1:155024116-155024875	GM12878	blood:	n/a	n/a
8	EBF1	chr1:155024165-155024447	GM12878	blood:	n/a	n/a
9	SIN3A	chr1:155022846-155024406	H1-hESC	embryonic stem cell:	n/a	chr1:155024322-155024335
10	MAZ	chr1:155022074-155025318	IMR90	lung:	n/a	chr1:155024142-155024152
11	MAX	chr1:155022559-155024470	A549	lung:	n/a	chr1:155024142-155024152
12	MAX	chr1:155024249-155025563	NB4	blood:	n/a	n/a
13	MXI1	chr1:155022898-155024761	Hela-S3	cervix:	n/a	n/a
14	MAX	chr1:155022304-155024993	A549	lung:	n/a	chr1:155024142-155024152
15	E2F6	chr1:155022529-155024394	A549	lung:	n/a	chr1:155023541-155023551 chr1:155023046-155023053 chr1:155023045-155023057 chr1:155023558-155023567 chr1:155024135-155024145 chr1:155023046-155023053 chr1:155023044-155023055 chr1:155023046-155023053
16	UBTF	chr1:155022800-155024548	K562	blood:	n/a	n/a
17	SIN3AK20	chr1:155024120-155024763	PANC-1	pancreas:	n/a	n/a
18	MAX	chr1:155022484-155024462	HepG2	liver:	n/a	chr1:155024142-155024152
19	NFIC	chr1:155024215-155025001	ECC-1	luminal epithelium:	n/a	n/a
20	POLR2A	chr1:155022746-155024574	Hela-S3	cervix:	n/a	n/a
21	CTCF	chr1:155022092-155025540	SK-N-SH	brain:	n/a	chr1:155022948-155022957
22	GABPA	chr1:155023714-155024526	H1-hESC	embryonic stem cell:	n/a	n/a
23	MAX	chr1:155024144-155024939	SK-N-SH	brain:	n/a	n/a
24	ZBTB7A	chr1:155023350-155024992	ECC-1	luminal epithelium:	n/a	chr1:155024138-155024147
25	POLR2A	chr1:155024202-155025075	HUVEC	blood vessel:	n/a	n/a
26	MAZ	chr1:155022554-155025332	Hela-S3	cervix:	n/a	chr1:155024142-155024152
27	POLR2A	chr1:155022720-155024443	HL-60	blood:	n/a	n/a
28	ELF1	chr1:155023704-155025015	GM12878	blood:	n/a	n/a
29	MAX	chr1:155022722-155024310	ECC-1	luminal epithelium:	n/a	chr1:155024142-155024152
30	MXI1	chr1:155022033-155025750	SK-N-SH	brain:	n/a	n/a
31	ZNF263	chr1:155022667-155024404	HEK293-T-REx	kidney:	n/a	chr1:155023036-155023057
32	POLR2A	chr1:155024112-155026330	HUVEC	blood vessel:	n/a	n/a
33	MAX	chr1:155022591-155025597	MCF-7	breast:	n/a	chr1:155024142-155024152
34	MXI1	chr1:155022485-155025062	IMR90	lung:	n/a	n/a
35	CTCF	chr1:155024260-155024410	AG04449	skin:	n/a	n/a
36	ZBTB7A	chr1:155022796-155024416	ECC-1	luminal epithelium:	n/a	chr1:155024138-155024147
37	CTCF	chr1:155024185-155025503	A549	lung:	n/a	n/a
38	SMARCB1	chr1:155022856-155025422	Hela-S3	cervix:	n/a	n/a
39	MTA3	chr1:155022674-155024325	GM12878	blood:	n/a	n/a
40	CTCF	chr1:155024180-155024330	Hela-S3	cervix:	n/a	n/a

(count:61 , 50 per page) page: 1 2

No.	Chromosome Location	Cell Line	Cell type	Cell Stage
1	chr1:155024281-155024331	GM12878	blood:	n/a
2	chr1:155024281-155024331	HEEpiC	esophagus:	n/a
3	chr1:155024281-155024331	BE2_C	brain:	n/a
4	chr1:155024281-155024331	HCF	heart:	n/a
5	chr1:155024281-155024331	Hela-S3	cervix:	n/a
6	chr1:155024281-155024331	HNPCEpiC	eye:	n/a
7	chr1:155024281-155024331	PANC-1	pancreas:	n/a
8	chr1:155024281-155024331	BJ	skin:	n/a
9	chr1:155024281-155024331	NHDF-neo	bronchial:	n/a
10	chr1:155024281-155024331	HUVEC	blood vessel:	n/a
11	chr1:155024281-155024331	SAEC	small airway:	n/a
12	chr1:155024281-155024331	MCF10A-Er-Src	breast:	n/a
13	chr1:155024281-155024331	IMR90	lung:	fetal
14	chr1:155024281-155024331	H1-hESC	embryonic stem cell:	embryo
15	chr1:155024281-155024331	K562	blood:	n/a
16	chr1:155024281-155024331	CMK	blood:	n/a
17	chr1:155024281-155024331	AG04450	lung:	fetal
18	chr1:155024281-155024331	HCT-116	colon:	n/a
19	chr1:155024281-155024331	NB4	blood:	n/a
20	chr1:155024281-155024331	SK-N-SH_RA	brain:	n/a
21	chr1:155024281-155024331	GM06990	blood:	n/a
22	chr1:155024281-155024331	PrEC	prostate:	n/a
23	chr1:155024281-155024331	NHBE	bronchial:	n/a
24	chr1:155024281-155024331	LNCaP	prostate:	n/a
25	chr1:155024281-155024331	Jurkat	blood:	n/a
26	chr1:155024281-155024331	GM19239	blood:	n/a
27	chr1:155024281-155024331	HepG2	liver:	n/a
28	chr1:155024281-155024331	RPTEC	kidney:	n/a
29	chr1:155024281-155024331	GM12892	blood:	n/a
30	chr1:155024281-155024331	GM12891	blood:	n/a
31	chr1:155024281-155024331	SKMC	muscle:	n/a
32	chr1:155024281-155024331	HCPEpiC	choroid plexus:	n/a
33	chr1:155024281-155024331	HRPEpiC	eye:	n/a
34	chr1:155024281-155024331	ECC-1	luminal epithelium:	n/a
35	chr1:155024281-155024331	AG10803	skin:	n/a
36	chr1:155024281-155024331	ovcar-3	ovarian:	n/a
37	chr1:155024281-155024331	HIPEpiC	eye:	n/a
38	chr1:155024281-155024331	HRCEpiC	kidney:	n/a
39	chr1:155024281-155024331	HL-60	blood:	n/a
40	chr1:155024281-155024331	HRE	kidney:	n/a
41	chr1:155024281-155024331	HMEC	breast:	n/a
42	chr1:155024281-155024331	SK-N-SH	brain:	n/a
43	chr1:155024281-155024331	HCM	heart:	n/a
44	chr1:155024281-155024331	AG09309	skin:	n/a
45	chr1:155024281-155024331	AG09319	gingival:	n/a
46	chr1:155024281-155024331	HEK293	kidney:	embryo
47	chr1:155024281-155024331	A549	lung:	n/a
48	chr1:155024281-155024331	U87	brain:	n/a
49	chr1:155024281-155024331	MCF-7	breast:	n/a
50	chr1:155024281-155024331	T-47D	breast:	n/a

(count:34 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr1:154968418..154978887-chr1:155021582..155027516,28	MCF-7	breast:
2	chr1:155023966..155024815-chr15:93354070..93354859,2	Hela-S3	cervix:
3	chr1:154944682..154948805-chr1:155021065..155026491,10	K562	blood:
4	chr1:155022054..155026411-chr1:155097710..155103379,8	MCF-7	breast:
5	chr1:155017487..155020103-chr1:155021736..155024994,7	K562	blood:
6	chr1:154932783..154935696-chr1:155023491..155025451,2	K562	blood:
7	chr1:155023801..155025386-chr1:155162454..155164656,2	MCF-7	breast:
8	chr1:154941816..154947838-chr1:155021873..155026372,7	K562	blood:
9	chr1:155022097..155024403-chr1:155195809..155198176,3	MCF-7	breast:
10	chr1:154947156..154950628-chr1:155023259..155025337,3	MCF-7	breast:
11	chr1:154972344..154977668-chr1:155022111..155025561,8	K562	blood:
12	chr1:154932678..154935762-chr1:155021459..155026414,6	MCF-7	breast:
13	chr1:154944569..154947043-chr1:155022801..155024885,3	MCF-7	breast:
14	chr1:155023406..155024318-chr13:53029329..53030119,2	NB4	blood:
15	chr1:154965302..154967303-chr1:155021616..155024587,2	MCF-7	breast:
16	chr1:154907814..154911845-chr1:155021941..155025304,6	MCF-7	breast:
17	chr1:154937703..154939754-chr1:155022536..155025142,2	MCF-7	breast:
18	chr1:155023157..155025347-chr1:155091508..155094393,2	MCF-7	breast:
19	chr1:155020796..155024695-chr1:155055166..155059924,7	K562	blood:
20	chr1:154954181..154957294-chr1:155022241..155026637,5	MCF-7	breast:
21	chr1:154927595..154930613-chr1:155023082..155024913,3	K562	blood:
22	chr1:154972444..154977644-chr1:155020190..155026477,10	K562	blood:
23	chr1:154927691..154930617-chr1:155023229..155025423,2	MCF-7	breast:
24	chr1:154940784..154943173-chr1:155024006..155025972,2	MCF-7	breast:
25	chr1:155013927..155032770-chr1:155044175..155061131,53	MCF-7	breast:
26	chr1:155023320..155025791-chr1:155164716..155166404,2	K562	blood:
27	chr1:154927402..154930292-chr1:155021901..155025717,6	MCF-7	breast:
28	chr1:155023770..155024496-chrX:47092090..47092872,2	Hela-S3	cervix:
29	chr1:155021809..155025289-chr1:155144477..155147497,3	K562	blood:
30	chr1:155023137..155025267-chr1:155097110..155100006,3	MCF-7	breast:
31	chr1:154993321..154996248-chr1:155024180..155027135,2	K562	blood:
32	chr1:154955834..154958215-chr1:155023141..155024962,2	K562	blood:
33	chr1:154932378..154935696-chr1:155021679..155024991,3	K562	blood:
34	chr1:154872023..154874487-chr1:155024249..155025873,2	MCF-7	breast:

No data

Variant related genes	Relation type
ADAM15	TF binding region
ADAM15	CpG island
ENSG00000169242	Chromatin interaction
ENSG00000271380	Chromatin interaction
ENSG00000232093	Chromatin interaction
ENSG00000163462	Chromatin interaction
ENSG00000163463	Chromatin interaction
ENSG00000185499	Chromatin interaction
ENSG00000202027	Chromatin interaction
ENSG00000163344	Chromatin interaction
ENSG00000271748	Chromatin interaction
ENSG00000102226	Chromatin interaction
ENSG00000264349	Chromatin interaction
ENSG00000163352	Chromatin interaction
ENSG00000173207	Chromatin interaction
ENSG00000270361	Chromatin interaction
ENSG00000169231	Chromatin interaction
ENSG00000160691	Chromatin interaction
ENSG00000160766	Chromatin interaction
ENSG00000160688	Chromatin interaction
ENSG00000143590	Chromatin interaction
ENSG00000163346	Chromatin interaction
ENSG00000136108	Chromatin interaction
ENSG00000160685	Chromatin interaction
ENSG00000163348	Chromatin interaction

Extended variants
information (count: 51 )
Associated
traits (count: 11 )

rSNPs within LD-proxies of this variant (count:47)

rs_ID	r²[population]
rs1001848	1.00[JPT][hapmap]
rs10157801	0.85[JPT][hapmap]
rs10908454	1.00[JPT][hapmap]
rs10908455	1.00[JPT][hapmap]
rs10908456	1.00[JPT][hapmap]
rs10908458	0.85[JPT][hapmap]
rs11264304	0.85[JPT][hapmap]
rs11264306	1.00[JPT][hapmap]
rs11264314	1.00[JPT][hapmap]
rs11264319	1.00[JPT][hapmap]
rs11264329	1.00[JPT][hapmap]
rs12023499	0.86[CHB][hapmap]
rs12025371	0.85[JPT][hapmap]
rs12028043	0.85[JPT][hapmap]
rs12040970	1.00[JPT][hapmap]
rs12145362	1.00[JPT][hapmap]
rs12743272	1.00[ASW][hapmap];1.00[LWK][hapmap];0.86[MEX][hapmap];0.88[MKK][hapmap];0.83[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.81[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs12904	0.85[JPT][hapmap]
rs1462855	1.00[JPT][hapmap]
rs17723260	1.00[ASW][hapmap];1.00[LWK][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes]
rs1870939	1.00[JPT][hapmap]
rs2306124	1.00[JPT][hapmap]
rs35902694	0.85[JPT][hapmap]
rs3765087	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs3766916	1.00[JPT][hapmap]
rs3806256	0.85[JPT][hapmap]
rs4045192	0.85[JPT][hapmap]
rs4246529	0.85[JPT][hapmap]
rs4276913	0.85[JPT][hapmap]
rs4745	0.85[JPT][hapmap]
rs4845408	1.00[JPT][hapmap]
rs4971052	1.00[JPT][hapmap]
rs4971066	0.85[JPT][hapmap]
rs4971073	0.85[JPT][hapmap]
rs4971076	0.85[JPT][hapmap]
rs4971079	0.85[JPT][hapmap]
rs6427158	1.00[JPT][hapmap]
rs6665822	1.00[JPT][hapmap]
rs6693477	1.00[JPT][hapmap]
rs7364524	0.85[JPT][hapmap]
rs7365544	1.00[JPT][hapmap]
rs7367207	1.00[JPT][hapmap]
rs7367897	1.00[JPT][hapmap]
rs7368345	1.00[JPT][hapmap]
rs7534162	1.00[JPT][hapmap]
rs7548955	1.00[JPT][hapmap]
rs9297	0.85[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	nsv532579	chr1:154548165-155262692	Flanking Active TSS Enhancers Strong transcription Flanking Bivalent TSS/Enh Active TSS Weak transcription Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	575 gene(s)	inside rSNPs	diseases
2	nsv872454	chr1:154904840-155079477	Weak transcription Bivalent Enhancer Enhancers Active TSS Flanking Bivalent TSS/Enh Genic enhancers Flanking Active TSS Strong transcription Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	181 gene(s)	inside rSNPs	diseases
3	esv1823746	chr1:154965207-155231904	Enhancers Flanking Active TSS Active TSS Weak transcription Genic enhancers Strong transcription Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	469 gene(s)	inside rSNPs	diseases
4	nsv872455	chr1:155003954-155106550	Enhancers Active TSS Flanking Active TSS Weak transcription Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Strong transcription Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	74 gene(s)	inside rSNPs	diseases

mRNA abundance (count:11)

SNP	Gene	Cis/trans	Tissue	Source
rs4845407	ARHGEF11	cis	parietal	SCAN
rs4845407	TDRKH	cis	cerebellum	SCAN
rs4845407	APOA1BP	cis	cerebellum	SCAN
rs4845407	TPM3	cis	parietal	SCAN
rs4845407	ADAM15	cis	brain	BrainEAC
rs4845407	C1orf56	cis	parietal	SCAN
rs4845407	RXFP4	cis	parietal	SCAN
rs4845407	SMCP	cis	cerebellum	SCAN
rs4845407	ADAM15	cis	intralobular white matter	BrainEAC
rs4845407	S100A3	cis	parietal	SCAN
rs4845407	C1orf54	cis	cerebellum	SCAN

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:155022400-155025200	Flanking Active TSS	Skeletal Muscle Female	skeletal muscle
2	chr1:155022400-155025400	Flanking Active TSS	Foreskin Fibroblast Primary Cells skin02	Skin
3	chr1:155022400-155025400	Flanking Active TSS	Colonic Mucosa	Colon
4	chr1:155022400-155025600	Flanking Active TSS	Stomach Smooth Muscle	stomach
5	chr1:155022600-155025200	Flanking Active TSS	Primary B cells from cord blood	blood
6	chr1:155022600-155025200	Flanking Active TSS	Cortex derived primary cultured neurospheres	brain
7	chr1:155022600-155026000	Flanking Active TSS	Monocytes-CD14+_RO01746	blood
8	chr1:155022800-155024400	Active TSS	Primary T cells effector/memory enriched fromperipheralblood	blood
9	chr1:155022800-155024800	Active TSS	H9 Cell Line	embryonic stem cell
10	chr1:155022800-155024800	Active TSS	Aorta	Aorta
11	chr1:155022800-155025000	Flanking Active TSS	Foreskin Melanocyte Primary Cells skin03	Skin
12	chr1:155022800-155025000	Active TSS	Pancreatic Islets	Pancreatic Islet
13	chr1:155022800-155025200	Active TSS	Ovary	ovary
14	chr1:155022800-155025400	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Female	--
15	chr1:155022800-155026000	Flanking Active TSS	Primary hematopoietic stem cells short term culture	blood
16	chr1:155022800-155026200	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
17	chr1:155023000-155024400	Active TSS	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
18	chr1:155023000-155024400	Active TSS	Primary T helper naive cells from peripheral blood	blood
19	chr1:155023000-155024600	Active TSS	Brain Dorsolateral Prefrontal Cortex	brain
20	chr1:155023000-155024600	Active TSS	Brain Substantia Nigra	brain
21	chr1:155023000-155024600	Active TSS	Duodenum Smooth Muscle	Duodenum
22	chr1:155023000-155024800	Active TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
23	chr1:155023000-155024800	Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
24	chr1:155023000-155024800	Active TSS	Brain Angular Gyrus	brain
25	chr1:155023000-155024800	Active TSS	Brain Anterior Caudate	brain
26	chr1:155023000-155024800	Active TSS	Colon Smooth Muscle	Colon
27	chr1:155023000-155024800	Active TSS	Hela-S3	cervix
28	chr1:155023000-155025200	Active TSS	Fetal Kidney	kidney
29	chr1:155023000-155025200	Active TSS	Psoas Muscle	Psoas
30	chr1:155023000-155025200	Active TSS	Sigmoid Colon	Sigmoid Colon
31	chr1:155023000-155025600	Active TSS	Left Ventricle	heart
32	chr1:155023200-155024400	Active TSS	Primary T helper memory cells from peripheral blood 2	blood
33	chr1:155023200-155024600	Active TSS	Brain Cingulate Gyrus	brain
34	chr1:155023200-155024600	Active TSS	Brain Inferior Temporal Lobe	brain
35	chr1:155023200-155024600	Active TSS	Stomach Mucosa	stomach
36	chr1:155023200-155024800	Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
37	chr1:155023200-155024800	Active TSS	Rectal Smooth Muscle	rectum
38	chr1:155023200-155024800	Active TSS	A549	lung
39	chr1:155023200-155025000	Active TSS	Gastric	stomach
40	chr1:155023200-155025000	Active TSS	Small Intestine	intestine
41	chr1:155023200-155025800	Active TSS	HSMM	muscle
42	chr1:155023200-155026000	Active TSS	Right Atrium	heart
43	chr1:155023400-155024400	Active TSS	Primary T cells from cord blood	blood
44	chr1:155023400-155024400	Active TSS	Brain Hippocampus Middle	brain
45	chr1:155023400-155024400	Active TSS	Rectal Mucosa Donor 31	rectum
46	chr1:155023400-155024600	Active TSS	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
47	chr1:155023400-155024600	Active TSS	Primary T helper cells PMA-I stimulated	--
48	chr1:155023400-155024600	Transcr. at gene 5' and 3'	Primary T helper 17 cells PMA-I stimulated	--
49	chr1:155023400-155024600	Active TSS	Muscle Satellite Cultured Cells	--
50	chr1:155023400-155024600	Active TSS	NHLF	lung

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