Variant report

Variant	rs2245455
Chromosome Location	chr21:40548087-40548088
allele	A/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	CTCF	chr21:40546911-40548103	SK-N-SH	brain:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr21:40539973..40543967-chr21:40547698..40550109,4	MCF-7	breast:
2	chr21:40542935..40544954-chr21:40544958..40548517,4	MCF-7	breast:
3	chr21:40547840..40550021-chr21:40578363..40579954,2	K562	blood:
4	chr21:40547282..40550044-chr21:40824037..40825934,2	K562	blood:

Variant related genes	Relation type
PCBP2P1	TF binding region
ENSG00000185437	Chromatin interaction
ENSG00000235701	Chromatin interaction

Extended variants
information (count: 105 )
Associated
traits (count: 13 )

rSNPs within LD-proxies of this variant (count:103)

rs_ID	r²[population]
rs1011413	0.89[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs10154057	0.81[ASN][1000 genomes]
rs11088471	0.90[CEU][hapmap]
rs11911822	0.96[CEU][hapmap];0.89[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs12482181	0.92[ASW][hapmap];0.83[MEX][hapmap];0.81[YRI][hapmap];0.83[AFR][1000 genomes]
rs12626405	0.85[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs13050247	0.83[ASN][1000 genomes]
rs13625	0.92[ASW][hapmap];0.81[YRI][hapmap]
rs14194	0.92[ASW][hapmap];0.82[MEX][hapmap];0.81[YRI][hapmap];0.82[AFR][1000 genomes]
rs1541102	0.92[ASW][hapmap];0.81[YRI][hapmap]
rs1888487	0.80[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs1888488	1.00[ASW][hapmap];0.89[CEU][hapmap];0.90[GIH][hapmap];0.82[JPT][hapmap];0.81[LWK][hapmap];0.81[TSI][hapmap];0.89[YRI][hapmap];0.82[AMR][1000 genomes]
rs1984022	0.81[YRI][hapmap]
rs2026265	0.81[YRI][hapmap]
rs2037925	1.00[ASW][hapmap];0.88[CEU][hapmap];0.88[GIH][hapmap];0.86[JPT][hapmap];0.82[MEX][hapmap];0.86[TSI][hapmap];0.80[AMR][1000 genomes]
rs2142111	1.00[CEU][hapmap];0.95[CHB][hapmap];0.95[JPT][hapmap];0.81[YRI][hapmap];0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2150413	0.92[ASW][hapmap];0.92[YRI][hapmap]
rs2150414	0.92[ASW][hapmap];0.92[YRI][hapmap]
rs2150415	0.92[ASW][hapmap]
rs2183573	0.92[CEU][hapmap];0.97[GIH][hapmap];0.95[TSI][hapmap];0.89[AMR][1000 genomes];0.97[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs2234543	0.92[ASW][hapmap];0.81[YRI][hapmap]
rs2410123	1.00[ASW][hapmap];0.89[CEU][hapmap];0.88[GIH][hapmap];0.82[JPT][hapmap];0.82[MEX][hapmap];0.86[TSI][hapmap];0.80[AMR][1000 genomes]
rs2836925	0.92[ASW][hapmap];0.83[MEX][hapmap];0.81[YRI][hapmap]
rs2836929	0.92[ASW][hapmap];0.83[MEX][hapmap];0.81[YRI][hapmap]
rs2836932	0.92[ASW][hapmap];0.83[MEX][hapmap];0.81[YRI][hapmap]
rs2836933	0.81[YRI][hapmap]
rs2836956	0.92[ASW][hapmap];0.92[YRI][hapmap]
rs2836957	0.81[YRI][hapmap]
rs2836958	0.92[ASW][hapmap];0.92[YRI][hapmap]
rs2836964	0.92[ASW][hapmap];0.81[YRI][hapmap]
rs2836965	0.92[ASW][hapmap];0.81[YRI][hapmap]
rs2836967	0.81[YRI][hapmap]
rs2836968	0.92[ASW][hapmap];0.81[YRI][hapmap]
rs2836969	1.00[CEU][hapmap];0.91[JPT][hapmap];0.89[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs2836971	0.90[JPT][hapmap];0.86[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs2836974	0.92[ASW][hapmap];0.81[YRI][hapmap]
rs2836975	0.96[CEU][hapmap];0.97[GIH][hapmap];0.91[JPT][hapmap];0.88[MEX][hapmap];0.91[TSI][hapmap];0.87[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs2836981	1.00[ASW][hapmap];0.92[CEU][hapmap];0.90[GIH][hapmap];0.82[JPT][hapmap];0.90[LWK][hapmap];0.82[MEX][hapmap];0.86[TSI][hapmap];0.81[YRI][hapmap];0.80[AMR][1000 genomes]
rs2836982	1.00[ASW][hapmap];0.92[CEU][hapmap];0.90[GIH][hapmap];0.82[JPT][hapmap];0.90[LWK][hapmap];0.82[MEX][hapmap];0.86[TSI][hapmap];0.81[YRI][hapmap];0.80[AMR][1000 genomes]
rs2836985	0.92[ASW][hapmap]
rs2836986	0.92[CEU][hapmap]
rs2836987	1.00[ASW][hapmap];0.92[CEU][hapmap];0.88[GIH][hapmap];0.82[JPT][hapmap];0.82[MEX][hapmap];0.84[TSI][hapmap];0.85[YRI][hapmap];0.80[AMR][1000 genomes]
rs2836988	1.00[ASW][hapmap];0.89[CEU][hapmap];0.88[GIH][hapmap];0.82[JPT][hapmap];0.82[MEX][hapmap];0.84[TSI][hapmap];0.80[AMR][1000 genomes]
rs34176878	0.83[AFR][1000 genomes]
rs35909862	0.89[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs371625	0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs377098	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs383967	0.83[ASN][1000 genomes]
rs391062	0.85[CHB][hapmap];0.83[ASN][1000 genomes]
rs413078	0.85[CHB][hapmap];0.83[ASN][1000 genomes]
rs414850	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs418298	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[GIH][hapmap];0.95[JPT][hapmap];1.00[MEX][hapmap];0.93[TSI][hapmap];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs418359	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[GIH][hapmap];0.95[JPT][hapmap];1.00[MEX][hapmap];0.93[TSI][hapmap];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs419469	0.85[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[GIH][hapmap];0.95[JPT][hapmap];1.00[MEX][hapmap];0.93[TSI][hapmap];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs425988	0.83[ASN][1000 genomes]
rs428602	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.92[YRI][hapmap];0.98[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs429955	0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs442972	0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs444130	0.83[ASN][1000 genomes]
rs452377	0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs452776	0.83[ASN][1000 genomes]
rs4624474	1.00[ASW][hapmap];0.89[CEU][hapmap];0.90[GIH][hapmap];0.82[JPT][hapmap];0.81[LWK][hapmap];0.82[MEX][hapmap];0.88[TSI][hapmap];0.89[YRI][hapmap]
rs4816620	0.86[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs4817999	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4818005	0.89[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs4818015	0.96[CEU][hapmap];0.97[GIH][hapmap];0.91[JPT][hapmap];0.88[MEX][hapmap];0.91[TSI][hapmap];0.83[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs4818017	0.80[AMR][1000 genomes]
rs61300849	0.84[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs6517519	0.92[ASW][hapmap];0.83[MEX][hapmap];0.81[YRI][hapmap]
rs6517520	0.85[CHB][hapmap];0.83[ASN][1000 genomes]
rs6517521	0.83[AFR][1000 genomes]
rs6517523	0.92[ASW][hapmap];0.81[YRI][hapmap]
rs6517526	0.92[ASW][hapmap];0.81[YRI][hapmap]
rs6517535	0.89[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs6517538	0.92[ASW][hapmap];0.81[YRI][hapmap]
rs6650847	0.83[ASN][1000 genomes]
rs66519408	0.83[ASN][1000 genomes]
rs66746936	0.83[ASN][1000 genomes]
rs67212994	0.83[ASN][1000 genomes]
rs67382266	0.81[ASN][1000 genomes]
rs67649754	0.83[ASN][1000 genomes]
rs68086041	0.81[ASN][1000 genomes]
rs68114370	0.83[ASN][1000 genomes]
rs719230	0.83[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs7276774	1.00[CEU][hapmap];0.90[JPT][hapmap];0.91[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs7278297	0.92[YRI][hapmap]
rs7278985	0.87[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs7280375	0.92[ASW][hapmap];0.83[MEX][hapmap];0.81[YRI][hapmap];0.81[AFR][1000 genomes]
rs7281853	1.00[ASW][hapmap];0.92[CEU][hapmap];0.90[GIH][hapmap];0.82[JPT][hapmap];0.90[LWK][hapmap];0.82[MEX][hapmap];0.86[TSI][hapmap];0.81[YRI][hapmap];0.80[AMR][1000 genomes]
rs7282604	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[GIH][hapmap];0.95[JPT][hapmap];1.00[MEX][hapmap];0.93[TSI][hapmap];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs8127087	0.81[YRI][hapmap]
rs8127986	0.80[AMR][1000 genomes]
rs8130795	0.96[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs8130854	0.80[AMR][1000 genomes]
rs8130984	0.84[YRI][hapmap]
rs8132285	0.81[YRI][hapmap]
rs9636957	0.80[AMR][1000 genomes]
rs997147	0.80[AMR][1000 genomes]
rs9974757	0.86[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs9978775	0.80[AMR][1000 genomes]
rs9981301	0.92[CEU][hapmap];0.86[JPT][hapmap];0.88[YRI][hapmap]
rs9982111	0.85[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs9982122	0.85[CHB][hapmap];0.83[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:2 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1061831	chr21:40376316-40583555	Enhancers Strong transcription Weak transcription Active TSS Flanking Active TSS Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	34 gene(s)	inside rSNPs	diseases
2	nsv544443	chr21:40376316-40583555	Enhancers Flanking Active TSS Weak transcription Active TSS Transcr. at gene 5' and 3' Strong transcription Bivalent Enhancer ZNF genes & repeats Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	34 gene(s)	inside rSNPs	diseases

mRNA abundance (count:13)

SNP	Gene	Cis/trans	Tissue	Source
rs2245455	BRWD1	cis	Lymphoblastoid	GTEx
rs2245455	PSMG1	cis	lung	GTEx
rs2245455	DSCR2	cis	lesional skin	skin_eQTL
rs2245455	BRWD1	cis	Cerebellum	GTEx
rs2245455	BRWD1	cis	Brain Pons	GTEx
rs2245455	PSMG1	cis	Esophagus Mucosa	GTEx
rs2245455	BRWD1	cis	Temporal Cortex	GTEx
rs2245455	DSCR2	cis	normal skin	skin_eQTL
rs2245455	PSMG1	cis	Artery Tibial	GTEx
rs2245455	PSMG1	cis	Skin Sun Exposed Lower leg	GTEx
rs2245455	PSMG1	cis	Nerve Tibial	GTEx
rs2245455	C21orf107	cis	multi-tissue	Pritchard
rs2245455	BRWD1	cis	Frontal Cortex	GTEx

Chromatin state (count:124 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr21:40537600-40553800	Weak transcription	Pancreatic Islets	Pancreatic Islet
2	chr21:40538800-40550400	Weak transcription	Placenta Amnion	Placenta Amnion
3	chr21:40539000-40550800	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
4	chr21:40539600-40554000	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
5	chr21:40539800-40554000	Weak transcription	iPS-15b Cell Line	embryonic stem cell
6	chr21:40540200-40554200	Weak transcription	Psoas Muscle	Psoas
7	chr21:40541200-40548400	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
8	chr21:40541200-40550600	Strong transcription	Dnd41	blood
9	chr21:40541200-40552600	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
10	chr21:40541200-40552800	Strong transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
11	chr21:40541200-40553000	Strong transcription	HUES48 Cell Line	embryonic stem cell
12	chr21:40541200-40553000	Strong transcription	HUES6 Cell Line	embryonic stem cell
13	chr21:40541200-40553600	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
14	chr21:40541200-40553800	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
15	chr21:40541200-40554000	Weak transcription	Brain Substantia Nigra	brain
16	chr21:40541400-40553000	Strong transcription	HUES64 Cell Line	embryonic stem cell
17	chr21:40541600-40553800	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
18	chr21:40541600-40554000	Weak transcription	ES-I3 Cell Line	embryonic stem cell
19	chr21:40541600-40554000	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
20	chr21:40541600-40554000	Weak transcription	Colon Smooth Muscle	Colon
21	chr21:40541800-40554400	Weak transcription	Brain Germinal Matrix	brain
22	chr21:40542000-40554000	Weak transcription	Rectal Smooth Muscle	rectum
23	chr21:40542000-40554000	Weak transcription	Stomach Mucosa	stomach
24	chr21:40542200-40551600	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
25	chr21:40542400-40548600	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
26	chr21:40542400-40554400	Weak transcription	Right Atrium	heart
27	chr21:40542800-40554000	Weak transcription	Primary neutrophils fromperipheralblood	blood
28	chr21:40543000-40549400	Strong transcription	HepG2	liver
29	chr21:40543000-40552400	Strong transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
30	chr21:40543000-40552400	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
31	chr21:40543000-40552600	Strong transcription	Osteobl	bone
32	chr21:40543200-40548200	Strong transcription	NH-A	brain
33	chr21:40543200-40549000	Strong transcription	Rectal Mucosa Donor 29	rectum
34	chr21:40543200-40549400	Strong transcription	Rectal Mucosa Donor 31	rectum
35	chr21:40543200-40551800	Strong transcription	Primary T helper cells fromperipheralblood	blood
36	chr21:40543400-40554000	Weak transcription	Primary T helper naive cells from peripheral blood	blood
37	chr21:40543600-40553200	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
38	chr21:40543800-40550600	Weak transcription	Fetal Kidney	kidney
39	chr21:40543800-40553200	Weak transcription	Small Intestine	intestine
40	chr21:40543800-40554000	Weak transcription	Brain Cingulate Gyrus	brain
41	chr21:40543800-40554000	Weak transcription	Brain Inferior Temporal Lobe	brain
42	chr21:40543800-40554200	Weak transcription	Right Ventricle	heart
43	chr21:40543800-40554600	Weak transcription	Left Ventricle	heart
44	chr21:40544000-40550800	Weak transcription	Aorta	Aorta
45	chr21:40544000-40553800	Weak transcription	HSMMtube	muscle
46	chr21:40544000-40554000	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
47	chr21:40544000-40554000	Weak transcription	Brain Anterior Caudate	brain
48	chr21:40544200-40554000	Weak transcription	Brain Hippocampus Middle	brain
49	chr21:40544200-40554000	Weak transcription	Colonic Mucosa	Colon
50	chr21:40544600-40551200	Strong transcription	NHEK	skin

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