Variant report

Variant	rs8132424
Chromosome Location	chr21:40584412-40584413
allele	A/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:8)
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	POLR2A	chr21:40583893-40585094	K562	blood:	n/a	n/a
2	MYC	chr21:40584381-40584450	H1-hESC	embryonic stem cell:	n/a	n/a

No data

(count:8 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr21:40583924..40586852-chr21:40588522..40591681,4	MCF-7	breast:
2	chr21:40582888..40584633-chr21:40585013..40587494,2	MCF-7	breast:
3	21:40583765-40590917..21:40718004-40719183	GM12878	blood:
4	chr21:40584192..40587063-chr21:40587263..40589363,2	K562	blood:
5	21:40583765-40590917..21:40796857-40798340	Hela-S3	cervix:
6	chr21:40579851..40582767-chr21:40583225..40585456,3	K562	blood:
7	chr21:40574695..40577813-chr21:40579621..40584653,4	K562	blood:
8	chr21:40582005..40584488-chr8:97183248..97185340,2	MCF-7	breast:

No data

Variant related genes	Relation type
TIMM9P2	TF binding region
ENSG00000205581	Chromatin interaction
ENSG00000232608	Chromatin interaction
ENSG00000185658	Chromatin interaction
ENSG00000182093	Chromatin interaction

Extended variants
information (count: 85 )
Associated
traits (count: 23 )

rSNPs within LD-proxies of this variant (count:82)

rs_ID	r²[population]
rs1029004	0.88[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs11088466	0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11088470	0.89[AMR][1000 genomes];0.87[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs11700813	0.82[EUR][1000 genomes]
rs11701805	0.89[AMR][1000 genomes];0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs11702505	0.85[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs11910232	0.90[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs11911087	0.82[AMR][1000 genomes];0.87[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs11911822	1.00[YRI][hapmap]
rs12483559	0.88[AMR][1000 genomes];0.90[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs12627205	0.85[AMR][1000 genomes];0.92[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs13049907	0.83[AMR][1000 genomes];0.89[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs1571709	0.90[YRI][hapmap]
rs1980407	0.83[AFR][1000 genomes];0.93[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs2056844	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.85[AMR][1000 genomes];0.91[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2070865	0.96[CEU][hapmap];0.86[CHB][hapmap];0.89[GIH][hapmap];0.90[JPT][hapmap];0.82[MEX][hapmap];0.82[TSI][hapmap]
rs2150411	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.86[AFR][1000 genomes];0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs2150413	0.80[ASW][hapmap];0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];0.91[MEX][hapmap];0.96[TSI][hapmap];0.91[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2150414	0.80[ASW][hapmap];0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];0.91[MEX][hapmap];0.96[TSI][hapmap];0.91[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2183573	0.93[ASW][hapmap];0.84[MKK][hapmap];0.89[YRI][hapmap]
rs2297256	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];0.83[LWK][hapmap];0.95[MEX][hapmap];0.83[MKK][hapmap];0.98[TSI][hapmap];0.93[AMR][1000 genomes];0.93[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs2836922	0.82[EUR][1000 genomes]
rs2836926	0.96[CEU][hapmap];0.95[JPT][hapmap];0.88[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs2836930	0.96[CEU][hapmap];0.95[JPT][hapmap];1.00[YRI][hapmap];0.93[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs2836931	0.96[CEU][hapmap];0.94[JPT][hapmap];1.00[YRI][hapmap];0.91[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs2836934	0.96[CEU][hapmap];0.91[CHB][hapmap];1.00[CHD][hapmap];0.98[GIH][hapmap];0.95[JPT][hapmap];0.81[LWK][hapmap];0.89[AMR][1000 genomes];0.93[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs2836940	0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2836942	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2836943	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2836945	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2836948	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2836949	1.00[CEU][hapmap];0.91[CHB][hapmap];0.95[JPT][hapmap];0.95[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2836952	0.96[CEU][hapmap];0.95[CHB][hapmap];0.95[JPT][hapmap];0.87[AMR][1000 genomes];0.94[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2836956	0.80[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];0.95[MEX][hapmap];0.98[TSI][hapmap];0.91[AMR][1000 genomes];0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2836958	0.80[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];0.95[MEX][hapmap];0.98[TSI][hapmap];0.91[AMR][1000 genomes];0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2836959	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.98[CHD][hapmap];0.98[GIH][hapmap];0.95[JPT][hapmap];0.85[LWK][hapmap];0.95[MEX][hapmap];0.81[MKK][hapmap];0.98[TSI][hapmap];0.96[YRI][hapmap];0.80[AFR][1000 genomes];0.90[AMR][1000 genomes];0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2836966	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];0.87[MEX][hapmap];0.98[TSI][hapmap];0.85[AMR][1000 genomes];0.92[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2836969	1.00[YRI][hapmap]
rs2836971	1.00[YRI][hapmap]
rs2836975	0.93[ASW][hapmap];1.00[YRI][hapmap]
rs2836980	1.00[ASW][hapmap];0.96[CEU][hapmap];0.91[CHB][hapmap];0.88[CHD][hapmap];0.91[GIH][hapmap];0.90[JPT][hapmap];0.80[LWK][hapmap];0.91[MEX][hapmap];0.95[TSI][hapmap];0.89[YRI][hapmap];0.89[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs2836983	0.96[CEU][hapmap];1.00[CHB][hapmap];0.90[JPT][hapmap];0.89[YRI][hapmap];0.89[AMR][1000 genomes];0.87[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2836984	0.85[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs2836985	0.80[ASW][hapmap];0.96[CEU][hapmap];0.87[CHB][hapmap];0.82[CHD][hapmap];0.91[GIH][hapmap];0.90[JPT][hapmap];0.86[MEX][hapmap];0.95[TSI][hapmap];0.84[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs3171465	0.96[CEU][hapmap];0.86[CHD][hapmap];0.95[GIH][hapmap];0.95[JPT][hapmap];0.87[MEX][hapmap];0.98[TSI][hapmap];0.89[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs34705151	0.88[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs35769610	0.88[AMR][1000 genomes];0.91[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs35994303	0.85[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs377098	1.00[YRI][hapmap]
rs418298	0.93[ASW][hapmap];0.80[LWK][hapmap];1.00[YRI][hapmap]
rs418359	0.93[ASW][hapmap];0.80[LWK][hapmap];1.00[YRI][hapmap]
rs419469	0.93[ASW][hapmap];1.00[YRI][hapmap]
rs4816617	0.88[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs4816618	0.92[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4818001	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.85[AFR][1000 genomes];0.96[AMR][1000 genomes];0.95[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs4818015	0.93[ASW][hapmap];1.00[YRI][hapmap]
rs4818018	0.89[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs4818019	0.89[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs59916147	0.80[AFR][1000 genomes];0.90[AMR][1000 genomes];0.94[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs62223011	0.91[AMR][1000 genomes];0.94[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs62223039	0.85[AMR][1000 genomes];0.89[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs62223052	0.83[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs6517522	0.86[ASW][hapmap];0.80[LWK][hapmap];0.90[YRI][hapmap]
rs7276046	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7276774	0.96[YRI][hapmap]
rs7278297	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[AMR][1000 genomes];0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7279497	0.96[CEU][hapmap];0.86[CHD][hapmap];0.95[GIH][hapmap];0.95[JPT][hapmap];0.87[MEX][hapmap];0.82[MKK][hapmap];0.98[TSI][hapmap];0.86[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs7282582	0.92[CEU][hapmap];0.91[CHB][hapmap];0.83[CHD][hapmap];0.80[GIH][hapmap];0.90[JPT][hapmap];0.86[MEX][hapmap];0.86[AMR][1000 genomes]
rs7282604	0.93[ASW][hapmap];0.80[LWK][hapmap];1.00[YRI][hapmap]
rs8127379	0.87[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs8128191	0.90[YRI][hapmap]
rs8129595	0.85[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs8130162	0.84[AMR][1000 genomes];0.92[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs8130240	0.83[AFR][1000 genomes];0.92[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs8130320	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];0.83[LWK][hapmap];0.91[MEX][hapmap];0.83[MKK][hapmap];1.00[TSI][hapmap];0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs8131132	0.88[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs8132143	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs8132295	0.86[ASW][hapmap];0.90[YRI][hapmap]
rs8132333	0.86[ASW][hapmap];0.90[YRI][hapmap]
rs8133928	0.89[AMR][1000 genomes];0.87[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs8134214	0.84[AFR][1000 genomes];0.91[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs8134843	0.83[AMR][1000 genomes];0.91[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1056683	chr21:40570023-40673210	Weak transcription Strong transcription Enhancers ZNF genes & repeats Genic enhancers Flanking Active TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	17 gene(s)	inside rSNPs	diseases
2	nsv459259	chr21:40571246-40701169	Weak transcription Flanking Active TSS Strong transcription Genic enhancers Enhancers Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	38 gene(s)	inside rSNPs	diseases
3	nsv587480	chr21:40571246-40701169	Strong transcription Active TSS Weak transcription Flanking Active TSS Enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	38 gene(s)	inside rSNPs	diseases

mRNA abundance (count:23)

SNP	Gene	Cis/trans	Tissue	Source
rs8132424	BRWD1	cis	Lymphoblastoid	GTEx
rs8132424	HMGN1	cis	lymphoblastoid	seeQTL
rs8132424	HMGN1	cis	multi-tissue	Pritchard
rs8132424	BRWD1	cis	Frontal Cortex	GTEx
rs8132424	BRWD1	cis	Liver	GTEx
rs8132424	C21orf107	cis	multi-tissue	Pritchard
rs8132424	BRWD1	cis	multi-tissue	Pritchard
rs8132424	HMGN1	trans	brain	seeQTL
rs8132424	SLC16A1	cis	Liver	GTEx
rs8132424	BRWD1	cis	Temporal Cortex	GTEx
rs8132424	DSCR2	cis	multi-tissue	Pritchard
rs8132424	BRWD1	cis	lymphoblastoid	seeQTL
rs8132424	HMGN1	cis	brain	seeQTL
rs8132424	PSMG1	cis	Artery Tibial	GTEx
rs8132424	SLC16A1	trans	multi-tissue	Pritchard
rs8132424	PSMG1	cis	Skin Sun Exposed Lower leg	GTEx
rs8132424	LOC643790	trans	multi-tissue	Pritchard
rs8132424	BRWD1	cis	Brain Pons	GTEx
rs8132424	WRB	cis	multi-tissue	Pritchard
rs8132424	PSMG1	cis	parietal	SCAN
rs8132424	BRWD1	cis	cerebellum	SCAN
rs8132424	BRWD1	cis	parietal	SCAN
rs8132424	BRWD1	cis	Cerebellum	GTEx

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr21:40556200-40602600	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
2	chr21:40563000-40640600	Strong transcription	Placenta	Placenta
3	chr21:40563000-40643600	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
4	chr21:40563400-40653400	Strong transcription	HUES64 Cell Line	embryonic stem cell
5	chr21:40563400-40660000	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
6	chr21:40563600-40588600	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
7	chr21:40563600-40653600	Strong transcription	Monocytes-CD14+_RO01746	blood
8	chr21:40564600-40612600	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
9	chr21:40564800-40587800	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
10	chr21:40565000-40592600	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
11	chr21:40565000-40654600	Strong transcription	HUES48 Cell Line	embryonic stem cell
12	chr21:40565200-40653600	Strong transcription	iPS-20b Cell Line	embryonic stem cell
13	chr21:40565400-40604200	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
14	chr21:40565400-40612600	Strong transcription	Primary monocytes fromperipheralblood	blood
15	chr21:40565400-40653600	Strong transcription	Dnd41	blood
16	chr21:40565600-40585600	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
17	chr21:40565600-40590200	Strong transcription	Liver	Liver
18	chr21:40565600-40615000	Strong transcription	HUES6 Cell Line	embryonic stem cell
19	chr21:40565800-40590600	Strong transcription	Fetal Thymus	thymus
20	chr21:40566000-40653600	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
21	chr21:40566200-40590600	Strong transcription	iPS-18 Cell Line	embryonic stem cell
22	chr21:40566200-40590600	Strong transcription	Adipose Nuclei	Adipose
23	chr21:40566400-40613200	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
24	chr21:40567400-40585400	Strong transcription	H1 Cell Line	embryonic stem cell
25	chr21:40567400-40592400	Strong transcription	Duodenum Smooth Muscle	Duodenum
26	chr21:40567600-40585000	Strong transcription	Primary hematopoietic stem cells short term culture	blood
27	chr21:40568200-40584600	Strong transcription	Stomach Smooth Muscle	stomach
28	chr21:40569800-40607800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
29	chr21:40570600-40589800	Weak transcription	Stomach Mucosa	stomach
30	chr21:40571400-40602400	Weak transcription	Fetal Brain Male	brain
31	chr21:40572000-40636800	Weak transcription	Psoas Muscle	Psoas
32	chr21:40573800-40593600	Weak transcription	A549	lung
33	chr21:40573800-40631000	Weak transcription	Small Intestine	intestine
34	chr21:40575200-40589400	Weak transcription	NHEK	skin
35	chr21:40576200-40590400	Strong transcription	Duodenum Mucosa	Duodenum
36	chr21:40576200-40597400	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
37	chr21:40576400-40592400	Strong transcription	Primary B cells from peripheral blood	blood
38	chr21:40576600-40588600	Strong transcription	Skeletal Muscle Female	skeletal muscle
39	chr21:40576600-40589000	Strong transcription	Primary B cells from cord blood	blood
40	chr21:40576800-40589600	Weak transcription	HUVEC	blood vessel
41	chr21:40576800-40593600	Weak transcription	Right Atrium	heart
42	chr21:40577000-40586600	Strong transcription	HSMM	muscle
43	chr21:40577200-40593800	Weak transcription	Colon Smooth Muscle	Colon
44	chr21:40577200-40595400	Weak transcription	Colonic Mucosa	Colon
45	chr21:40577600-40586800	Weak transcription	Esophagus	oesophagus
46	chr21:40577600-40587000	Weak transcription	Brain Angular Gyrus	brain
47	chr21:40577600-40589400	Weak transcription	Brain Hippocampus Middle	brain
48	chr21:40577600-40596000	Weak transcription	H9 Cell Line	embryonic stem cell
49	chr21:40577800-40598800	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
50	chr21:40578000-40586800	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin

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