Variant report

Variant	rs945179
Chromosome Location	chr1:45992460-45992461
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:2)
CpG islands
(count:0)
Chromatin interactive
region (count:5)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

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

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	FOXA2	chr1:45991811-45992599	HepG2	liver:	n/a	n/a
2	FAM48A	chr1:45992330-45992497	GM12878	blood:	n/a	n/a

No data

(count:5 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr1:45990085..45992504-chr1:45996653..45999903,3	MCF-7	breast:
2	chr1:45990878..45992460-chr1:46016513..46018764,2	K562	blood:
3	chr1:45984791..45989119-chr1:45989451..45994043,12	MCF-7	breast:
4	chr1:45980210..45995142-chr1:46046095..46057139,89	K562	blood:
5	chr1:45974558..45995867-chr1:46046173..46057010,94	K562	blood:

No data

Variant related genes	Relation type
PRDX1	TF binding region
HMGB1P48	TF binding region
ENSG00000132780	Chromatin interaction
ENSG00000117448	Chromatin interaction
ENSG00000117450	Chromatin interaction

Extended variants
information (count: 84 )
Associated
traits (count: 22 )

rSNPs within LD-proxies of this variant (count:76)

rs_ID	r²[population]
rs1006215	1.00[JPT][hapmap]
rs10157597	0.89[AFR][1000 genomes];0.93[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs1044717	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10493120	0.81[CHD][hapmap];0.86[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap]
rs10736426	0.96[CEU][hapmap];0.96[GIH][hapmap];0.89[MEX][hapmap];0.94[TSI][hapmap];0.93[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs10789466	0.84[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs1088099	0.88[AMR][1000 genomes];0.98[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs11211110	0.81[CHD][hapmap];0.86[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap]
rs11211113	0.86[GIH][hapmap];1.00[MEX][hapmap]
rs11211115	1.00[JPT][hapmap]
rs11211132	1.00[ASW][hapmap];0.96[CEU][hapmap];0.91[CHD][hapmap];0.96[GIH][hapmap];0.88[LWK][hapmap];1.00[MEX][hapmap];0.87[MKK][hapmap];0.97[TSI][hapmap];0.90[YRI][hapmap];0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs11211133	1.00[ASN][1000 genomes]
rs11211134	0.93[EUR][1000 genomes]
rs11211138	0.82[EUR][1000 genomes]
rs12021717	1.00[ASN][1000 genomes]
rs12038608	0.86[AFR][1000 genomes];0.96[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs12042481	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.88[ASN][1000 genomes]
rs12047498	0.88[ASN][1000 genomes]
rs12048936	0.87[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs12082256	0.88[EUR][1000 genomes]
rs12145526	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs12729974	0.89[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12749658	0.82[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs1337902	1.00[CEU][hapmap];0.85[CHB][hapmap];0.90[YRI][hapmap];0.90[AFR][1000 genomes];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs1494813	1.00[ASW][hapmap];1.00[CEU][hapmap];0.85[CHB][hapmap];0.83[CHD][hapmap];1.00[GIH][hapmap];0.88[LWK][hapmap];1.00[MEX][hapmap];0.97[MKK][hapmap];0.97[TSI][hapmap];0.90[YRI][hapmap];0.90[AFR][1000 genomes];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs1691217	0.86[GIH][hapmap];1.00[JPT][hapmap];0.89[MEX][hapmap]
rs1771549	1.00[JPT][hapmap]
rs1974271	0.84[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs2065708	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.80[MKK][hapmap];1.00[ASN][1000 genomes]
rs2077808	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs2152077	0.95[CEU][hapmap];0.93[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs2356555	0.93[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs2356559	1.00[ASW][hapmap];0.96[CEU][hapmap];0.90[CHD][hapmap];0.96[GIH][hapmap];0.88[LWK][hapmap];1.00[MEX][hapmap];0.86[MKK][hapmap];0.97[TSI][hapmap];0.90[YRI][hapmap]
rs2356560	0.93[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs2356561	0.93[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs2991966	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2993257	0.86[AFR][1000 genomes];0.87[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs2993259	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs34315657	0.82[EUR][1000 genomes]
rs3748643	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[YRI][hapmap];0.92[AFR][1000 genomes];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs3748644	1.00[JPT][hapmap]
rs4233498	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs4660306	1.00[ASW][hapmap];0.96[CEU][hapmap];0.91[CHD][hapmap];0.96[GIH][hapmap];0.88[LWK][hapmap];1.00[MEX][hapmap];0.87[MKK][hapmap];0.97[TSI][hapmap];0.90[YRI][hapmap];0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs4660309	0.88[EUR][1000 genomes]
rs4660860	1.00[CEU][hapmap];0.85[CHB][hapmap];0.90[YRI][hapmap];0.90[AFR][1000 genomes];0.93[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs4660862	1.00[ASW][hapmap];1.00[CEU][hapmap];0.85[CHB][hapmap];0.84[CHD][hapmap];1.00[GIH][hapmap];0.88[LWK][hapmap];1.00[MEX][hapmap];0.97[MKK][hapmap];0.97[TSI][hapmap];0.90[YRI][hapmap];0.90[AFR][1000 genomes];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs4660864	1.00[ASW][hapmap];1.00[CEU][hapmap];0.85[CHB][hapmap];0.84[CHD][hapmap];1.00[GIH][hapmap];0.95[LWK][hapmap];1.00[MEX][hapmap];0.97[MKK][hapmap];0.97[TSI][hapmap];0.90[YRI][hapmap];0.95[AFR][1000 genomes];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs4660866	0.85[EUR][1000 genomes]
rs4660867	0.86[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs4660868	0.86[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs4660871	0.83[EUR][1000 genomes]
rs4660872	0.92[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs6429566	0.86[GIH][hapmap];0.89[MEX][hapmap]
rs6429567	1.00[CEU][hapmap];0.85[CHB][hapmap];0.90[YRI][hapmap];0.89[AFR][1000 genomes];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs6429569	0.96[CEU][hapmap];0.96[GIH][hapmap];0.95[TSI][hapmap];0.93[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs6667191	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6673477	0.83[EUR][1000 genomes]
rs6688424	0.81[AFR][1000 genomes];0.84[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs6688516	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7516006	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7522705	0.96[CEU][hapmap];0.96[GIH][hapmap];0.89[MEX][hapmap];0.97[TSI][hapmap];0.93[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs7534467	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs7536557	0.96[CEU][hapmap];0.96[GIH][hapmap];0.89[MEX][hapmap];0.97[TSI][hapmap];0.93[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs7539253	0.90[AFR][1000 genomes];0.93[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs7543076	0.95[AFR][1000 genomes];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs7546268	0.95[AFR][1000 genomes];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs7549093	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs781057	1.00[JPT][hapmap]
rs781059	0.84[GIH][hapmap];1.00[MEX][hapmap]
rs781060	0.86[GIH][hapmap];1.00[MEX][hapmap]
rs781062	1.00[JPT][hapmap]
rs781066	0.91[AMR][1000 genomes];0.98[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs882803	0.96[CEU][hapmap];0.96[GIH][hapmap];0.88[MEX][hapmap];0.94[TSI][hapmap];0.93[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs937290	1.00[ASW][hapmap];1.00[CEU][hapmap];0.85[CHB][hapmap];0.84[CHD][hapmap];1.00[GIH][hapmap];0.88[LWK][hapmap];1.00[MEX][hapmap];0.97[MKK][hapmap];0.97[TSI][hapmap];0.90[YRI][hapmap];0.90[AFR][1000 genomes];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs9725380	0.92[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs9803979	0.93[AMR][1000 genomes];0.95[EUR][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	nsv498036	chr1:45428030-46050934	Active TSS Enhancers Flanking Active TSS Genic enhancers Weak transcription Strong transcription Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	191 gene(s)	inside rSNPs	diseases
2	esv1795802	chr1:45819489-46009818	Enhancers Weak transcription Active TSS Genic enhancers Flanking Active TSS Strong transcription Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	126 gene(s)	inside rSNPs	diseases
3	esv1831217	chr1:45819489-46009818	Strong transcription Enhancers Genic enhancers Active TSS Weak transcription Flanking Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	126 gene(s)	inside rSNPs	diseases
4	nsv530016	chr1:45868543-46069020	Flanking Active TSS Genic enhancers Weak transcription Active TSS Enhancers Transcr. at gene 5' and 3' Strong transcription Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	149 gene(s)	inside rSNPs	diseases
5	nsv829726	chr1:45897581-46103186	Weak transcription Enhancers Flanking Active TSS Strong transcription Active TSS Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	148 gene(s)	inside rSNPs	diseases
6	nsv529631	chr1:45905936-46335246	Enhancers Flanking Active TSS Transcr. at gene 5' and 3' Strong transcription Weak transcription Active TSS Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	207 gene(s)	inside rSNPs	diseases
7	nsv932680	chr1:45935520-46686477	Strong transcription Weak transcription Flanking Active TSS Active TSS Enhancers Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	232 gene(s)	inside rSNPs	diseases
8	nsv868828	chr1:45953923-46686477	Active TSS Weak transcription Enhancers Flanking Active TSS Strong transcription Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	232 gene(s)	inside rSNPs	diseases

mRNA abundance (count:22)

SNP	Gene	Cis/trans	Tissue	Source
rs945179	TESK2	cis	multi-tissue	Pritchard
rs945179	CCDC163P	cis	Esophagus Muscularis	GTEx
rs945179	CCDC163P	cis	Thyroid	GTEx
rs945179	CCDC163P	cis	Heart Left Ventricle	GTEx
rs945179	CCDC163P	cis	Skin Sun Exposed Lower leg	GTEx
rs945179	CCDC163P	cis	Whole Blood	GTEx
rs945179	CYP4Z2P	cis	parietal	SCAN
rs945179	CCDC163P	cis	Artery Aorta	GTEx
rs945179	BEND5	cis	cerebellum	SCAN
rs945179	CCDC163P	cis	lymphoblastoid	seeQTL
rs945179	ST3GAL3	cis	parietal	SCAN
rs945179	CCDC163P	cis	Artery Tibial	GTEx
rs945179	TESK2	cis	lymphoblastoid	seeQTL
rs945179	CCDC163P	cis	Esophagus Mucosa	GTEx
rs945179	CCDC163P	cis	Adipose Subcutaneous	GTEx
rs945179	LOC126661	cis	multi-tissue	Pritchard
rs945179	CCDC163P	cis	Muscle Skeletal	GTEx
rs945179	LOC126661	cis	uninvolved skin	skin_eQTL
rs945179	CCDC163P	cis	lung	GTEx
rs945179	CYP4A11	cis	parietal	SCAN
rs945179	CCDC163P	cis	Stomach	GTEx
rs945179	CCDC163P	cis	Nerve Tibial	GTEx

Chromatin state (count:24 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:45988200-45993000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
2	chr1:45988400-45993400	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
3	chr1:45988400-45997200	Weak transcription	Monocytes-CD14+_RO01746	blood
4	chr1:45988600-45993400	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
5	chr1:45989000-45993200	Weak transcription	Placenta	Placenta
6	chr1:45989200-46000600	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
7	chr1:45990400-45992600	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
8	chr1:45990400-45992600	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
9	chr1:45990600-45992800	Enhancers	Stomach Mucosa	stomach
10	chr1:45990600-45992800	Enhancers	HepG2	liver
11	chr1:45991000-45993400	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
12	chr1:45991000-45993400	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
13	chr1:45991000-45993400	Weak transcription	K562	blood
14	chr1:45991200-45993400	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
15	chr1:45991200-45993400	Weak transcription	HUES6 Cell Line	embryonic stem cell
16	chr1:45992200-45992600	Enhancers	Fetal Heart	heart
17	chr1:45992200-45992600	Enhancers	Fetal Intestine Large	intestine
18	chr1:45992200-45992600	Enhancers	Fetal Kidney	kidney
19	chr1:45992200-45992600	Enhancers	Fetal Lung	lung
20	chr1:45992200-45992800	Enhancers	ES-I3 Cell Line	embryonic stem cell
21	chr1:45992200-45992800	Enhancers	iPS-15b Cell Line	embryonic stem cell
22	chr1:45992200-45992800	Enhancers	Fetal Intestine Small	intestine
23	chr1:45992400-45992600	Enhancers	Primary hematopoietic stem cells short term culture	blood
24	chr1:45992400-45992600	Enhancers	A549	lung

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