Variant report

Variant	rs3171465
Chromosome Location	chr21:40552307-40552308
allele	C/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:6)
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	chr21:40552201-40552615	HepG2	liver:	n/a	n/a
2	POLR2A	chr21:40552233-40553132	K562	blood:	n/a	n/a

No data

(count:6 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr21:40550674..40556725-chr21:40756529..40762932,9	MCF-7	breast:
2	chr21:40551398..40553559-chr21:40572324..40574736,2	K562	blood:
3	chr21:40550947..40553094-chr21:40816313..40818311,2	MCF-7	breast:
4	chr21:40177078..40179093-chr21:40551455..40553285,2	K562	blood:
5	chr21:40550424..40553042-chr21:40683249..40686279,3	K562	blood:
6	chr21:40551398..40560769-chr21:40565658..40576445,18	K562	blood:

No data

Variant related genes	Relation type
ENSG00000272991	TF binding region
PSMG1	TF binding region
ENSG00000182093	Chromatin interaction
ENSG00000185658	Chromatin interaction
ENSG00000157557	Chromatin interaction
ENSG00000157578	Chromatin interaction
ENSG00000185437	Chromatin interaction

Extended variants
information (count: 66 )
Associated
traits (count: 14 )

rSNPs within LD-proxies of this variant (count:64)

rs_ID	r²[population]
rs1029004	0.90[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs11088466	0.93[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs11088470	0.81[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs11700813	0.90[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs11701805	0.89[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs11910232	0.85[EUR][1000 genomes]
rs11911087	0.84[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs12483559	0.84[EUR][1000 genomes]
rs12627205	0.85[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs13049907	0.85[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs1980407	0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2037923	0.82[ASN][1000 genomes]
rs2056844	0.96[CEU][hapmap];0.95[JPT][hapmap];0.93[YRI][hapmap];0.83[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs2070865	0.92[CEU][hapmap];0.89[GIH][hapmap];0.85[JPT][hapmap];0.87[MEX][hapmap];0.80[TSI][hapmap]
rs2150411	0.96[CEU][hapmap];0.95[JPT][hapmap];0.89[AMR][1000 genomes];0.94[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs2150413	1.00[CEU][hapmap];0.86[CHD][hapmap];1.00[GIH][hapmap];0.95[JPT][hapmap];0.87[MEX][hapmap];0.93[TSI][hapmap];0.87[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs2150414	1.00[CEU][hapmap];0.86[CHD][hapmap];1.00[GIH][hapmap];0.95[JPT][hapmap];0.87[MEX][hapmap];0.93[TSI][hapmap];0.87[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs2297256	0.82[ASW][hapmap];0.96[CEU][hapmap];0.86[CHD][hapmap];0.98[GIH][hapmap];0.95[JPT][hapmap];0.95[LWK][hapmap];0.91[MEX][hapmap];0.96[MKK][hapmap];0.95[TSI][hapmap];0.93[YRI][hapmap];0.91[AFR][1000 genomes];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2836922	0.81[AMR][1000 genomes];0.90[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2836926	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[YRI][hapmap];0.83[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2836930	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2836931	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2836934	0.94[ASW][hapmap];1.00[CEU][hapmap];0.88[CHD][hapmap];0.98[GIH][hapmap];0.90[JPT][hapmap];0.98[LWK][hapmap];1.00[MKK][hapmap];0.92[YRI][hapmap];0.92[AFR][1000 genomes];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2836940	1.00[YRI][hapmap];0.94[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs2836942	0.96[CEU][hapmap];0.95[JPT][hapmap];1.00[YRI][hapmap];0.94[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs2836943	1.00[CEU][hapmap];0.95[JPT][hapmap];0.93[YRI][hapmap];0.96[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs2836945	1.00[CEU][hapmap];0.95[JPT][hapmap];1.00[YRI][hapmap];0.93[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs2836948	0.96[CEU][hapmap];0.95[JPT][hapmap];0.93[YRI][hapmap];0.90[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs2836949	0.96[CEU][hapmap];1.00[JPT][hapmap];0.96[YRI][hapmap];0.88[EUR][1000 genomes]
rs2836952	1.00[CEU][hapmap];0.90[JPT][hapmap];0.96[YRI][hapmap];0.91[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs2836956	0.96[CEU][hapmap];0.86[CHD][hapmap];0.98[GIH][hapmap];0.95[JPT][hapmap];0.82[MEX][hapmap];0.95[TSI][hapmap];0.83[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs2836958	0.96[CEU][hapmap];0.89[CHD][hapmap];0.98[GIH][hapmap];0.95[JPT][hapmap];0.82[MEX][hapmap];0.95[TSI][hapmap];0.83[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs2836959	0.96[CEU][hapmap];0.89[CHD][hapmap];0.98[GIH][hapmap];0.90[JPT][hapmap];0.82[MEX][hapmap];0.95[TSI][hapmap];0.82[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs2836966	0.88[ASW][hapmap];1.00[CEU][hapmap];0.86[CHD][hapmap];1.00[GIH][hapmap];0.95[JPT][hapmap];0.83[LWK][hapmap];0.91[MEX][hapmap];0.82[MKK][hapmap];0.95[TSI][hapmap];0.96[YRI][hapmap];0.87[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs2836980	0.92[CEU][hapmap];0.91[GIH][hapmap];0.85[JPT][hapmap];0.86[MEX][hapmap];0.93[TSI][hapmap];0.81[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs2836983	0.92[CEU][hapmap];0.85[JPT][hapmap];0.81[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs2836985	0.92[CEU][hapmap];0.91[GIH][hapmap];0.85[JPT][hapmap];0.82[MEX][hapmap];0.93[TSI][hapmap]
rs34705151	0.95[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs35769610	0.82[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs4816617	0.88[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4816618	0.90[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs4818001	0.96[CEU][hapmap];0.95[JPT][hapmap];0.89[AMR][1000 genomes];0.93[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs4818018	0.81[AMR][1000 genomes]
rs4818019	0.81[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs59916147	0.82[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs62223011	0.83[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs62223039	0.83[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs6517518	0.87[CHB][hapmap];0.83[ASN][1000 genomes]
rs6517522	0.83[MEX][hapmap]
rs7276046	0.89[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs7278297	0.96[CEU][hapmap];0.95[JPT][hapmap];0.83[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs7279497	0.94[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];0.97[MKK][hapmap];1.00[TSI][hapmap];0.96[YRI][hapmap];0.86[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7282582	0.88[CEU][hapmap];0.80[GIH][hapmap];0.85[JPT][hapmap];0.82[MEX][hapmap]
rs8127379	0.89[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs8129595	0.83[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs8130162	0.86[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs8130240	0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs8130320	0.82[ASW][hapmap];1.00[CEU][hapmap];0.86[CHD][hapmap];1.00[GIH][hapmap];0.95[JPT][hapmap];0.95[LWK][hapmap];0.95[MEX][hapmap];0.96[MKK][hapmap];0.98[TSI][hapmap];0.93[YRI][hapmap];0.96[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs8131132	0.84[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs8132143	0.96[CEU][hapmap];0.95[JPT][hapmap];0.89[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs8132424	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]
rs8133928	0.81[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs8134214	0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs8134843	0.91[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[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:14)

SNP	Gene	Cis/trans	Tissue	Source
rs3171465	HMGN1	Cis_1M	lymphoblastoid	RTeQTL
rs3171465	PSMG1	cis	parietal	SCAN
rs3171465	BRWD1	cis	Brain Pons	GTEx
rs3171465	HMGN1	cis	multi-tissue	Pritchard
rs3171465	PSMG1	cis	lung	GTEx
rs3171465	BRWD1	cis	parietal	SCAN
rs3171465	BRWD1	Cis_1M	lymphoblastoid	RTeQTL
rs3171465	BRWD1	cis	cerebellum	SCAN
rs3171465	BRWD1	cis	lymphoblastoid	seeQTL
rs3171465	BRWD1	cis	Frontal Cortex	GTEx
rs3171465	PSMG1	cis	Artery Tibial	GTEx
rs3171465	BRWD1	cis	Cerebellum	GTEx
rs3171465	BRWD1	cis	Temporal Cortex	GTEx
rs3171465	BRWD1	cis	multi-tissue	Pritchard

Chromatin state (count:125 , 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	chr21:40539600-40554000	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
3	chr21:40539800-40554000	Weak transcription	iPS-15b Cell Line	embryonic stem cell
4	chr21:40540200-40554200	Weak transcription	Psoas Muscle	Psoas
5	chr21:40541200-40552600	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
6	chr21:40541200-40552800	Strong transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
7	chr21:40541200-40553000	Strong transcription	HUES48 Cell Line	embryonic stem cell
8	chr21:40541200-40553000	Strong transcription	HUES6 Cell Line	embryonic stem cell
9	chr21:40541200-40553600	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
10	chr21:40541200-40553800	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
11	chr21:40541200-40554000	Weak transcription	Brain Substantia Nigra	brain
12	chr21:40541400-40553000	Strong transcription	HUES64 Cell Line	embryonic stem cell
13	chr21:40541600-40553800	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
14	chr21:40541600-40554000	Weak transcription	ES-I3 Cell Line	embryonic stem cell
15	chr21:40541600-40554000	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
16	chr21:40541600-40554000	Weak transcription	Colon Smooth Muscle	Colon
17	chr21:40541800-40554400	Weak transcription	Brain Germinal Matrix	brain
18	chr21:40542000-40554000	Weak transcription	Rectal Smooth Muscle	rectum
19	chr21:40542000-40554000	Weak transcription	Stomach Mucosa	stomach
20	chr21:40542400-40554400	Weak transcription	Right Atrium	heart
21	chr21:40542800-40554000	Weak transcription	Primary neutrophils fromperipheralblood	blood
22	chr21:40543000-40552400	Strong transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
23	chr21:40543000-40552400	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
24	chr21:40543000-40552600	Strong transcription	Osteobl	bone
25	chr21:40543400-40554000	Weak transcription	Primary T helper naive cells from peripheral blood	blood
26	chr21:40543600-40553200	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
27	chr21:40543800-40553200	Weak transcription	Small Intestine	intestine
28	chr21:40543800-40554000	Weak transcription	Brain Cingulate Gyrus	brain
29	chr21:40543800-40554000	Weak transcription	Brain Inferior Temporal Lobe	brain
30	chr21:40543800-40554200	Weak transcription	Right Ventricle	heart
31	chr21:40543800-40554600	Weak transcription	Left Ventricle	heart
32	chr21:40544000-40553800	Weak transcription	HSMMtube	muscle
33	chr21:40544000-40554000	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
34	chr21:40544000-40554000	Weak transcription	Brain Anterior Caudate	brain
35	chr21:40544200-40554000	Weak transcription	Brain Hippocampus Middle	brain
36	chr21:40544200-40554000	Weak transcription	Colonic Mucosa	Colon
37	chr21:40544600-40552400	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
38	chr21:40545400-40552400	Strong transcription	Hela-S3	cervix
39	chr21:40545600-40553000	Strong transcription	iPS-20b Cell Line	embryonic stem cell
40	chr21:40545600-40554200	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
41	chr21:40545800-40553800	Weak transcription	Cortex derived primary cultured neurospheres	brain
42	chr21:40546400-40552400	Strong transcription	Primary hematopoietic stem cells short term culture	blood
43	chr21:40546400-40553800	Weak transcription	NHLF	lung
44	chr21:40546400-40554000	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
45	chr21:40546400-40554000	Weak transcription	Brain Angular Gyrus	brain
46	chr21:40546400-40554000	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
47	chr21:40546400-40554000	Weak transcription	Esophagus	oesophagus
48	chr21:40546400-40554000	Weak transcription	Spleen	Spleen
49	chr21:40546400-40554200	Weak transcription	Lung	lung
50	chr21:40546400-40554200	Weak transcription	Ovary	ovary

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