Variant report

Variant	rs17189562
Chromosome Location	chr9:104358147-104358148
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:0)
CpG islands
(count:61)
Chromatin interactive
region (count:0)
LncRNA
region (count:1)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

(count:61 , 50 per page) page: 1 2

No.	Chromosome Location	Cell Line	Cell type	Cell Stage
1	chr9:104358101-104358151	NB4	blood:	n/a
2	chr9:104358101-104358151	HMEC	breast:	n/a
3	chr9:104358101-104358151	T-47D	breast:	n/a
4	chr9:104358101-104358151	HRPEpiC	eye:	n/a
5	chr9:104358101-104358151	PFSK-1	brain:	n/a
6	chr9:104358101-104358151	IMR90	lung:	fetal
7	chr9:104358101-104358151	HL-60	blood:	n/a
8	chr9:104358101-104358151	GM19239	blood:	n/a
9	chr9:104358101-104358151	NT2-D1	testis:	n/a
10	chr9:104358101-104358151	GM12892	blood:	n/a
11	chr9:104358101-104358151	ProgFib	skin:	n/a
12	chr9:104358101-104358151	HUVEC	blood vessel:	n/a
13	chr9:104358101-104358151	U87	brain:	n/a
14	chr9:104358101-104358151	HIPEpiC	eye:	n/a
15	chr9:104358101-104358151	SKMC	muscle:	n/a
16	chr9:104358101-104358151	SAEC	small airway:	n/a
17	chr9:104358101-104358151	K562	blood:	n/a
18	chr9:104358101-104358151	HepG2	liver:	n/a
19	chr9:104358101-104358151	Caco-2	colon:	n/a
20	chr9:104358101-104358151	Jurkat	blood:	n/a
21	chr9:104358101-104358151	BE2_C	brain:	n/a
22	chr9:104358101-104358151	SK-N-SH_RA	brain:	n/a
23	chr9:104358101-104358151	AG09319	gingival:	n/a
24	chr9:104358101-104358151	Hela-S3	cervix:	n/a
25	chr9:104358101-104358151	HRCEpiC	kidney:	n/a
26	chr9:104358101-104358151	AoSMC	blood vessel:	n/a
27	chr9:104358101-104358151	H1-hESC	embryonic stem cell:	embryo
28	chr9:104358101-104358151	RPTEC	kidney:	n/a
29	chr9:104358101-104358151	MCF10A-Er-Src	breast:	n/a
30	chr9:104358101-104358151	HNPCEpiC	eye:	n/a
31	chr9:104358101-104358151	LNCaP	prostate:	n/a
32	chr9:104358101-104358151	ECC-1	luminal epithelium:	n/a
33	chr9:104358101-104358151	CMK	blood:	n/a
34	chr9:104358101-104358151	AG10803	skin:	n/a
35	chr9:104358101-104358151	Hepatocyte	liver:	n/a
36	chr9:104358101-104358151	HEEpiC	esophagus:	n/a
37	chr9:104358101-104358151	HAEpiC	amniotic membrane:	n/a
38	chr9:104358101-104358151	GM06990	blood:	n/a
39	chr9:104358101-104358151	AG04449	skin:	fetal
40	chr9:104358101-104358151	A549	lung:	n/a
41	chr9:104358101-104358151	HPAEpiC	pulmonary alveolar:	n/a
42	chr9:104358101-104358151	NHBE	bronchial:	n/a
43	chr9:104358101-104358151	NHDF-neo	bronchial:	n/a
44	chr9:104358101-104358151	SK-N-MC	brain:	n/a
45	chr9:104358101-104358151	HEK293	kidney:	embryo
46	chr9:104358101-104358151	ovcar-3	ovarian:	n/a
47	chr9:104358101-104358151	GM12878	blood:	n/a
48	chr9:104358101-104358151	HCPEpiC	choroid plexus:	n/a
49	chr9:104358101-104358151	HCM	heart:	n/a
50	chr9:104358101-104358151	SK-N-SH	brain:	n/a

No data

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

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-RNF20-3	chr9:104357879-104358148	NONHSAT133747

No data

Variant related genes	Relation type
PPP3R2	CpG island

Extended variants
information (count: 46 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:42)

rs_ID	r²[population]
rs10512283	0.84[EUR][1000 genomes]
rs10512284	0.84[EUR][1000 genomes]
rs10512286	0.82[EUR][1000 genomes]
rs10819954	0.84[EUR][1000 genomes]
rs10819955	0.84[EUR][1000 genomes]
rs10819956	0.84[EUR][1000 genomes]
rs10819958	0.84[EUR][1000 genomes]
rs10819959	0.84[EUR][1000 genomes]
rs10819961	0.84[EUR][1000 genomes]
rs10819977	0.80[EUR][1000 genomes]
rs10989572	0.84[EUR][1000 genomes]
rs10989592	0.83[EUR][1000 genomes]
rs10989594	0.81[EUR][1000 genomes]
rs10989596	0.81[EUR][1000 genomes]
rs10989597	0.81[EUR][1000 genomes]
rs10989598	0.81[EUR][1000 genomes]
rs12708308	0.82[EUR][1000 genomes]
rs1323427	0.84[EUR][1000 genomes]
rs13289501	0.84[EUR][1000 genomes]
rs1407873	0.84[EUR][1000 genomes]
rs1407874	0.84[EUR][1000 genomes]
rs17189275	0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs17189604	1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs17189821	0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs17197124	0.84[EUR][1000 genomes]
rs17774987	0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs1853447	0.84[EUR][1000 genomes]
rs34888126	0.90[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs35227408	0.84[EUR][1000 genomes]
rs35569161	0.90[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs4266702	0.84[EUR][1000 genomes]
rs4442195	0.84[EUR][1000 genomes]
rs55731515	0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs55749212	0.85[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs55838720	0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs56052939	0.90[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs56073506	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs56246731	0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs58830774	0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6479060	0.83[EUR][1000 genomes]
rs72745350	0.85[AMR][1000 genomes];0.95[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs72745355	0.88[AMR][1000 genomes];0.96[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1046975	chr9:104167583-104659873	Weak transcription Flanking Active TSS Active TSS Enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS Strong transcription ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	15 gene(s)	inside rSNPs	diseases
2	nsv949579	chr9:104229820-104512923	Genic enhancers Enhancers Strong transcription Active TSS Bivalent/Poised TSS Bivalent Enhancer Weak transcription Flanking Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	14 gene(s)	inside rSNPs	diseases
3	nsv1052492	chr9:104263419-104387782	Weak transcription Enhancers Strong transcription Active TSS Flanking Active TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	7 gene(s)	inside rSNPs	diseases
4	nsv831672	chr9:104300755-104480849	Weak transcription Strong transcription Bivalent/Poised TSS Enhancers Flanking Active TSS Active TSS Genic enhancers Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	6 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:0 , 50 per page) page:

No data

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dbSNP/dbVar ID: rs12345 /nsv7879
a single nucleotide as 0-based coordinates: chr1:12345
chromosomal regions: chr1:12345-34567

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