Variant report

Variant	rs6508826
Chromosome Location	chr19:39425722-39425723
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:27)
CpG islands
(count:0)
Chromatin interactive
region (count:3)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:27 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	TCF12	chr19:39424981-39426012	A549	lung:	n/a	chr19:39425645-39425655
2	POLR2A	chr19:39425125-39425753	K562	blood:	n/a	n/a
3	POLR2A	chr19:39425051-39425856	GM12892	blood:	n/a	n/a
4	POLR2A	chr19:39425022-39426396	SK-N-MC	brain:	n/a	n/a
5	POLR2A	chr19:39425571-39425883	MCF10A-Er-Src	breast:	n/a	n/a
6	POLR2A	chr19:39425543-39425863	ECC-1	luminal epithelium:	n/a	n/a
7	POLR2A	chr19:39425529-39425891	HL-60	blood:	n/a	n/a
8	POLR2A	chr19:39418846-39427915	PANC-1	pancreas:	n/a	n/a
9	POLR2A	chr19:39425617-39425859	GM12878	blood:	n/a	n/a
10	POLR2A	chr19:39425581-39425795	MCF-7	breast:	n/a	n/a
11	POLR2A	chr19:39425666-39425834	A549	lung:	n/a	n/a
12	POLR2A	chr19:39425530-39425834	HCT-116	colon:	n/a	n/a
13	POLR2A	chr19:39425136-39426019	PFSK-1	brain:	n/a	n/a
14	POLR2A	chr19:39425136-39425872	GM12892	blood:	n/a	n/a
15	POLR2A	chr19:39425059-39425916	K562	blood:	n/a	n/a
16	POLR2A	chr19:39424987-39426056	K562	blood:	n/a	n/a
17	SPI1	chr19:39425285-39425781	HL-60	blood:	n/a	chr19:39425332-39425341 chr19:39425603-39425616
18	SETDB1	chr19:39425720-39426589	U2OS	brain:	n/a	n/a
19	POLR2A	chr19:39425664-39425856	A549	lung:	n/a	n/a
20	BCL3	chr19:39425131-39425942	A549	lung:	n/a	n/a
21	KAP1	chr19:39425657-39426607	K562	blood:	n/a	n/a
22	POLR2A	chr19:39419835-39427960	PANC-1	pancreas:	n/a	n/a
23	POLR2A	chr19:39425402-39425819	Hela-S3	cervix:	n/a	n/a
24	POLR2A	chr19:39425500-39425832	K562	blood:	n/a	n/a
25	POLR2A	chr19:39425254-39425800	GM12891	blood:	n/a	n/a
26	SETDB1	chr19:39425171-39426878	K562	blood:	n/a	n/a
27	POLR2A	chr19:39425626-39425858	A549	lung:	n/a	n/a

No data

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

No.	Distal block	Cell Line	Cell type
1	chr19:39421479..39423080-chr19:39424950..39427056,2	MCF-7	breast:
2	chr19:39338909..39344654-chr19:39419169..39426961,19	MCF-7	breast:
3	chr19:39424291..39427165-chr19:39431184..39433812,2	K562	blood:

No data

Variant related genes	Relation type
SARS2	TF binding region
ENSG00000104824	Chromatin interaction
ENSG00000104835	Chromatin interaction
ENSG00000128626	Chromatin interaction

Extended variants
information (count: 32 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:30)

rs_ID	r²[population]
rs10411209	0.86[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs10411301	0.83[AFR][1000 genomes];1.00[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs10423309	0.82[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs11083487	1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs12977453	1.00[ASN][1000 genomes]
rs13343573	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs16972885	0.91[YRI][hapmap];0.91[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs17883664	1.00[ASN][1000 genomes]
rs2070250	1.00[JPT][hapmap];0.87[YRI][hapmap];0.83[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs2070251	0.89[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs2082436	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs2116853	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs2163811	0.86[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs2304115	0.87[ASW][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.92[MKK][hapmap];1.00[TSI][hapmap];0.87[YRI][hapmap];0.83[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs2304116	0.87[ASW][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.92[MKK][hapmap];1.00[TSI][hapmap];0.87[YRI][hapmap];0.83[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs28808414	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28824318	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28844707	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28860185	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs34264048	0.83[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs45535036	1.00[ASN][1000 genomes]
rs59849895	1.00[ASN][1000 genomes]
rs61194027	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs61232096	0.89[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs61347610	1.00[ASN][1000 genomes]
rs6508827	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73537681	1.00[ASN][1000 genomes]
rs73930228	0.84[AMR][1000 genomes]
rs73930229	0.82[AFR][1000 genomes];0.84[AMR][1000 genomes]
rs8113749	0.93[AFR][1000 genomes];0.85[AMR][1000 genomes];1.00[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	nsv1057899	chr19:39088319-39475493	Flanking Active TSS Flanking Bivalent TSS/Enh Genic enhancers Weak transcription Transcr. at gene 5' and 3' Enhancers Bivalent Enhancer Active TSS Strong transcription Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	82 gene(s)	inside rSNPs	diseases
2	esv1837023	chr19:39190588-39425722	Active TSS Enhancers Weak transcription Genic enhancers Flanking Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer Strong transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	65 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs6508826	MRPS12	cis	multi-tissue	Pritchard

Chromatin state (count:100 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr19:39422400-39426600	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
2	chr19:39422400-39434600	Weak transcription	Fetal Kidney	kidney
3	chr19:39422400-39435000	Weak transcription	Fetal Lung	lung
4	chr19:39422400-39435000	Weak transcription	Placenta Amnion	Placenta Amnion
5	chr19:39422400-39440600	Weak transcription	NHDF-Ad	bronchial
6	chr19:39422600-39427000	Weak transcription	Rectal Mucosa Donor 31	rectum
7	chr19:39422600-39430200	Weak transcription	HUVEC	blood vessel
8	chr19:39422600-39430800	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
9	chr19:39422600-39435200	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
10	chr19:39422600-39435200	Weak transcription	HSMM	muscle
11	chr19:39422600-39440200	Weak transcription	NH-A	brain
12	chr19:39422600-39440600	Weak transcription	Duodenum Mucosa	Duodenum
13	chr19:39422600-39453000	Weak transcription	HSMMtube	muscle
14	chr19:39422800-39432600	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
15	chr19:39423000-39425800	ZNF genes & repeats	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
16	chr19:39423000-39425800	ZNF genes & repeats	HUES64 Cell Line	embryonic stem cell
17	chr19:39423000-39425800	ZNF genes & repeats	iPS DF 19.11 Cell Line	embryonic stem cell
18	chr19:39423000-39425800	Strong transcription	Rectal Mucosa Donor 29	rectum
19	chr19:39423200-39425800	Strong transcription	Primary T cells from cord blood	blood
20	chr19:39423200-39440800	Weak transcription	Fetal Heart	heart
21	chr19:39423400-39426000	Strong transcription	Fetal Muscle Trunk	muscle
22	chr19:39423400-39436800	Weak transcription	Aorta	Aorta
23	chr19:39423600-39425800	Strong transcription	Primary T helper naive cells fromperipheralblood	blood
24	chr19:39423600-39425800	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
25	chr19:39423600-39426000	Strong transcription	Foreskin Fibroblast Primary Cells skin01	Skin
26	chr19:39423600-39426000	Strong transcription	Foreskin Fibroblast Primary Cells skin02	Skin
27	chr19:39423600-39426200	Weak transcription	Hela-S3	cervix
28	chr19:39423600-39432400	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
29	chr19:39423600-39433400	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
30	chr19:39423600-39435000	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
31	chr19:39423600-39440400	Weak transcription	Right Atrium	heart
32	chr19:39423600-39440600	Weak transcription	Gastric	stomach
33	chr19:39424000-39426000	ZNF genes & repeats	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
34	chr19:39424000-39435200	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
35	chr19:39424200-39425800	Enhancers	HepG2	liver
36	chr19:39424200-39426000	ZNF genes & repeats	HUES6 Cell Line	embryonic stem cell
37	chr19:39424200-39426400	Weak transcription	Skeletal Muscle Female	skeletal muscle
38	chr19:39424200-39435400	Weak transcription	NHLF	lung
39	chr19:39424400-39426600	ZNF genes & repeats	Fetal Intestine Small	intestine
40	chr19:39424400-39432000	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
41	chr19:39424400-39435000	Weak transcription	Adipose Nuclei	Adipose
42	chr19:39424400-39436800	Weak transcription	Brain Angular Gyrus	brain
43	chr19:39424400-39440000	Weak transcription	Fetal Brain Female	brain
44	chr19:39424600-39425800	ZNF genes & repeats	iPS-20b Cell Line	embryonic stem cell
45	chr19:39424600-39426000	Enhancers	Pancreas	Pancrea
46	chr19:39424600-39426000	Weak transcription	Sigmoid Colon	Sigmoid Colon
47	chr19:39424600-39427800	Weak transcription	Small Intestine	intestine
48	chr19:39424600-39434400	Weak transcription	Fetal Intestine Large	intestine
49	chr19:39424600-39434600	Weak transcription	Muscle Satellite Cultured Cells	--
50	chr19:39424600-39434600	Weak transcription	Colon Smooth Muscle	Colon

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