Variant report

Variant	rs4845408
Chromosome Location	chr1:155065627-155065628
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:0)
CpG islands
(count:0)
Chromatin interactive
region (count:19)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

(count:19 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr1:155064094..155065891-chr1:155117626..155119134,2	MCF-7	breast:
2	chr1:155056065..155060440-chr1:155062354..155065779,6	K562	blood:
3	chr1:155063960..155065905-chr1:155106879..155109737,2	K562	blood:
4	chr1:155056491..155066482-chr1:155136760..155147519,21	K562	blood:
5	chr1:155064687..155066465-chr1:155098268..155100764,2	K562	blood:
6	chr1:155062448..155069217-chr1:155142816..155147773,12	MCF-7	breast:
7	chr1:155065499..155067791-chr1:155070241..155073223,2	MCF-7	breast:
8	chr1:155055416..155060440-chr1:155063419..155068026,8	K562	blood:
9	chr1:155064469..155067923-chr1:155161991..155164572,4	MCF-7	breast:
10	chr1:155063776..155066689-chr1:155134444..155136393,2	MCF-7	breast:
11	chr1:154931783..154934509-chr1:155065563..155068170,2	MCF-7	breast:
12	chr1:155063703..155067297-chr1:155143302..155147272,4	K562	blood:
13	chr1:155049589..155073019-chr1:155085330..155115362,149	MCF-7	breast:
14	chr1:155061878..155067935-chr1:155138836..155144212,15	MCF-7	breast:
15	chr1:155061833..155068204-chr1:155135824..155142287,19	MCF-7	breast:
16	chr1:155064648..155066932-chr1:155147928..155150182,2	K562	blood:
17	chr1:155062611..155066935-chr1:155144495..155147775,5	MCF-7	breast:
18	chr1:155064464..155066465-chr1:155098268..155100764,3	K562	blood:
19	chr1:155063203..155065869-chr1:155133125..155134696,2	K562	blood:

No data

Variant related genes	Relation type
ENSG00000163462	Chromatin interaction
ENSG00000163463	Chromatin interaction
ENSG00000202027	Chromatin interaction
ENSG00000271380	Chromatin interaction
ENSG00000169242	Chromatin interaction
ENSG00000179085	Chromatin interaction
ENSG00000163348	Chromatin interaction
ENSG00000143590	Chromatin interaction
ENSG00000169241	Chromatin interaction
ENSG00000185499	Chromatin interaction

Extended variants
information (count: 71 )
Associated
traits (count: 7 )

rSNPs within LD-proxies of this variant (count:66)

rs_ID	r²[population]
rs1001848	1.00[JPT][hapmap]
rs10157801	0.85[JPT][hapmap]
rs10796938	0.97[ASN][1000 genomes]
rs10796939	0.93[ASN][1000 genomes]
rs10908454	1.00[CHB][hapmap];0.94[CHD][hapmap];1.00[JPT][hapmap];0.97[ASN][1000 genomes]
rs10908455	1.00[CHB][hapmap];0.94[CHD][hapmap];1.00[JPT][hapmap];0.97[ASN][1000 genomes]
rs10908456	1.00[CHB][hapmap];0.88[CHD][hapmap];1.00[JPT][hapmap];0.97[ASN][1000 genomes]
rs10908458	0.85[JPT][hapmap]
rs11264304	0.85[JPT][hapmap]
rs11264306	1.00[JPT][hapmap]
rs11264312	0.97[ASN][1000 genomes]
rs11264313	0.95[ASN][1000 genomes]
rs11264314	1.00[CHB][hapmap];1.00[JPT][hapmap];0.97[ASN][1000 genomes]
rs11264319	1.00[CHB][hapmap];1.00[JPT][hapmap];0.97[ASN][1000 genomes]
rs11264321	0.97[ASN][1000 genomes]
rs11264322	0.95[ASN][1000 genomes]
rs11264327	0.95[ASN][1000 genomes]
rs11264328	0.95[ASN][1000 genomes]
rs11264329	1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[ASN][1000 genomes]
rs12025371	0.85[JPT][hapmap]
rs12026113	0.91[AFR][1000 genomes];0.97[AMR][1000 genomes];0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12028043	0.85[JPT][hapmap]
rs12039316	0.97[ASN][1000 genomes]
rs12040970	1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[ASN][1000 genomes]
rs12145362	1.00[CHB][hapmap];0.83[CHD][hapmap];1.00[JPT][hapmap];0.95[ASN][1000 genomes]
rs12904	0.85[JPT][hapmap]
rs1462855	1.00[CHB][hapmap];0.94[CHD][hapmap];1.00[JPT][hapmap];0.97[ASN][1000 genomes]
rs1870939	1.00[CHB][hapmap];1.00[JPT][hapmap];0.97[ASN][1000 genomes]
rs2306124	1.00[CHB][hapmap];0.94[CHD][hapmap];1.00[JPT][hapmap];0.97[ASN][1000 genomes]
rs2306125	1.00[LWK][hapmap]
rs34815285	0.81[ASN][1000 genomes]
rs35902694	0.85[JPT][hapmap]
rs3765087	1.00[JPT][hapmap]
rs3766916	1.00[JPT][hapmap]
rs3766918	0.97[ASN][1000 genomes]
rs3806256	0.85[JPT][hapmap]
rs4045192	0.85[JPT][hapmap]
rs4246529	0.85[JPT][hapmap]
rs4276913	0.85[JPT][hapmap]
rs4303067	0.93[ASN][1000 genomes]
rs4361977	0.97[ASN][1000 genomes]
rs4625273	0.97[ASN][1000 genomes]
rs4745	0.85[JPT][hapmap]
rs4845407	1.00[JPT][hapmap]
rs4971052	1.00[JPT][hapmap]
rs4971066	1.00[ASW][hapmap];0.85[JPT][hapmap];1.00[LWK][hapmap];0.83[MEX][hapmap];1.00[AFR][1000 genomes];0.81[AMR][1000 genomes]
rs4971073	0.85[JPT][hapmap]
rs4971076	0.85[JPT][hapmap]
rs4971079	0.85[JPT][hapmap]
rs56112907	0.97[ASN][1000 genomes]
rs6427158	1.00[CHB][hapmap];0.88[CHD][hapmap];1.00[JPT][hapmap];0.97[ASN][1000 genomes]
rs6665822	1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[ASN][1000 genomes]
rs6693477	1.00[CHB][hapmap];0.82[CHD][hapmap];1.00[JPT][hapmap];0.97[ASN][1000 genomes]
rs7364524	0.85[JPT][hapmap]
rs7364869	0.97[ASN][1000 genomes]
rs7365544	1.00[CHB][hapmap];0.88[CHD][hapmap];1.00[JPT][hapmap];0.97[ASN][1000 genomes]
rs7366138	0.98[ASN][1000 genomes]
rs7366355	0.97[ASN][1000 genomes]
rs7367207	1.00[CHB][hapmap];0.94[CHD][hapmap];1.00[JPT][hapmap];0.97[ASN][1000 genomes]
rs7367758	0.91[AFR][1000 genomes];0.94[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs7367897	1.00[CHB][hapmap];1.00[JPT][hapmap];0.97[ASN][1000 genomes]
rs7368345	1.00[CHB][hapmap];0.88[CHD][hapmap];1.00[JPT][hapmap];0.97[ASN][1000 genomes]
rs7534162	1.00[CHB][hapmap];0.88[CHD][hapmap];1.00[JPT][hapmap];0.97[ASN][1000 genomes]
rs7548955	1.00[CHB][hapmap];0.88[CHD][hapmap];1.00[JPT][hapmap];0.97[ASN][1000 genomes]
rs9297	0.85[JPT][hapmap]
rs9330263	0.90[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:5 , 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
5	esv2762194	chr1:155063145-155067283	Flanking Active TSS Weak transcription Bivalent Enhancer Enhancers Flanking Bivalent TSS/Enh Genic enhancers Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3'	Chromatin interactive region	14 gene(s)	inside rSNPs	diseases

mRNA abundance (count:7)

SNP	Gene	Cis/trans	Tissue	Source
rs4845408	NES	cis	parietal	SCAN
rs4845408	TPM3	cis	parietal	SCAN
rs4845408	OAZ3	cis	parietal	SCAN
rs4845408	SETDB1	cis	parietal	SCAN
rs4845408	PGLYRP4	cis	cerebellum	SCAN
rs4845408	C1orf56	cis	parietal	SCAN
rs4845408	UBE2Q1	cis	cerebellum	SCAN

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:155058600-155066000	Weak transcription	Right Atrium	heart
2	chr1:155059000-155066200	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
3	chr1:155059200-155066600	Weak transcription	Primary B cells from cord blood	blood
4	chr1:155059800-155066400	Weak transcription	Primary hematopoietic stem cells	blood
5	chr1:155063400-155067200	Bivalent Enhancer	Fetal Muscle Trunk	muscle
6	chr1:155063600-155067200	Enhancers	Right Ventricle	heart
7	chr1:155064000-155066000	Weak transcription	Primary monocytes fromperipheralblood	blood
8	chr1:155064200-155065800	Weak transcription	Duodenum Mucosa	Duodenum
9	chr1:155064200-155066200	Weak transcription	Duodenum Smooth Muscle	Duodenum
10	chr1:155064200-155066200	Weak transcription	Placenta Amnion	Placenta Amnion
11	chr1:155064200-155066600	Weak transcription	GM12878-XiMat	blood
12	chr1:155064400-155065800	Weak transcription	Brain Anterior Caudate	brain
13	chr1:155064400-155065800	Weak transcription	Brain Inferior Temporal Lobe	brain
14	chr1:155064400-155065800	Weak transcription	Brain Substantia Nigra	brain
15	chr1:155064400-155065800	Weak transcription	Colon Smooth Muscle	Colon
16	chr1:155064400-155065800	Weak transcription	Fetal Heart	heart
17	chr1:155064400-155065800	Weak transcription	Ovary	ovary
18	chr1:155064400-155066000	Weak transcription	Primary hematopoietic stem cells short term culture	blood
19	chr1:155064400-155066000	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
20	chr1:155064400-155066000	Weak transcription	Brain Angular Gyrus	brain
21	chr1:155064400-155066000	Weak transcription	Colonic Mucosa	Colon
22	chr1:155064400-155066000	Weak transcription	Lung	lung
23	chr1:155064400-155066000	Weak transcription	Rectal Smooth Muscle	rectum
24	chr1:155064400-155066200	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
25	chr1:155064400-155066200	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
26	chr1:155064400-155066200	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
27	chr1:155064400-155066200	Weak transcription	Adipose Nuclei	Adipose
28	chr1:155064400-155066200	Weak transcription	Esophagus	oesophagus
29	chr1:155064400-155066200	Weak transcription	Fetal Brain Female	brain
30	chr1:155064400-155066200	Weak transcription	Fetal Intestine Large	intestine
31	chr1:155064400-155066200	Weak transcription	Fetal Intestine Small	intestine
32	chr1:155064400-155066200	Weak transcription	Rectal Mucosa Donor 31	rectum
33	chr1:155064400-155066200	Weak transcription	Hela-S3	cervix
34	chr1:155064400-155066400	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
35	chr1:155064400-155066400	Weak transcription	Fetal Thymus	thymus
36	chr1:155064400-155066400	Weak transcription	Sigmoid Colon	Sigmoid Colon
37	chr1:155064400-155066400	Weak transcription	HSMM	muscle
38	chr1:155064400-155066600	Weak transcription	Stomach Mucosa	stomach
39	chr1:155064400-155066800	Weak transcription	Primary B cells from peripheral blood	blood
40	chr1:155064600-155065800	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
41	chr1:155064600-155066000	Weak transcription	Liver	Liver
42	chr1:155064600-155066000	Weak transcription	Brain Cingulate Gyrus	brain
43	chr1:155064600-155066000	Weak transcription	Skeletal Muscle Female	skeletal muscle
44	chr1:155064600-155066200	Weak transcription	Breast Myoepithelial Primary Cells	Breast
45	chr1:155064600-155066200	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
46	chr1:155064600-155066400	Weak transcription	Left Ventricle	heart
47	chr1:155064600-155066400	Enhancers	Stomach Smooth Muscle	stomach
48	chr1:155064600-155066600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
49	chr1:155064600-155066600	Weak transcription	Pancreas	Pancrea
50	chr1:155064600-155067000	Enhancers	iPS DF 19.11 Cell Line	embryonic stem cell

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