Variant report

Variant	rs2298787
Chromosome Location	chr18:43669980-43669981
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:5)
CpG islands
(count:0)
Chromatin interactive
region (count:4)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

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

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	POLR2A	chr18:43669892-43670569	HepG2	liver:	n/a	n/a
2	POLR2A	chr18:43669665-43670097	GM12878	blood:	n/a	n/a
3	POLR2A	chr18:43669792-43670027	HepG2	liver:	n/a	n/a
4	POLR2A	chr18:43669524-43671921	K562	blood:	n/a	n/a
5	POLR2A	chr18:43669846-43670119	GM12878	blood:	n/a	n/a

No data

(count:4 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr18:43669948..43672641-chr18:43676747..43679041,2	K562	blood:
2	chr18:43669796..43671297-chr18:43673823..43676678,2	K562	blood:
3	chr18:43666467..43668997-chr18:43669505..43672301,3	K562	blood:
4	chr18:43668900..43671493-chr18:43677433..43680075,2	MCF-7	breast:

No data

Variant related genes	Relation type
ATP5A1	TF binding region
ENSG00000152234	Chromatin interaction

Extended variants
information (count: 73 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:69)

rs_ID	r²[population]
rs11082509	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.86[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.98[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];0.92[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs11082510	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];0.92[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs11659357	0.97[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs11659478	0.84[AMR][1000 genomes];0.83[ASN][1000 genomes]
rs11659795	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11661945	0.91[EUR][1000 genomes]
rs11664764	0.96[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11872954	0.93[EUR][1000 genomes]
rs11872985	0.93[EUR][1000 genomes]
rs11874712	1.00[CEU][hapmap];0.94[EUR][1000 genomes]
rs12954944	1.00[ASW][hapmap];0.96[CEU][hapmap];1.00[CHB][hapmap];0.85[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];0.98[LWK][hapmap];0.90[MEX][hapmap];1.00[MKK][hapmap];0.98[TSI][hapmap];0.96[YRI][hapmap];0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12955201	0.89[GIH][hapmap]
rs13381709	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];0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1800636	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.98[LWK][hapmap];0.95[MEX][hapmap];0.99[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap]
rs1800637	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1800639	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];0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1800640	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];0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28457840	0.91[AFR][1000 genomes];0.97[AMR][1000 genomes];0.90[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs28504655	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28532950	0.85[EUR][1000 genomes]
rs28699609	0.96[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28757346	0.85[EUR][1000 genomes]
rs34907121	0.96[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs35507656	0.87[AFR][1000 genomes];0.97[AMR][1000 genomes];0.91[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs3753069	0.83[GIH][hapmap]
rs3765636	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[YRI][hapmap];0.89[AFR][1000 genomes];1.00[AMR][1000 genomes];0.91[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs56075249	0.80[AMR][1000 genomes];0.99[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs56181324	0.98[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs62096500	0.96[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs71364522	0.85[EUR][1000 genomes]
rs7227508	1.00[CHB][hapmap]
rs7230064	0.93[AFR][1000 genomes];0.92[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7231846	1.00[CHB][hapmap]
rs7235373	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];0.91[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs7244921	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.98[LWK][hapmap];1.00[MEX][hapmap];0.97[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7244950	0.95[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7359798	0.89[GIH][hapmap]
rs8083998	0.96[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs8085444	0.91[EUR][1000 genomes]
rs8085743	0.81[AFR][1000 genomes];0.94[AMR][1000 genomes];0.80[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs8088881	1.00[ASW][hapmap];0.92[CEU][hapmap];1.00[CHB][hapmap];0.87[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.95[LWK][hapmap];1.00[MEX][hapmap];0.98[MKK][hapmap];0.98[TSI][hapmap];1.00[YRI][hapmap];0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs8089150	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];0.96[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs8091452	0.91[AFR][1000 genomes];0.92[AMR][1000 genomes];0.88[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs8092674	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];0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs8093880	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs8094902	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs8095031	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs8095608	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];0.98[MKK][hapmap];0.98[TSI][hapmap];1.00[YRI][hapmap];0.95[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs8097521	0.86[AFR][1000 genomes];0.88[AMR][1000 genomes];0.90[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs9304326	0.93[AFR][1000 genomes];0.99[AMR][1000 genomes];0.89[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs9304327	0.93[AFR][1000 genomes];0.97[AMR][1000 genomes];0.89[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs9304328	0.91[AFR][1000 genomes];0.97[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs9304330	0.83[EUR][1000 genomes]
rs9783884	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];0.91[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs9783886	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap]
rs9783887	0.99[AMR][1000 genomes];0.91[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs9783888	0.80[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs9807399	0.89[GIH][hapmap]
rs9944637	0.91[EUR][1000 genomes]
rs9945606	0.89[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9945751	0.96[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9947908	0.80[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs9950234	0.83[GIH][hapmap]
rs9954278	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9955008	0.83[GIH][hapmap]
rs9961065	1.00[JPT][hapmap];0.95[YRI][hapmap];0.88[AFR][1000 genomes];1.00[AMR][1000 genomes];0.91[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs9962380	0.95[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9962458	0.98[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs9965812	0.81[GIH][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	nsv1064882	chr18:43558343-43687674	Bivalent Enhancer Flanking Active TSS Enhancers Strong transcription Weak transcription Bivalent/Poised TSS Active TSS Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	15 gene(s)	inside rSNPs	diseases
2	nsv543693	chr18:43558343-43687674	Flanking Active TSS Enhancers Weak transcription Strong transcription Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Genic enhancers Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	15 gene(s)	inside rSNPs	diseases
3	nsv1062024	chr18:43589516-43749410	Active TSS Strong transcription Enhancers Flanking Active TSS Weak transcription Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	15 gene(s)	inside rSNPs	diseases
4	nsv543694	chr18:43589516-43749410	Strong transcription Weak transcription Active TSS Enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3' Flanking Active TSS ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	15 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs2298787	ATP5A1	cis	parietal	SCAN

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr18:43657000-43672200	Strong transcription	Breast Myoepithelial Primary Cells	Breast
2	chr18:43657200-43673800	Strong transcription	Primary neutrophils fromperipheralblood	blood
3	chr18:43657200-43674800	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
4	chr18:43657200-43674800	Strong transcription	Ganglion Eminence derived primary cultured neurospheres	brain
5	chr18:43657200-43675000	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
6	chr18:43657200-43675400	Strong transcription	HUES64 Cell Line	embryonic stem cell
7	chr18:43657200-43675400	Strong transcription	Primary hematopoietic stem cells short term culture	blood
8	chr18:43657200-43675600	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
9	chr18:43657200-43676000	Strong transcription	Osteobl	bone
10	chr18:43657200-43676200	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
11	chr18:43657400-43673400	Strong transcription	Primary T helper cells fromperipheralblood	blood
12	chr18:43657400-43674600	Strong transcription	Liver	Liver
13	chr18:43657400-43674800	Strong transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
14	chr18:43657400-43675000	Strong transcription	iPS-20b Cell Line	embryonic stem cell
15	chr18:43657400-43675200	Strong transcription	Monocytes-CD14+_RO01746	blood
16	chr18:43657400-43675400	Strong transcription	Placenta	Placenta
17	chr18:43657400-43675800	Strong transcription	Primary monocytes fromperipheralblood	blood
18	chr18:43657400-43675800	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
19	chr18:43657600-43672400	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
20	chr18:43657600-43673400	Strong transcription	Dnd41	blood
21	chr18:43657600-43674400	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
22	chr18:43657600-43674600	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
23	chr18:43657600-43675200	Strong transcription	Sigmoid Colon	Sigmoid Colon
24	chr18:43657800-43675200	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
25	chr18:43657800-43675800	Strong transcription	Fetal Muscle Leg	muscle
26	chr18:43657800-43676600	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
27	chr18:43658000-43670000	Strong transcription	Fetal Stomach	stomach
28	chr18:43658000-43670600	Strong transcription	Primary T helper cells PMA-I stimulated	--
29	chr18:43658000-43670800	Strong transcription	Skeletal Muscle Female	skeletal muscle
30	chr18:43658000-43675400	Strong transcription	Fetal Muscle Trunk	muscle
31	chr18:43658200-43671800	Weak transcription	Right Atrium	heart
32	chr18:43658600-43675000	Strong transcription	iPS-18 Cell Line	embryonic stem cell
33	chr18:43658600-43675400	Strong transcription	HUES48 Cell Line	embryonic stem cell
34	chr18:43658800-43674200	Strong transcription	Duodenum Smooth Muscle	Duodenum
35	chr18:43658800-43674400	Strong transcription	Foreskin Fibroblast Primary Cells skin01	Skin
36	chr18:43659000-43674800	Strong transcription	HUVEC	blood vessel
37	chr18:43659000-43675200	Strong transcription	Primary B cells from peripheral blood	blood
38	chr18:43659000-43675200	Strong transcription	Cortex derived primary cultured neurospheres	brain
39	chr18:43659000-43676000	Strong transcription	HUES6 Cell Line	embryonic stem cell
40	chr18:43659200-43672000	Strong transcription	Muscle Satellite Cultured Cells	--
41	chr18:43659200-43675000	Strong transcription	Fetal Brain Female	brain
42	chr18:43659200-43675800	Strong transcription	H1 Cell Line	embryonic stem cell
43	chr18:43659400-43671800	Strong transcription	Primary T cells fromperipheralblood	blood
44	chr18:43659400-43675800	Strong transcription	HMEC	breast
45	chr18:43659600-43674800	Strong transcription	Stomach Smooth Muscle	stomach
46	chr18:43659800-43672200	Strong transcription	Primary T cells from cord blood	blood
47	chr18:43659800-43672800	Strong transcription	Skeletal Muscle Male	skeletal muscle
48	chr18:43659800-43674400	Strong transcription	Primary T helper 17 cells PMA-I stimulated	--
49	chr18:43660000-43670200	Strong transcription	Brain Angular Gyrus	brain
50	chr18:43660000-43672000	Strong transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived

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