Variant report

Variant	rs10413847
Chromosome Location	chr19:52690514-52690515
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:1)
LncRNA
region (count:0)
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	chr19:52690490-52690540	LNCaP	prostate:	n/a
2	chr19:52690490-52690540	HUVEC	blood vessel:	n/a
3	chr19:52690490-52690540	ovcar-3	ovarian:	n/a
4	chr19:52690490-52690540	BJ	skin:	n/a
5	chr19:52690490-52690540	MCF-7	breast:	n/a
6	chr19:52690490-52690540	CMK	blood:	n/a
7	chr19:52690490-52690540	PANC-1	pancreas:	n/a
8	chr19:52690490-52690540	T-47D	breast:	n/a
9	chr19:52690490-52690540	Jurkat	blood:	n/a
10	chr19:52690490-52690540	Hepatocyte	liver:	n/a
11	chr19:52690490-52690540	HCM	heart:	n/a
12	chr19:52690490-52690540	A549	lung:	n/a
13	chr19:52690490-52690540	HepG2	liver:	n/a
14	chr19:52690490-52690540	HAEpiC	amniotic membrane:	n/a
15	chr19:52690490-52690540	MCF10A-Er-Src	breast:	n/a
16	chr19:52690490-52690540	GM06990	blood:	n/a
17	chr19:52690490-52690540	NH-A	brain:	n/a
18	chr19:52690490-52690540	SK-N-SH	brain:	n/a
19	chr19:52690490-52690540	Caco-2	colon:	n/a
20	chr19:52690490-52690540	SK-N-SH_RA	brain:	n/a
21	chr19:52690490-52690540	AG10803	skin:	n/a
22	chr19:52690490-52690540	RPTEC	kidney:	n/a
23	chr19:52690490-52690540	K562	blood:	n/a
24	chr19:52690490-52690540	NB4	blood:	n/a
25	chr19:52690490-52690540	AG04449	skin:	fetal
26	chr19:52690490-52690540	HL-60	blood:	n/a
27	chr19:52690490-52690540	AG09309	skin:	n/a
28	chr19:52690490-52690540	GM12892	blood:	n/a
29	chr19:52690490-52690540	GM12891	blood:	n/a
30	chr19:52690490-52690540	PFSK-1	brain:	n/a
31	chr19:52690490-52690540	HEK293	kidney:	embryo
32	chr19:52690490-52690540	PrEC	prostate:	n/a
33	chr19:52690490-52690540	SK-N-MC	brain:	n/a
34	chr19:52690490-52690540	HNPCEpiC	eye:	n/a
35	chr19:52690490-52690540	HMEC	breast:	n/a
36	chr19:52690490-52690540	ECC-1	luminal epithelium:	n/a
37	chr19:52690490-52690540	SAEC	small airway:	n/a
38	chr19:52690490-52690540	HCF	heart:	n/a
39	chr19:52690490-52690540	HCPEpiC	choroid plexus:	n/a
40	chr19:52690490-52690540	AG04450	lung:	fetal
41	chr19:52690490-52690540	AoSMC	blood vessel:	n/a
42	chr19:52690490-52690540	H1-hESC	embryonic stem cell:	embryo
43	chr19:52690490-52690540	SKMC	muscle:	n/a
44	chr19:52690490-52690540	HPAEpiC	pulmonary alveolar:	n/a
45	chr19:52690490-52690540	NT2-D1	testis:	n/a
46	chr19:52690490-52690540	HCT-116	colon:	n/a
47	chr19:52690490-52690540	HRCEpiC	kidney:	n/a
48	chr19:52690490-52690540	NHBE	bronchial:	n/a
49	chr19:52690490-52690540	U87	brain:	n/a
50	chr19:52690490-52690540	HEEpiC	esophagus:	n/a

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

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr19:52689327..52690920-chr19:52699885..52701616,2	MCF-7	breast:

No data

Variant related genes	Relation type
PPP2R1A	CpG island

Extended variants
information (count: 44 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:37)

rs_ID	r²[population]
rs1025279	1.00[CHB][hapmap];0.84[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs10404867	0.85[ASN][1000 genomes]
rs10405103	0.85[ASN][1000 genomes]
rs10405293	0.91[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[YRI][hapmap];0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs10405519	0.87[ASN][1000 genomes]
rs10405856	0.91[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs10405862	0.80[AFR][1000 genomes];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs10407987	1.00[CEU][hapmap];1.00[CHB][hapmap];0.86[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs10410506	0.85[ASN][1000 genomes]
rs10410908	0.85[CEU][hapmap];0.85[ASN][1000 genomes]
rs10411335	0.85[CEU][hapmap]
rs10411382	0.85[ASN][1000 genomes]
rs10412525	0.90[AMR][1000 genomes];0.86[ASN][1000 genomes]
rs10413274	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10413372	0.90[AMR][1000 genomes];0.86[ASN][1000 genomes]
rs10413470	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10414423	1.00[JPT][hapmap]
rs10415203	0.90[AMR][1000 genomes];0.86[ASN][1000 genomes]
rs10416195	0.94[AFR][1000 genomes];0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs10422583	0.84[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs10423610	1.00[CEU][hapmap];1.00[CHB][hapmap];0.84[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs10423794	1.00[CEU][hapmap];1.00[CHB][hapmap];0.84[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs10424348	1.00[CEU][hapmap];1.00[CHB][hapmap];0.85[YRI][hapmap];0.84[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs10425393	0.82[ASN][1000 genomes]
rs10426066	1.00[CEU][hapmap];0.84[EUR][1000 genomes]
rs13344984	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs16983548	1.00[CEU][hapmap];1.00[CHB][hapmap];0.84[AMR][1000 genomes];0.84[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs16983549	1.00[CEU][hapmap];1.00[CHB][hapmap];0.84[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs16983557	1.00[CEU][hapmap];1.00[CHB][hapmap];0.86[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs1984750	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs61435553	0.84[AMR][1000 genomes];0.84[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs7253157	0.84[AMR][1000 genomes];0.84[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs73935026	0.85[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs73937434	0.84[AMR][1000 genomes];0.85[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs8101364	0.84[AMR][1000 genomes];0.84[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs8103874	1.00[CEU][hapmap];1.00[CHB][hapmap];0.85[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs8107377	1.00[CEU][hapmap];1.00[CHB][hapmap];0.86[EUR][1000 genomes];0.85[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:7 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1065410	chr19:52103914-52889530	Genic enhancers Enhancers ZNF genes & repeats Weak transcription Strong transcription Active TSS Flanking Active TSS Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	596 gene(s)	inside rSNPs	diseases
2	esv3366000	chr19:52491073-52842946	Strong transcription ZNF genes & repeats Weak transcription Genic enhancers Flanking Active TSS Enhancers Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	48 gene(s)	inside rSNPs	diseases
3	nsv1066015	chr19:52502213-52890308	Flanking Active TSS ZNF genes & repeats Enhancers Weak transcription Genic enhancers Active TSS Strong transcription Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	49 gene(s)	inside rSNPs	diseases
4	nsv544059	chr19:52502213-52890308	Active TSS Weak transcription Flanking Active TSS Strong transcription ZNF genes & repeats Enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	49 gene(s)	inside rSNPs	diseases
5	nsv580007	chr19:52660279-52693277	Active TSS ZNF genes & repeats Bivalent/Poised TSS Flanking Active TSS Weak transcription Enhancers Transcr. at gene 5' and 3' Strong transcription Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	12 gene(s)	inside rSNPs	diseases
6	nsv1059417	chr19:52662380-52703801	Enhancers Active TSS Weak transcription Flanking Active TSS Genic enhancers Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	14 gene(s)	inside rSNPs	diseases
7	esv2760529	chr19:52662380-52703813	Weak transcription Enhancers Strong transcription ZNF genes & repeats Flanking Active TSS Genic enhancers Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	14 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs10413847	PPP2R1A	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:5 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr19:52680200-52692200	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
2	chr19:52680400-52691800	Weak transcription	Placenta Amnion	Placenta Amnion
3	chr19:52688600-52691600	Weak transcription	Brain Anterior Caudate	brain
4	chr19:52690200-52691800	Weak transcription	Right Ventricle	heart
5	chr19:52690400-52691800	Enhancers	Breast Myoepithelial Primary Cells	Breast

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