Variant report

Variant	rs34705151
Chromosome Location	chr21:40553344-40553345
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:1)
CpG islands
(count:0)
Chromatin interactive
region (count:10)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

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

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	ZNF263	chr21:40552583-40553576	HEK293-T-REx	kidney:	n/a	chr21:40553105-40553126

No data

(count:10 , 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	chr21:40551398..40553559-chr21:40572324..40574736,2	K562	blood:
4	chr21:40552682..40557546-chr21:40815502..40820280,12	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	chr21:40552640..40555791-chr21:40749339..40752310,3	K562	blood:
9	chr21:40032723..40034705-chr21:40552796..40555245,2	MCF-7	breast:
10	chr21:40551398..40560769-chr21:40565658..40576445,18	K562	blood:

No data

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

Extended variants
information (count: 58 )
Associated
traits (count: 5 )

rSNPs within LD-proxies of this variant (count:56)

rs_ID	r²[population]
rs1029004	0.87[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs11088466	0.92[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs11088470	0.80[EUR][1000 genomes]
rs11700813	0.89[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs11701805	0.86[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs11910232	0.83[EUR][1000 genomes]
rs11911087	0.81[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs12483559	0.82[EUR][1000 genomes]
rs12627205	0.84[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs13049907	0.82[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs1980407	0.92[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2037923	0.82[ASN][1000 genomes]
rs2056844	0.83[EUR][1000 genomes]
rs2150411	0.88[AMR][1000 genomes];0.94[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs2150413	0.84[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs2150414	0.84[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs2297256	0.90[AFR][1000 genomes];0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2836922	0.89[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2836926	0.81[AFR][1000 genomes];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2836930	0.92[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2836931	0.90[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2836934	0.90[AFR][1000 genomes];0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs2836940	0.91[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs2836942	0.91[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs2836943	0.92[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs2836945	0.90[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs2836948	0.89[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs2836949	0.87[EUR][1000 genomes]
rs2836952	0.88[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs2836956	0.86[EUR][1000 genomes]
rs2836958	0.86[EUR][1000 genomes]
rs2836959	0.86[EUR][1000 genomes]
rs2836966	0.84[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs2836983	0.80[EUR][1000 genomes]
rs3171465	0.95[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs35769610	0.83[EUR][1000 genomes]
rs4816617	0.85[AFR][1000 genomes];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4816618	0.89[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs4818001	0.88[AMR][1000 genomes];0.93[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs59916147	0.84[EUR][1000 genomes]
rs62223011	0.84[EUR][1000 genomes]
rs62223039	0.82[EUR][1000 genomes]
rs6517518	0.84[ASN][1000 genomes]
rs7276046	0.88[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs7278297	0.86[EUR][1000 genomes]
rs7279497	0.83[AFR][1000 genomes];0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs8127379	0.88[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs8130162	0.83[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs8130240	0.91[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs8130320	0.94[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs8131132	0.81[AFR][1000 genomes];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs8132143	0.88[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs8132424	0.88[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs8133928	0.80[EUR][1000 genomes]
rs8134214	0.90[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs8134843	0.90[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[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:5)

SNP	Gene	Cis/trans	Tissue	Source
rs34705151	HMGN1	cis	multi-tissue	Pritchard
rs34705151	PSMG1	cis	Artery Tibial	GTEx
rs34705151	PSMG1	cis	lung	GTEx
rs34705151	BRWD1	Cis_1M	lymphoblastoid	RTeQTL
rs34705151	HMGN1	Cis_1M	lymphoblastoid	RTeQTL

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	chr21:40541200-40553600	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
6	chr21:40541200-40553800	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
7	chr21:40541200-40554000	Weak transcription	Brain Substantia Nigra	brain
8	chr21:40541600-40553800	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
9	chr21:40541600-40554000	Weak transcription	ES-I3 Cell Line	embryonic stem cell
10	chr21:40541600-40554000	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
11	chr21:40541600-40554000	Weak transcription	Colon Smooth Muscle	Colon
12	chr21:40541800-40554400	Weak transcription	Brain Germinal Matrix	brain
13	chr21:40542000-40554000	Weak transcription	Rectal Smooth Muscle	rectum
14	chr21:40542000-40554000	Weak transcription	Stomach Mucosa	stomach
15	chr21:40542400-40554400	Weak transcription	Right Atrium	heart
16	chr21:40542800-40554000	Weak transcription	Primary neutrophils fromperipheralblood	blood
17	chr21:40543400-40554000	Weak transcription	Primary T helper naive cells from peripheral blood	blood
18	chr21:40543800-40554000	Weak transcription	Brain Cingulate Gyrus	brain
19	chr21:40543800-40554000	Weak transcription	Brain Inferior Temporal Lobe	brain
20	chr21:40543800-40554200	Weak transcription	Right Ventricle	heart
21	chr21:40543800-40554600	Weak transcription	Left Ventricle	heart
22	chr21:40544000-40553800	Weak transcription	HSMMtube	muscle
23	chr21:40544000-40554000	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
24	chr21:40544000-40554000	Weak transcription	Brain Anterior Caudate	brain
25	chr21:40544200-40554000	Weak transcription	Brain Hippocampus Middle	brain
26	chr21:40544200-40554000	Weak transcription	Colonic Mucosa	Colon
27	chr21:40545600-40554200	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
28	chr21:40545800-40553800	Weak transcription	Cortex derived primary cultured neurospheres	brain
29	chr21:40546400-40553800	Weak transcription	NHLF	lung
30	chr21:40546400-40554000	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
31	chr21:40546400-40554000	Weak transcription	Brain Angular Gyrus	brain
32	chr21:40546400-40554000	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
33	chr21:40546400-40554000	Weak transcription	Esophagus	oesophagus
34	chr21:40546400-40554000	Weak transcription	Spleen	Spleen
35	chr21:40546400-40554200	Weak transcription	Lung	lung
36	chr21:40546400-40554200	Weak transcription	Ovary	ovary
37	chr21:40546400-40554600	Weak transcription	Gastric	stomach
38	chr21:40546600-40553800	Weak transcription	Fetal Lung	lung
39	chr21:40548000-40553800	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
40	chr21:40548000-40554000	Weak transcription	Pancreas	Pancrea
41	chr21:40548400-40554000	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
42	chr21:40548400-40554000	Weak transcription	Skeletal Muscle Female	skeletal muscle
43	chr21:40548400-40554400	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
44	chr21:40548400-40554600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
45	chr21:40548800-40554000	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
46	chr21:40548800-40554000	Weak transcription	Fetal Heart	heart
47	chr21:40549000-40553800	Weak transcription	Adipose Nuclei	Adipose
48	chr21:40549200-40554000	Weak transcription	Stomach Smooth Muscle	stomach
49	chr21:40549400-40554000	Weak transcription	Rectal Mucosa Donor 31	rectum
50	chr21:40550800-40554000	Weak transcription	Primary B cells from peripheral blood	blood

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