Variant report

Variant	rs11715459
Chromosome Location	chr3:142440299-142440300
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	chr3:142440284-142440334	NB4	blood:	n/a
2	chr3:142440284-142440334	GM06990	blood:	n/a
3	chr3:142440284-142440334	HCPEpiC	choroid plexus:	n/a
4	chr3:142440284-142440334	IMR90	lung:	fetal
5	chr3:142440284-142440334	HRCEpiC	kidney:	n/a
6	chr3:142440284-142440334	Hela-S3	cervix:	n/a
7	chr3:142440284-142440334	NHDF-neo	bronchial:	n/a
8	chr3:142440284-142440334	LNCaP	prostate:	n/a
9	chr3:142440284-142440334	GM19239	blood:	n/a
10	chr3:142440284-142440334	MCF10A-Er-Src	breast:	n/a
11	chr3:142440284-142440334	GM12891	blood:	n/a
12	chr3:142440284-142440334	AoSMC	blood vessel:	n/a
13	chr3:142440284-142440334	HCM	heart:	n/a
14	chr3:142440284-142440334	GM12878	blood:	n/a
15	chr3:142440284-142440334	HAEpiC	amniotic membrane:	n/a
16	chr3:142440284-142440334	BJ	skin:	n/a
17	chr3:142440284-142440334	RPTEC	kidney:	n/a
18	chr3:142440284-142440334	Hepatocyte	liver:	n/a
19	chr3:142440284-142440334	CMK	blood:	n/a
20	chr3:142440284-142440334	AG04449	skin:	fetal
21	chr3:142440284-142440334	HRPEpiC	eye:	n/a
22	chr3:142440284-142440334	HCF	heart:	n/a
23	chr3:142440284-142440334	HPAEpiC	pulmonary alveolar:	n/a
24	chr3:142440284-142440334	HEK293	kidney:	embryo
25	chr3:142440284-142440334	AG09319	gingival:	n/a
26	chr3:142440284-142440334	AG10803	skin:	n/a
27	chr3:142440284-142440334	H1-hESC	embryonic stem cell:	embryo
28	chr3:142440284-142440334	T-47D	breast:	n/a
29	chr3:142440284-142440334	PrEC	prostate:	n/a
30	chr3:142440284-142440334	AG09309	skin:	n/a
31	chr3:142440284-142440334	HIPEpiC	eye:	n/a
32	chr3:142440284-142440334	K562	blood:	n/a
33	chr3:142440284-142440334	HEEpiC	esophagus:	n/a
34	chr3:142440284-142440334	SK-N-MC	brain:	n/a
35	chr3:142440284-142440334	PFSK-1	brain:	n/a
36	chr3:142440284-142440334	ProgFib	skin:	n/a
37	chr3:142440284-142440334	HUVEC	blood vessel:	n/a
38	chr3:142440284-142440334	Jurkat	blood:	n/a
39	chr3:142440284-142440334	HepG2	liver:	n/a
40	chr3:142440284-142440334	GM12892	blood:	n/a
41	chr3:142440284-142440334	ovcar-3	ovarian:	n/a
42	chr3:142440284-142440334	AG04450	lung:	fetal
43	chr3:142440284-142440334	HL-60	blood:	n/a
44	chr3:142440284-142440334	A549	lung:	n/a
45	chr3:142440284-142440334	Caco-2	colon:	n/a
46	chr3:142440284-142440334	SK-N-SH	brain:	n/a
47	chr3:142440284-142440334	NT2-D1	testis:	n/a
48	chr3:142440284-142440334	HRE	kidney:	n/a
49	chr3:142440284-142440334	HMEC	breast:	n/a
50	chr3:142440284-142440334	PANC-1	pancreas:	n/a

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

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr3:142437025..142440945-chr3:142442939..142444971,3	K562	blood:

No data

Variant related genes	Relation type
TRPC1	CpG island
ENSG00000144935	Chromatin interaction

Extended variants
information (count: 57 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:53)

rs_ID	r²[population]
rs11717993	0.81[ASN][1000 genomes]
rs11915805	0.85[AMR][1000 genomes];0.90[ASN][1000 genomes]
rs1604	0.89[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs2049328	0.89[CHB][hapmap];0.89[ASN][1000 genomes]
rs2354856	0.94[CHB][hapmap];0.81[JPT][hapmap];0.81[ASN][1000 genomes]
rs28571594	0.95[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs28658009	0.81[ASN][1000 genomes]
rs34445140	0.81[ASN][1000 genomes]
rs35467195	0.86[AMR][1000 genomes];0.87[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs35862982	0.86[AMR][1000 genomes];0.84[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs3773504	0.82[MEX][hapmap];0.83[TSI][hapmap];0.83[AMR][1000 genomes]
rs3821647	0.83[CHB][hapmap]
rs4259003	0.94[CHB][hapmap]
rs4530572	0.90[ASN][1000 genomes]
rs4539980	0.86[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs55722370	0.81[ASN][1000 genomes]
rs55722917	0.89[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs56775607	0.86[AMR][1000 genomes];0.85[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs57026466	0.81[ASN][1000 genomes]
rs60294656	0.81[ASN][1000 genomes]
rs60319320	0.81[ASN][1000 genomes]
rs60752859	0.81[ASN][1000 genomes]
rs6440104	0.87[ASW][hapmap];0.96[CEU][hapmap];0.88[CHB][hapmap];1.00[CHD][hapmap];0.94[GIH][hapmap];1.00[JPT][hapmap];0.97[LWK][hapmap];1.00[MEX][hapmap];0.96[MKK][hapmap];0.98[TSI][hapmap];0.93[YRI][hapmap];0.87[AFR][1000 genomes];0.95[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs6440106	0.86[AMR][1000 genomes];0.88[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6440107	0.95[MEX][hapmap];0.91[TSI][hapmap];0.89[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs66897945	0.81[ASN][1000 genomes]
rs6777466	0.81[ASN][1000 genomes]
rs6784998	0.82[MEX][hapmap];0.91[TSI][hapmap];0.89[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs6790959	0.89[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs6798849	0.81[ASN][1000 genomes]
rs7623762	0.92[CEU][hapmap];0.88[CHB][hapmap];1.00[CHD][hapmap];0.92[GIH][hapmap];0.94[JPT][hapmap];0.81[LWK][hapmap];0.95[MEX][hapmap];0.84[MKK][hapmap];0.98[TSI][hapmap];0.95[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs7623977	0.81[ASN][1000 genomes]
rs7626908	0.91[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs7628728	0.89[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs7629129	0.92[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs7631245	0.83[CHB][hapmap]
rs7635768	0.87[ASN][1000 genomes]
rs7637826	0.87[ASN][1000 genomes]
rs7637846	0.94[CHB][hapmap];0.81[JPT][hapmap];0.80[ASN][1000 genomes]
rs7641514	0.89[CHB][hapmap];0.97[CHD][hapmap]
rs7642332	0.81[ASN][1000 genomes]
rs7644704	0.89[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs7646197	0.81[ASN][1000 genomes]
rs7647291	0.89[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs953239	0.94[CHB][hapmap];1.00[CHD][hapmap];0.92[GIH][hapmap];0.87[JPT][hapmap];0.95[MEX][hapmap];0.91[TSI][hapmap];0.86[AMR][1000 genomes];0.87[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs953641	0.88[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap]
rs9758429	0.81[ASN][1000 genomes]
rs9815607	0.94[CHB][hapmap];1.00[CHD][hapmap];0.81[JPT][hapmap];0.80[ASN][1000 genomes]
rs9820721	0.88[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs9823836	0.81[AMR][1000 genomes]
rs9861598	0.83[AMR][1000 genomes]
rs9865053	0.89[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs9868886	0.83[CHB][hapmap]

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	nsv591920	chr3:142411200-142496951	Flanking Active TSS Enhancers Flanking Bivalent TSS/Enh Weak transcription Strong transcription Active TSS Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region miRNA target site	8 gene(s)	inside rSNPs	diseases
2	nsv521098	chr3:142411200-142503605	Weak transcription Active TSS Enhancers Bivalent/Poised TSS ZNF genes & repeats Flanking Active TSS Strong transcription Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region miRNA target site	8 gene(s)	inside rSNPs	diseases
3	nsv520533	chr3:142417070-142440299	Weak transcription Strong transcription Enhancers	TF binding region CpG island Chromatin interactive region miRNA target site	3 gene(s)	inside rSNPs	diseases
4	nsv518623	chr3:142417070-142503605	Weak transcription Active TSS Enhancers Bivalent/Poised TSS Strong transcription Flanking Bivalent TSS/Enh Flanking Active TSS ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region miRNA target site	8 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs11715459	PLS1	cis	cerebellum	SCAN
rs11715459	ATP1B3	cis	parietal	SCAN

Chromatin state (count:6 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:142389800-142442400	Weak transcription	iPS-20b Cell Line	embryonic stem cell
2	chr3:142429400-142442400	Weak transcription	NH-A	brain
3	chr3:142429600-142442200	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
4	chr3:142431600-142442400	Weak transcription	Duodenum Mucosa	Duodenum
5	chr3:142431800-142442600	Weak transcription	Rectal Mucosa Donor 31	rectum
6	chr3:142434200-142442200	Weak transcription	A549	lung

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