Variant report

Variant	rs6517522
Chromosome Location	chr21:40553845-40553846
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:3)
CpG islands
(count:0)
Chromatin interactive
region (count:12)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:3 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	MXI1	chr21:40553519-40556556	IMR90	lung:	n/a	chr21:40554025-40554034
2	ZNF274	chr21:40553665-40554268	K562	blood:	n/a	n/a
3	IRF1	chr21:40553796-40554356	K562	blood:	n/a	n/a

No data

(count:12 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr21:40550674..40556725-chr21:40756529..40762932,9	MCF-7	breast:
2	chr21:40552516..40555515-chr21:40758943..40760790,2	MCF-7	breast:
3	chr21:40552682..40557546-chr21:40815502..40820280,12	K562	blood:
4	chr21:40553821..40557385-chr21:40719764..40724370,6	K562	blood:
5	chr21:40552682..40557091-chr21:40814575..40819975,14	K562	blood:
6	chr21:40552621..40554134-chr21:40759011..40760578,2	K562	blood:
7	chr21:40552621..40555799-chr21:40758034..40760615,3	K562	blood:
8	chr21:40175328..40180167-chr21:40553641..40558387,7	K562	blood:
9	chr21:40552640..40555791-chr21:40749339..40752310,3	K562	blood:
10	chr21:40553454..40557456-chr21:40682892..40687176,12	K562	blood:
11	chr21:40032723..40034705-chr21:40552796..40555245,2	MCF-7	breast:
12	chr21:40551398..40560769-chr21:40565658..40576445,18	K562	blood:

No data

Variant related genes	Relation type
PSMG1	TF binding region
ENSG00000272991	TF binding region
ENSG00000205581	Chromatin interaction
ENSG00000185658	Chromatin interaction
ENSG00000185437	Chromatin interaction
ENSG00000157554	Chromatin interaction
ENSG00000182093	Chromatin interaction
ENSG00000157557	Chromatin interaction
ENSG00000157578	Chromatin interaction
ENSG00000255568	Chromatin interaction

Extended variants
information (count: 69 )
Associated
traits (count: 17 )

rSNPs within LD-proxies of this variant (count:67)

rs_ID	r²[population]
rs11910151	0.82[AFR][1000 genomes]
rs11911822	0.90[YRI][hapmap]
rs13052882	0.81[AFR][1000 genomes]
rs1571709	1.00[YRI][hapmap];0.87[AFR][1000 genomes]
rs1888490	0.82[CHB][hapmap]
rs1980407	0.81[AFR][1000 genomes]
rs2037925	0.86[YRI][hapmap]
rs2150411	0.90[YRI][hapmap];0.82[AFR][1000 genomes]
rs2183573	0.93[ASW][hapmap]
rs2239384	0.83[JPT][hapmap]
rs2297255	0.82[CHB][hapmap]
rs2776311	0.89[CEU][hapmap];1.00[JPT][hapmap]
rs2836930	0.90[YRI][hapmap];0.87[AFR][1000 genomes]
rs2836931	0.89[YRI][hapmap];0.87[AFR][1000 genomes]
rs2836936	0.82[CHB][hapmap]
rs2836937	0.82[CHB][hapmap]
rs2836941	0.82[CHB][hapmap]
rs2836946	0.82[CHB][hapmap]
rs2836947	0.82[CHB][hapmap]
rs2836959	0.86[ASW][hapmap];0.86[YRI][hapmap]
rs2836962	0.82[CHB][hapmap]
rs2836963	0.82[CHB][hapmap]
rs2836969	0.90[YRI][hapmap]
rs2836970	0.82[CHB][hapmap]
rs2836971	0.90[YRI][hapmap]
rs2836975	0.93[ASW][hapmap];0.90[YRI][hapmap]
rs2836976	0.82[CHB][hapmap]
rs2836978	0.82[CHB][hapmap]
rs2836979	0.82[CHB][hapmap]
rs2836980	0.86[ASW][hapmap];0.86[YRI][hapmap]
rs2836983	0.86[YRI][hapmap]
rs2836985	0.86[YRI][hapmap]
rs2836988	0.86[YRI][hapmap]
rs2836992	0.83[JPT][hapmap]
rs2854727	0.89[CEU][hapmap];0.85[GIH][hapmap];1.00[JPT][hapmap];0.86[MEX][hapmap]
rs3171465	0.83[MEX][hapmap]
rs36113648	0.81[AFR][1000 genomes]
rs377098	0.90[YRI][hapmap]
rs379291	0.82[CHB][hapmap]
rs418298	0.93[ASW][hapmap];0.90[YRI][hapmap]
rs418359	0.93[ASW][hapmap];0.89[YRI][hapmap]
rs419469	0.92[ASW][hapmap];0.90[YRI][hapmap]
rs420888	0.82[CHB][hapmap]
rs4817997	0.82[CHB][hapmap]
rs4818001	0.90[YRI][hapmap];0.82[AFR][1000 genomes]
rs4818015	0.93[ASW][hapmap];0.90[YRI][hapmap]
rs4818027	0.83[JPT][hapmap]
rs6517516	0.82[CHB][hapmap]
rs6517517	0.82[CHB][hapmap]
rs7276774	0.85[YRI][hapmap]
rs7278048	0.82[CHB][hapmap]
rs7279497	0.83[MEX][hapmap]
rs7281540	0.82[CHB][hapmap]
rs7282604	0.93[ASW][hapmap];0.90[YRI][hapmap]
rs741795	0.89[CEU][hapmap];1.00[JPT][hapmap]
rs8128191	1.00[YRI][hapmap]
rs8129850	0.82[CHB][hapmap]
rs8132143	0.90[YRI][hapmap]
rs8132295	1.00[ASW][hapmap];1.00[YRI][hapmap]
rs8132333	1.00[ASW][hapmap];1.00[YRI][hapmap]
rs8132424	0.86[ASW][hapmap];0.80[LWK][hapmap];0.90[YRI][hapmap]
rs8132993	0.88[CEU][hapmap];0.85[GIH][hapmap];0.92[JPT][hapmap];0.86[MEX][hapmap]
rs9305669	0.82[CHB][hapmap]
rs997146	0.82[CHB][hapmap]
rs9979691	0.82[CHB][hapmap]
rs9981595	0.81[CHB][hapmap]
rs9981884	0.83[AMR][1000 genomes];0.89[EUR][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:17)

SNP	Gene	Cis/trans	Tissue	Source
rs6517522	DSCR6	cis	parietal	SCAN
rs6517522	BRWD1	cis	Temporal Cortex	GTEx
rs6517522	BRWD1	Cis_1M	lymphoblastoid	RTeQTL
rs6517522	HMGN1	Cis_1M	lymphoblastoid	RTeQTL
rs6517522	BRWD1	cis	Brain Pons	GTEx
rs6517522	BRWD1	cis	parietal	SCAN
rs6517522	DSCR2	cis	normal skin	skin_eQTL
rs6517522	BRWD1	cis	Frontal Cortex	GTEx
rs6517522	PSMG1	cis	Artery Tibial	GTEx
rs6517522	DSCR3	cis	cerebellum	SCAN
rs6517522	HMGN1	cis	multi-tissue	Pritchard
rs6517522	PSMG1	cis	Skin Sun Exposed Lower leg	GTEx
rs6517522	BRWD1	cis	Cerebellum	GTEx
rs6517522	PSMG1	cis	Esophagus Mucosa	GTEx
rs6517522	C21orf107	cis	multi-tissue	Pritchard
rs6517522	HMGN1	cis	lymphoblastoid	seeQTL
rs6517522	PSMG1	cis	parietal	SCAN

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr21:40539600-40554000	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
2	chr21:40539800-40554000	Weak transcription	iPS-15b Cell Line	embryonic stem cell
3	chr21:40540200-40554200	Weak transcription	Psoas Muscle	Psoas
4	chr21:40541200-40554000	Weak transcription	Brain Substantia Nigra	brain
5	chr21:40541600-40554000	Weak transcription	ES-I3 Cell Line	embryonic stem cell
6	chr21:40541600-40554000	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
7	chr21:40541600-40554000	Weak transcription	Colon Smooth Muscle	Colon
8	chr21:40541800-40554400	Weak transcription	Brain Germinal Matrix	brain
9	chr21:40542000-40554000	Weak transcription	Rectal Smooth Muscle	rectum
10	chr21:40542000-40554000	Weak transcription	Stomach Mucosa	stomach
11	chr21:40542400-40554400	Weak transcription	Right Atrium	heart
12	chr21:40542800-40554000	Weak transcription	Primary neutrophils fromperipheralblood	blood
13	chr21:40543400-40554000	Weak transcription	Primary T helper naive cells from peripheral blood	blood
14	chr21:40543800-40554000	Weak transcription	Brain Cingulate Gyrus	brain
15	chr21:40543800-40554000	Weak transcription	Brain Inferior Temporal Lobe	brain
16	chr21:40543800-40554200	Weak transcription	Right Ventricle	heart
17	chr21:40543800-40554600	Weak transcription	Left Ventricle	heart
18	chr21:40544000-40554000	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
19	chr21:40544000-40554000	Weak transcription	Brain Anterior Caudate	brain
20	chr21:40544200-40554000	Weak transcription	Brain Hippocampus Middle	brain
21	chr21:40544200-40554000	Weak transcription	Colonic Mucosa	Colon
22	chr21:40545600-40554200	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
23	chr21:40546400-40554000	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
24	chr21:40546400-40554000	Weak transcription	Brain Angular Gyrus	brain
25	chr21:40546400-40554000	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
26	chr21:40546400-40554000	Weak transcription	Esophagus	oesophagus
27	chr21:40546400-40554000	Weak transcription	Spleen	Spleen
28	chr21:40546400-40554200	Weak transcription	Lung	lung
29	chr21:40546400-40554200	Weak transcription	Ovary	ovary
30	chr21:40546400-40554600	Weak transcription	Gastric	stomach
31	chr21:40548000-40554000	Weak transcription	Pancreas	Pancrea
32	chr21:40548400-40554000	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
33	chr21:40548400-40554000	Weak transcription	Skeletal Muscle Female	skeletal muscle
34	chr21:40548400-40554400	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
35	chr21:40548400-40554600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
36	chr21:40548800-40554000	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
37	chr21:40548800-40554000	Weak transcription	Fetal Heart	heart
38	chr21:40549200-40554000	Weak transcription	Stomach Smooth Muscle	stomach
39	chr21:40549400-40554000	Weak transcription	Rectal Mucosa Donor 31	rectum
40	chr21:40550800-40554000	Weak transcription	Primary B cells from peripheral blood	blood
41	chr21:40551000-40554200	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
42	chr21:40551200-40554000	Weak transcription	Fetal Muscle Trunk	muscle
43	chr21:40551200-40554000	Weak transcription	Fetal Muscle Leg	muscle
44	chr21:40551200-40554000	Weak transcription	Thymus	Thymus
45	chr21:40551400-40554000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
46	chr21:40551400-40554000	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
47	chr21:40551400-40554000	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
48	chr21:40551400-40554000	Weak transcription	Fetal Kidney	kidney
49	chr21:40551400-40554000	Weak transcription	Fetal Stomach	stomach
50	chr21:40551400-40554200	Weak transcription	Aorta	Aorta

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