Variant report

Variant	rs4818858
Chromosome Location	chr21:45083097-45083098
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	YY1	chr21:45082945-45083178	GM12878	blood:	n/a	chr21:45083019-45083041
2	EP300	chr21:45083043-45083107	Hela-S3	cervix:	n/a	n/a
3	YY1	chr21:45082937-45083133	GM12891	blood:	n/a	chr21:45083019-45083041
4	BATF	chr21:45082950-45083228	GM12878	blood:	n/a	n/a
5	BATF	chr21:45082935-45083307	GM12878	blood:	n/a	n/a
6	ATF2	chr21:45082944-45083353	GM12878	blood:	n/a	n/a
7	RUNX3	chr21:45082869-45083244	GM12878	blood:	n/a	n/a
8	YY1	chr21:45082913-45083260	GM12878	blood:	n/a	chr21:45083019-45083041
9	RUNX3	chr21:45082846-45083276	GM12878	blood:	n/a	n/a
10	POLR2A	chr21:45083078-45083665	HepG2	liver:	n/a	n/a
11	BCLAF1	chr21:45082939-45083361	GM12878	blood:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr21:44922604..44925012-chr21:45081747..45084022,2	MCF-7	breast:
2	chr21:45081592..45084345-chr21:45095328..45097020,2	MCF-7	breast:
3	chr21:44526005..44528845-chr21:45081704..45083461,2	K562	blood:
4	chr21:45079841..45084102-chr21:45134985..45140333,7	K562	blood:
5	chr21:45082895..45085626-chr21:45107142..45109564,2	MCF-7	breast:

Variant related genes	Relation type
HSF2BP	TF binding region
ENSG00000160209	Chromatin interaction
ENSG00000160201	Chromatin interaction

Extended variants
information (count: 136 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:131)

rs_ID	r²[population]
rs1003280	0.87[JPT][hapmap]
rs10211901	0.85[EUR][1000 genomes]
rs1073522	0.87[JPT][hapmap]
rs11089093	0.88[EUR][1000 genomes]
rs1122873	0.81[CEU][hapmap];0.87[JPT][hapmap]
rs11700909	0.96[CEU][hapmap];0.86[CHB][hapmap];0.82[CHD][hapmap];0.95[GIH][hapmap];0.93[JPT][hapmap];0.81[MEX][hapmap];0.98[TSI][hapmap];0.91[EUR][1000 genomes]
rs11700913	0.96[EUR][1000 genomes]
rs11702544	0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11909064	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12627667	0.87[JPT][hapmap]
rs13051953	0.94[EUR][1000 genomes]
rs1378079	0.82[CHD][hapmap]
rs1378080	0.87[JPT][hapmap]
rs141521	0.82[CHD][hapmap];0.87[JPT][hapmap]
rs1454648	0.81[CEU][hapmap];0.87[JPT][hapmap]
rs1454650	0.81[CEU][hapmap];0.82[CHD][hapmap];0.87[JPT][hapmap];0.86[TSI][hapmap]
rs1454651	0.81[CEU][hapmap];0.87[JPT][hapmap]
rs1584917	0.81[CEU][hapmap];0.87[JPT][hapmap]
rs1584918	0.81[CEU][hapmap];0.87[JPT][hapmap]
rs1598206	0.82[CHD][hapmap];0.87[JPT][hapmap]
rs162344	0.82[CHD][hapmap]
rs162345	0.80[JPT][hapmap]
rs162366	0.82[CHD][hapmap]
rs162371	0.80[JPT][hapmap]
rs162372	0.80[JPT][hapmap]
rs162375	0.82[CHD][hapmap];0.80[JPT][hapmap];0.84[TSI][hapmap]
rs162376	0.82[CHD][hapmap];0.80[JPT][hapmap];0.84[TSI][hapmap]
rs162377	0.82[CHD][hapmap];0.80[JPT][hapmap]
rs162378	0.80[JPT][hapmap]
rs162398	0.82[CHD][hapmap]
rs162400	0.82[CHD][hapmap];0.86[TSI][hapmap]
rs2006113	0.94[EUR][1000 genomes]
rs2051407	0.87[EUR][1000 genomes]
rs2070533	0.96[CEU][hapmap];0.86[CHB][hapmap];0.85[CHD][hapmap];0.90[GIH][hapmap];0.93[JPT][hapmap];0.98[TSI][hapmap];0.96[EUR][1000 genomes]
rs2155722	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];0.98[TSI][hapmap];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2186924	0.81[CHB][hapmap];0.86[JPT][hapmap]
rs2236665	0.90[AMR][1000 genomes];0.91[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2236666	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.83[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2236667	0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2246602	0.82[CHD][hapmap];0.87[JPT][hapmap]
rs2250773	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2251253	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2282526	0.81[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs229341	0.96[CHD][hapmap]
rs229357	0.87[JPT][hapmap]
rs2298561	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs2298562	0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs230642	0.82[CHD][hapmap]
rs2329442	0.81[CEU][hapmap];0.82[CHD][hapmap];0.87[JPT][hapmap];0.86[TSI][hapmap]
rs2329593	0.96[CEU][hapmap];0.86[CHB][hapmap];0.93[JPT][hapmap];0.96[EUR][1000 genomes]
rs2838316	0.82[CHD][hapmap];0.87[JPT][hapmap]
rs2838317	0.87[JPT][hapmap]
rs2838319	0.87[JPT][hapmap]
rs2838320	0.92[CHB][hapmap];0.96[CHD][hapmap];0.93[JPT][hapmap];0.86[TSI][hapmap]
rs2838321	0.87[JPT][hapmap]
rs2838323	0.87[JPT][hapmap]
rs2838324	0.87[JPT][hapmap]
rs2838328	0.87[JPT][hapmap]
rs2838330	0.87[JPT][hapmap]
rs2838331	0.81[CEU][hapmap];0.82[CHD][hapmap];0.87[JPT][hapmap]
rs2838336	0.82[JPT][hapmap]
rs2838337	0.87[JPT][hapmap]
rs2838338	0.81[CEU][hapmap];0.82[JPT][hapmap]
rs2838339	0.81[CEU][hapmap];0.82[CHD][hapmap];0.82[JPT][hapmap]
rs2838341	0.87[JPT][hapmap]
rs2838343	0.81[JPT][hapmap]
rs2838344	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.92[GIH][hapmap];1.00[JPT][hapmap];0.83[TSI][hapmap];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2838345	0.92[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2838348	1.00[CEU][hapmap];1.00[CHB][hapmap];0.92[CHD][hapmap];0.92[GIH][hapmap];1.00[JPT][hapmap];0.85[MEX][hapmap];0.85[TSI][hapmap];0.90[AMR][1000 genomes];0.91[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2838350	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2838351	0.85[CEU][hapmap];0.93[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.94[AMR][1000 genomes];0.90[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2838353	0.89[CEU][hapmap];0.86[CHB][hapmap];0.93[JPT][hapmap];0.83[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs2838354	0.86[CHB][hapmap];0.93[JPT][hapmap];0.90[AMR][1000 genomes];0.97[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs3788062	0.87[JPT][hapmap]
rs3819161	0.90[ASW][hapmap];0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.95[TSI][hapmap];0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs389278	0.92[CHB][hapmap];0.86[JPT][hapmap]
rs4818850	0.87[JPT][hapmap]
rs4818859	0.96[CEU][hapmap];0.86[CHB][hapmap];0.82[CHD][hapmap];0.95[GIH][hapmap];0.93[JPT][hapmap];0.81[MEX][hapmap];0.98[TSI][hapmap];0.97[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs4818860	1.00[CEU][hapmap];0.86[CHB][hapmap];0.93[JPT][hapmap];0.96[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs4818861	0.90[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs4819270	0.81[CEU][hapmap];0.87[JPT][hapmap]
rs4819283	0.87[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4819285	0.96[CEU][hapmap];0.86[CHB][hapmap];0.95[GIH][hapmap];0.93[JPT][hapmap];0.81[MEX][hapmap];0.98[TSI][hapmap];0.96[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs4819286	0.96[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs4819287	0.90[AMR][1000 genomes];0.97[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs4819288	0.83[ASW][hapmap];1.00[CEU][hapmap];0.86[CHB][hapmap];0.82[CHD][hapmap];0.95[GIH][hapmap];0.93[JPT][hapmap];1.00[MEX][hapmap];0.98[TSI][hapmap];0.90[AMR][1000 genomes];0.97[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs4819289	0.96[CEU][hapmap];0.86[CHB][hapmap];0.82[CHD][hapmap];0.95[GIH][hapmap];0.93[JPT][hapmap];0.98[TSI][hapmap];0.96[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs4819290	0.87[EUR][1000 genomes]
rs4819291	0.96[CEU][hapmap];0.86[CHB][hapmap];0.92[JPT][hapmap];0.94[EUR][1000 genomes]
rs4819292	0.94[EUR][1000 genomes]
rs4819293	0.81[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs4819294	0.81[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs4819295	0.93[JPT][hapmap]
rs4819296	0.82[CHD][hapmap];0.93[JPT][hapmap]
rs6518301	0.87[JPT][hapmap]
rs6518302	0.81[CEU][hapmap];0.82[CHD][hapmap];0.87[JPT][hapmap];0.86[TSI][hapmap]
rs6518309	0.86[JPT][hapmap]
rs6518310	0.85[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[ASN][1000 genomes]
rs7276215	0.87[JPT][hapmap]
rs7276633	0.82[JPT][hapmap]
rs7277539	0.81[CEU][hapmap];0.82[CHD][hapmap];0.87[JPT][hapmap];0.86[TSI][hapmap];0.84[EUR][1000 genomes]
rs7279958	0.87[JPT][hapmap]
rs7279959	0.92[CHB][hapmap];1.00[JPT][hapmap];0.90[ASN][1000 genomes]
rs7279968	0.82[JPT][hapmap]
rs7282122	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7282405	0.94[EUR][1000 genomes]
rs7283428	0.93[EUR][1000 genomes]
rs762400	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];1.00[TSI][hapmap];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs8129601	0.85[CEU][hapmap];0.86[CHB][hapmap];0.92[GIH][hapmap];0.93[JPT][hapmap];0.81[TSI][hapmap];0.83[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs8131027	0.85[CEU][hapmap];0.81[CHB][hapmap]
rs8131111	0.93[EUR][1000 genomes]
rs8133276	0.94[EUR][1000 genomes]
rs8133523	0.81[CEU][hapmap];0.87[JPT][hapmap]
rs86139	0.80[JPT][hapmap]
rs914197	0.97[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs914198	0.97[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs9306159	0.81[CEU][hapmap];0.82[JPT][hapmap]
rs9306160	1.00[CEU][hapmap];0.93[JPT][hapmap];0.83[TSI][hapmap];0.91[AMR][1000 genomes];0.91[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs969060	0.81[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs9941787	0.87[AMR][1000 genomes];0.97[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs9976441	0.87[JPT][hapmap]
rs9977076	0.81[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9978811	0.87[JPT][hapmap]
rs9978858	0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9980185	0.82[CHD][hapmap];0.87[JPT][hapmap]
rs9981291	0.81[CEU][hapmap];0.82[CHD][hapmap];0.87[JPT][hapmap];0.86[TSI][hapmap]
rs9981790	0.82[CHB][hapmap];0.87[JPT][hapmap]
rs9982727	0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs9983670	0.87[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9983763	0.81[CEU][hapmap];0.82[CHD][hapmap];0.87[JPT][hapmap]
rs9984002	0.87[JPT][hapmap]

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	nsv913873	chr21:44879869-45142427	Enhancers Weak transcription Flanking Active TSS ZNF genes & repeats Bivalent Enhancer Active TSS Transcr. at gene 5' and 3' Strong transcription Bivalent/Poised TSS Genic enhancers Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	64 gene(s)	inside rSNPs	diseases
2	nsv834106	chr21:44992387-45109489	Strong transcription Bivalent Enhancer Enhancers Weak transcription Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region miRNA	15 gene(s)	inside rSNPs	diseases
3	nsv587700	chr21:45007956-45095200	Enhancers Weak transcription Active TSS Genic enhancers Strong transcription Bivalent Enhancer Flanking Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region miRNA	14 gene(s)	inside rSNPs	diseases
4	nsv913874	chr21:45041790-45191005	Enhancers Strong transcription Weak transcription ZNF genes & repeats Flanking Active TSS Genic enhancers Bivalent/Poised TSS Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	36 gene(s)	inside rSNPs	diseases
5	nsv531544	chr21:45071371-45202912	Enhancers Flanking Active TSS Weak transcription Strong transcription Genic enhancers Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	39 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs4818858	DNMT3L	cis	cerebellum	SCAN
rs4818858	HSF2BP	cis	lymphoblastoid	seeQTL

Chromatin state (count:125 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr21:45080200-45089800	Weak transcription	Aorta	Aorta
2	chr21:45080600-45122400	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
3	chr21:45080800-45084200	Weak transcription	iPS-15b Cell Line	embryonic stem cell
4	chr21:45080800-45084400	Weak transcription	Brain Hippocampus Middle	brain
5	chr21:45080800-45084800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
6	chr21:45080800-45084800	Weak transcription	Brain Angular Gyrus	brain
7	chr21:45080800-45084800	Weak transcription	Rectal Mucosa Donor 31	rectum
8	chr21:45080800-45085400	Weak transcription	Rectal Smooth Muscle	rectum
9	chr21:45080800-45085600	Weak transcription	Right Ventricle	heart
10	chr21:45080800-45085600	Weak transcription	Stomach Mucosa	stomach
11	chr21:45080800-45087000	Weak transcription	Osteobl	bone
12	chr21:45080800-45089200	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
13	chr21:45080800-45089400	Weak transcription	Sigmoid Colon	Sigmoid Colon
14	chr21:45080800-45092000	Weak transcription	Esophagus	oesophagus
15	chr21:45080800-45094600	Weak transcription	NHLF	lung
16	chr21:45080800-45094800	Weak transcription	Primary neutrophils fromperipheralblood	blood
17	chr21:45080800-45094800	Weak transcription	Placenta Amnion	Placenta Amnion
18	chr21:45080800-45096200	Weak transcription	Psoas Muscle	Psoas
19	chr21:45080800-45121800	Weak transcription	Fetal Heart	heart
20	chr21:45080800-45122600	Weak transcription	Small Intestine	intestine
21	chr21:45081000-45083600	Genic enhancers	Primary T cells fromperipheralblood	blood
22	chr21:45081000-45089800	Weak transcription	NH-A	brain
23	chr21:45081200-45083200	Genic enhancers	Primary T killer memory cells from peripheral blood	blood
24	chr21:45081200-45083400	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
25	chr21:45081200-45083400	Transcr. at gene 5' and 3'	GM12878-XiMat	blood
26	chr21:45081200-45085600	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
27	chr21:45081200-45085800	Genic enhancers	Primary T regulatory cells fromperipheralblood	blood
28	chr21:45081200-45085800	Weak transcription	Colon Smooth Muscle	Colon
29	chr21:45081200-45089200	Weak transcription	Skeletal Muscle Male	skeletal muscle
30	chr21:45081200-45096400	Weak transcription	Pancreatic Islets	Pancreatic Islet
31	chr21:45081400-45083200	Genic enhancers	Primary T helper cells fromperipheralblood	blood
32	chr21:45081400-45083200	Weak transcription	Gastric	stomach
33	chr21:45081400-45083400	Strong transcription	Fetal Muscle Trunk	muscle
34	chr21:45081400-45084000	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
35	chr21:45081400-45084400	Weak transcription	Brain Substantia Nigra	brain
36	chr21:45081400-45084400	Weak transcription	Thymus	Thymus
37	chr21:45081400-45085000	Strong transcription	HSMMtube	muscle
38	chr21:45081400-45085600	Weak transcription	Liver	Liver
39	chr21:45081400-45085600	Weak transcription	Fetal Lung	lung
40	chr21:45081400-45085600	Strong transcription	Fetal Stomach	stomach
41	chr21:45081400-45086000	Strong transcription	Fetal Muscle Leg	muscle
42	chr21:45081400-45086200	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
43	chr21:45081400-45086200	Strong transcription	Fetal Intestine Small	intestine
44	chr21:45081400-45089800	Weak transcription	NHDF-Ad	bronchial
45	chr21:45081600-45083400	Strong transcription	iPS DF 6.9 Cell Line	embryonic stem cell
46	chr21:45081600-45085800	Weak transcription	Cortex derived primary cultured neurospheres	brain
47	chr21:45081600-45086400	Strong transcription	H1 Cell Line	embryonic stem cell
48	chr21:45081600-45086400	Strong transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
49	chr21:45081600-45086400	Strong transcription	HUES64 Cell Line	embryonic stem cell
50	chr21:45081600-45086400	Strong transcription	iPS-20b Cell Line	embryonic stem cell

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