Variant report

Variant	rs4478801
Chromosome Location	chr1:154464572-154464573
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	NFIC	chr1:154464494-154465122	GM12878	blood:	n/a	n/a
2	RUNX3	chr1:154464264-154465102	GM12878	blood:	n/a	n/a
3	EP300	chr1:154464475-154464957	GM12878	blood:	n/a	n/a
4	RUNX3	chr1:154464292-154465185	GM12878	blood:	n/a	n/a
5	ATF2	chr1:154464513-154465019	GM12878	blood:	n/a	n/a
6	EBF1	chr1:154464568-154464941	GM12878	blood:	n/a	n/a
7	EBF1	chr1:154464474-154465450	GM12878	blood:	n/a	n/a
8	FOXM1	chr1:154464567-154465048	GM12878	blood:	n/a	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr1:154463006..154464587-chr1:154519369..154521445,2	K562	blood:

Variant related genes	Relation type
SHE	TF binding region

Extended variants
information (count: 42 )
Associated
traits (count: 5 )

rSNPs within LD-proxies of this variant (count:39)

rs_ID	r²[population]
rs10908841	0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10908842	1.00[YRI][hapmap];0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10908843	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];0.94[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10908845	0.82[AMR][1000 genomes];0.94[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs10908847	0.99[AMR][1000 genomes];0.94[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs11265621	0.96[CEU][hapmap];0.89[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.90[AMR][1000 genomes];0.96[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs11265622	1.00[ASW][hapmap];1.00[CEU][hapmap];0.92[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.92[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11265628	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11265632	0.90[AFR][1000 genomes];0.98[AMR][1000 genomes];0.92[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs12037271	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.87[AFR][1000 genomes];0.93[AMR][1000 genomes];0.93[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12118018	0.88[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12119111	0.87[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12128408	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12136771	1.00[ASW][hapmap];0.96[CEU][hapmap];0.92[CHB][hapmap];0.94[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.95[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.90[AFR][1000 genomes];0.98[AMR][1000 genomes];0.92[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12407048	0.84[AFR][1000 genomes];1.00[AMR][1000 genomes];0.94[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12568083	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];0.92[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12740969	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12753666	0.91[AFR][1000 genomes];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs12753680	0.96[AMR][1000 genomes];0.95[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs4074436	0.86[LWK][hapmap]
rs4345797	0.88[AMR][1000 genomes];0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4382717	0.88[AMR][1000 genomes];0.86[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs4584384	0.96[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.88[AMR][1000 genomes];0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4638123	0.84[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.99[AMR][1000 genomes];0.94[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4845637	0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4845638	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4845639	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4845642	0.88[AMR][1000 genomes];0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4845647	0.86[AMR][1000 genomes];0.92[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs5018567	1.00[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.88[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6658175	0.87[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6664608	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6684921	1.00[ASW][hapmap];1.00[CEU][hapmap];0.92[CHB][hapmap];0.97[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];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs6686276	1.00[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6689965	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6700296	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.95[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7518694	0.88[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7519499	0.88[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs9660786	0.88[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv948413	chr1:153974621-154797272	Enhancers Weak transcription Strong transcription Flanking Active TSS Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3' Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	132 gene(s)	inside rSNPs	diseases
2	nsv1000402	chr1:153991106-154527053	Strong transcription Flanking Active TSS Enhancers Genic enhancers Flanking Bivalent TSS/Enh Weak transcription Transcr. at gene 5' and 3' Active TSS Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	106 gene(s)	inside rSNPs	diseases
3	nsv521887	chr1:154236570-154684106	Strong transcription Flanking Active TSS Active TSS Weak transcription Enhancers Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	65 gene(s)	inside rSNPs	diseases

mRNA abundance (count:5)

SNP	Gene	Cis/trans	Tissue	Source
rs4478801	LCE2B	cis	cerebellum	SCAN
rs4478801	EFNA4	cis	parietal	SCAN
rs4478801	SHC1	cis	parietal	SCAN
rs4478801	CRNN	cis	cerebellum	SCAN
rs4478801	S100A3	cis	parietal	SCAN

Chromatin state (count:39 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:154427800-154464800	Weak transcription	Ovary	ovary
2	chr1:154441600-154465200	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
3	chr1:154451600-154465600	Weak transcription	ES-I3 Cell Line	embryonic stem cell
4	chr1:154458600-154469000	Weak transcription	Small Intestine	intestine
5	chr1:154459200-154464800	Weak transcription	Brain Anterior Caudate	brain
6	chr1:154459400-154465600	Weak transcription	Liver	Liver
7	chr1:154461400-154466400	Enhancers	Spleen	Spleen
8	chr1:154461600-154464600	Weak transcription	Breast Myoepithelial Primary Cells	Breast
9	chr1:154461800-154465600	Enhancers	Adipose Nuclei	Adipose
10	chr1:154461800-154465800	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
11	chr1:154461800-154467000	Enhancers	Primary monocytes fromperipheralblood	blood
12	chr1:154461800-154473800	Weak transcription	Pancreas	Pancrea
13	chr1:154462800-154464800	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
14	chr1:154462800-154465400	Enhancers	Primary B cells from cord blood	blood
15	chr1:154462800-154467200	Enhancers	Primary B cells from peripheral blood	blood
16	chr1:154463000-154465000	Enhancers	Right Atrium	heart
17	chr1:154463000-154468000	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
18	chr1:154463200-154465000	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
19	chr1:154463200-154466200	Weak transcription	Duodenum Mucosa	Duodenum
20	chr1:154463200-154467600	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
21	chr1:154463600-154465400	Genic enhancers	HUVEC	blood vessel
22	chr1:154463800-154465400	Weak transcription	Sigmoid Colon	Sigmoid Colon
23	chr1:154464000-154465000	Genic enhancers	Fetal Adrenal Gland	Adrenal Gland
24	chr1:154464000-154465000	Weak transcription	K562	blood
25	chr1:154464000-154466600	Enhancers	Skeletal Muscle Male	skeletal muscle
26	chr1:154464000-154472400	Weak transcription	Lung	lung
27	chr1:154464200-154464600	Enhancers	Rectal Mucosa Donor 29	rectum
28	chr1:154464200-154464800	Genic enhancers	Left Ventricle	heart
29	chr1:154464200-154465400	Enhancers	Primary hematopoietic stem cells short term culture	blood
30	chr1:154464200-154465400	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
31	chr1:154464200-154465400	Enhancers	Placenta	Placenta
32	chr1:154464200-154465800	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
33	chr1:154464200-154466600	Enhancers	Primary neutrophils fromperipheralblood	blood
34	chr1:154464200-154466800	Enhancers	Primary hematopoietic stem cells	blood
35	chr1:154464200-154467600	Weak transcription	Right Ventricle	heart
36	chr1:154464400-154464600	Enhancers	Colon Smooth Muscle	Colon
37	chr1:154464400-154464600	Enhancers	GM12878-XiMat	blood
38	chr1:154464400-154464600	Flanking Active TSS	Monocytes-CD14+_RO01746	blood
39	chr1:154464400-154465600	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--

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