Variant report

Variant	rs9657054
Chromosome Location	chr8:48882899-48882900
allele	C/T
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	POLR2A	chr8:48881989-48884271	GM12878	blood:	n/a	n/a
2	POLR2A	chr8:48882864-48884242	H1-hESC	embryonic stem cell:	n/a	n/a
3	POLR2A	chr8:48882570-48882969	K562	blood:	n/a	n/a
4	POLR2A	chr8:48882638-48882911	H1-hESC	embryonic stem cell:	n/a	n/a
5	POLR2A	chr8:48882534-48883830	HL-60	blood:	n/a	n/a
6	POLR2A	chr8:48879371-48884177	GM12892	blood:	n/a	n/a
7	POLR2A	chr8:48882564-48884047	GM12878	blood:	n/a	n/a
8	POLR2A	chr8:48882002-48883995	K562	blood:	n/a	n/a
9	POLR2A	chr8:48882758-48882905	HepG2	liver:	n/a	n/a
10	POLR2A	chr8:48882623-48882937	H1-hESC	embryonic stem cell:	n/a	n/a
11	POLR2A	chr8:48882898-48884402	GM12892	blood:	n/a	n/a
12	POLR2A	chr8:48882109-48883845	K562	blood:	n/a	n/a
13	POLR2A	chr8:48882589-48882978	Hela-S3	cervix:	n/a	n/a
14	POLR2A	chr8:48882087-48884028	Hela-S3	cervix:	n/a	n/a
15	POLR2A	chr8:48882638-48882933	GM12891	blood:	n/a	n/a
16	POLR2A	chr8:48882550-48882939	K562	blood:	n/a	n/a
17	POLR2A	chr8:48881901-48882938	PFSK-1	brain:	n/a	n/a
18	POLR2A	chr8:48882543-48883130	K562	blood:	n/a	n/a
19	POLR2A	chr8:48882008-48883978	Hela-S3	cervix:	n/a	n/a
20	POLR2A	chr8:48882638-48882958	GM12892	blood:	n/a	n/a
21	POLR2A	chr8:48882166-48884360	K562	blood:	n/a	n/a
22	POLR2A	chr8:48879336-48884417	SK-N-MC	brain:	n/a	n/a
23	POLR2A	chr8:48882142-48882908	H1-hESC	embryonic stem cell:	n/a	n/a
24	POLR2A	chr8:48882127-48883986	K562	blood:	n/a	n/a

Variant related genes	Relation type
MCM4	TF binding region

Extended variants
information (count: 49 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:41)

rs_ID	r²[population]
rs10091017	1.00[ASW][hapmap];0.85[CHB][hapmap];1.00[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];0.91[LWK][hapmap];0.97[MKK][hapmap];0.96[YRI][hapmap];0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10097783	1.00[CEU][hapmap];0.92[CHB][hapmap];0.82[JPT][hapmap];0.84[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs10106778	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.83[JPT][hapmap];0.95[MEX][hapmap];0.94[TSI][hapmap];0.87[AMR][1000 genomes];0.90[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs10481294	0.92[AFR][1000 genomes];0.97[AMR][1000 genomes];0.90[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs10808897	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.94[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];0.81[TSI][hapmap];1.00[YRI][hapmap];0.87[AMR][1000 genomes];0.83[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs10958438	0.89[AFR][1000 genomes];0.97[AMR][1000 genomes];0.90[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs11986191	0.87[AFR][1000 genomes];0.96[AMR][1000 genomes];0.90[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs12156246	0.83[AMR][1000 genomes]
rs12334811	1.00[CEU][hapmap];1.00[CHB][hapmap];0.94[CHD][hapmap];0.83[JPT][hapmap];0.95[MEX][hapmap];0.94[TSI][hapmap];0.87[AMR][1000 genomes];0.90[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs13251871	0.81[AMR][1000 genomes]
rs1551655	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];0.94[TSI][hapmap];1.00[YRI][hapmap];0.93[AFR][1000 genomes];0.97[AMR][1000 genomes];0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1894311	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.95[MEX][hapmap];0.94[TSI][hapmap];0.87[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1903082	0.81[AFR][1000 genomes];0.94[AMR][1000 genomes];0.88[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs28457765	0.82[CEU][hapmap];0.92[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap]
rs28485144	0.88[AMR][1000 genomes]
rs28578331	0.83[AMR][1000 genomes];0.86[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs28641816	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.93[LWK][hapmap];1.00[MEX][hapmap];0.92[MKK][hapmap];0.94[TSI][hapmap];1.00[YRI][hapmap];0.87[AFR][1000 genomes];0.97[AMR][1000 genomes];0.90[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs28702696	0.86[AFR][1000 genomes];0.97[AMR][1000 genomes];0.88[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs4618724	0.87[AMR][1000 genomes];0.90[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs4873266	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.95[MEX][hapmap];0.94[TSI][hapmap];0.87[AMR][1000 genomes];0.90[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4873737	0.88[AMR][1000 genomes]
rs4873770	1.00[CEU][hapmap];0.95[MEX][hapmap];0.94[TSI][hapmap];0.81[EUR][1000 genomes]
rs4873771	0.84[AMR][1000 genomes];0.88[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs4873773	0.81[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs58108179	0.80[AMR][1000 genomes];0.82[ASN][1000 genomes]
rs6993292	0.88[AFR][1000 genomes];0.97[AMR][1000 genomes];0.90[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs6993483	0.88[AMR][1000 genomes]
rs7014544	0.83[AMR][1000 genomes]
rs72633911	0.81[AMR][1000 genomes];0.88[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs72647906	0.83[AMR][1000 genomes]
rs72647914	0.81[EUR][1000 genomes]
rs72647916	0.84[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs72647918	0.83[EUR][1000 genomes]
rs72647922	0.83[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs7824066	0.89[AFR][1000 genomes];0.94[AMR][1000 genomes];0.81[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs7838910	0.94[ASW][hapmap];1.00[CEU][hapmap];0.92[CHB][hapmap];0.82[CHD][hapmap];0.92[GIH][hapmap];0.83[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.96[MKK][hapmap];0.94[TSI][hapmap];1.00[YRI][hapmap]
rs7839407	0.88[AMR][1000 genomes]
rs8178016	1.00[CEU][hapmap];0.94[MEX][hapmap];0.94[TSI][hapmap];0.83[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs8178079	0.84[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs8178095	1.00[CEU][hapmap];0.95[MEX][hapmap];0.94[TSI][hapmap];0.81[AMR][1000 genomes]
rs8178238	1.00[CEU][hapmap]

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	nsv931032	chr8:48744329-49091359	Strong transcription Flanking Active TSS Enhancers Active TSS Weak transcription Transcr. at gene 5' and 3' Bivalent Enhancer Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	20 gene(s)	inside rSNPs	diseases
2	esv2758156	chr8:48788293-49008014	Strong transcription Active TSS Genic enhancers Enhancers Weak transcription ZNF genes & repeats Flanking Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	17 gene(s)	inside rSNPs	diseases
3	esv2759611	chr8:48788293-49008014	Strong transcription Active TSS Weak transcription Enhancers Genic enhancers ZNF genes & repeats Flanking Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	17 gene(s)	inside rSNPs	diseases
4	nsv427820	chr8:48788293-49008014	Strong transcription Weak transcription Active TSS Enhancers Transcr. at gene 5' and 3' Genic enhancers Flanking Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	17 gene(s)	inside rSNPs	diseases
5	nsv831309	chr8:48815290-48977856	Strong transcription Genic enhancers Weak transcription Active TSS Enhancers Flanking Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	17 gene(s)	inside rSNPs	diseases
6	nsv1033760	chr8:48852925-48961374	Active TSS Strong transcription Weak transcription Genic enhancers Enhancers Flanking Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	16 gene(s)	inside rSNPs	diseases
7	nsv1020619	chr8:48871586-48932988	Genic enhancers Active TSS Enhancers Flanking Active TSS Strong transcription Flanking Bivalent TSS/Enh Weak transcription Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region miRNA target site	16 gene(s)	inside rSNPs	diseases
8	nsv1032750	chr8:48877179-48924828	Active TSS Flanking Active TSS Enhancers Weak transcription Strong transcription Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region miRNA target site	10 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:126 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr8:48874400-48888800	Weak transcription	Primary T helper naive cells from peripheral blood	blood
2	chr8:48874600-48888800	Weak transcription	Pancreatic Islets	Pancreatic Islet
3	chr8:48874600-48891600	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
4	chr8:48874600-48891800	Weak transcription	Colon Smooth Muscle	Colon
5	chr8:48874800-48890000	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
6	chr8:48874800-48890400	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
7	chr8:48874800-48890800	Strong transcription	ES-I3 Cell Line	embryonic stem cell
8	chr8:48874800-48890800	Strong transcription	Placenta	Placenta
9	chr8:48874800-48905800	Weak transcription	Stomach Mucosa	stomach
10	chr8:48875000-48887600	Strong transcription	Muscle Satellite Cultured Cells	--
11	chr8:48875000-48887800	Strong transcription	Osteobl	bone
12	chr8:48875000-48888400	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
13	chr8:48875000-48890200	Strong transcription	HSMM	muscle
14	chr8:48875000-48891400	Strong transcription	H1 Cell Line	embryonic stem cell
15	chr8:48875000-48891400	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
16	chr8:48875000-48891400	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
17	chr8:48875000-48891600	Strong transcription	H9 Cell Line	embryonic stem cell
18	chr8:48875000-48891600	Weak transcription	Primary T killer memory cells from peripheral blood	blood
19	chr8:48875000-48891600	Strong transcription	Fetal Stomach	stomach
20	chr8:48875000-48891800	Strong transcription	Fetal Intestine Small	intestine
21	chr8:48875000-48892200	Strong transcription	HUES6 Cell Line	embryonic stem cell
22	chr8:48875000-48892600	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
23	chr8:48875000-48898800	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
24	chr8:48875200-48890400	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
25	chr8:48875200-48890600	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
26	chr8:48875200-48891600	Strong transcription	Cortex derived primary cultured neurospheres	brain
27	chr8:48875200-48892000	Strong transcription	HUES48 Cell Line	embryonic stem cell
28	chr8:48875200-48892200	Strong transcription	iPS-18 Cell Line	embryonic stem cell
29	chr8:48875200-48892600	Strong transcription	Fetal Thymus	thymus
30	chr8:48875400-48884400	Strong transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
31	chr8:48875400-48890600	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
32	chr8:48875400-48890800	Strong transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
33	chr8:48875400-48890800	Strong transcription	Skeletal Muscle Female	skeletal muscle
34	chr8:48875400-48890800	Strong transcription	HMEC	breast
35	chr8:48875400-48891800	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
36	chr8:48875400-48892000	Strong transcription	iPS-20b Cell Line	embryonic stem cell
37	chr8:48875400-48892200	Strong transcription	HUES64 Cell Line	embryonic stem cell
38	chr8:48875400-48892200	Strong transcription	Primary hematopoietic stem cells short term culture	blood
39	chr8:48875600-48884400	Strong transcription	Ganglion Eminence derived primary cultured neurospheres	brain
40	chr8:48875600-48890400	Strong transcription	Duodenum Smooth Muscle	Duodenum
41	chr8:48875600-48891600	Strong transcription	Breast Myoepithelial Primary Cells	Breast
42	chr8:48875600-48892000	Strong transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
43	chr8:48875600-48892200	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
44	chr8:48875800-48887800	Strong transcription	K562	blood
45	chr8:48875800-48889800	Strong transcription	iPS-15b Cell Line	embryonic stem cell
46	chr8:48875800-48890200	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
47	chr8:48875800-48890200	Strong transcription	HUVEC	blood vessel
48	chr8:48875800-48890400	Strong transcription	Liver	Liver
49	chr8:48875800-48890400	Strong transcription	Brain Germinal Matrix	brain
50	chr8:48875800-48890400	Strong transcription	Fetal Intestine Large	intestine

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