Variant report

Variant	rs347684
Chromosome Location	chr3:141806655-141806656
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 57 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:48)

rs_ID	r²[population]
rs11569198	0.88[CHB][hapmap];0.87[JPT][hapmap]
rs11569216	0.82[CHB][hapmap];0.87[JPT][hapmap]
rs12495978	0.82[CHB][hapmap]
rs1397763	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs1543064	0.88[CHB][hapmap];0.84[CHD][hapmap];0.94[JPT][hapmap];0.91[MKK][hapmap];0.80[ASN][1000 genomes]
rs1704990	0.90[AMR][1000 genomes];0.97[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs1705612	1.00[ASW][hapmap];0.92[CEU][hapmap];0.94[CHB][hapmap];0.82[CHD][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.90[MKK][hapmap];1.00[TSI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs1705613	0.92[CEU][hapmap];0.94[CHB][hapmap];1.00[JPT][hapmap];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs1705615	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs1705619	0.90[AMR][1000 genomes];0.97[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs1705628	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs1820941	0.81[ASN][1000 genomes]
rs2063453	0.88[CHB][hapmap];0.87[JPT][hapmap];0.91[MKK][hapmap]
rs2063454	0.88[CHB][hapmap];0.87[JPT][hapmap];0.91[MKK][hapmap]
rs2271386	0.88[CHB][hapmap];0.87[JPT][hapmap];0.91[MKK][hapmap]
rs2862126	0.90[AMR][1000 genomes];0.98[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs347680	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs347681	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs347682	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs347688	0.90[AMR][1000 genomes];0.97[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs347689	0.87[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs347690	0.90[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs3811708	0.82[CHB][hapmap];0.87[JPT][hapmap]
rs3817176	0.88[CHB][hapmap];0.87[JPT][hapmap];0.91[MKK][hapmap]
rs4683666	0.88[AMR][1000 genomes];0.95[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs4683668	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs62284561	0.97[ASN][1000 genomes]
rs62284562	0.87[ASN][1000 genomes]
rs62284565	0.84[ASN][1000 genomes]
rs62284573	0.93[ASN][1000 genomes]
rs6440062	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs6764833	0.82[ASN][1000 genomes]
rs6766782	1.00[AFR][1000 genomes];0.88[AMR][1000 genomes];0.95[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs6773343	0.82[JPT][hapmap]
rs6773377	1.00[AFR][1000 genomes];0.88[AMR][1000 genomes];0.91[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs6778085	0.88[CHB][hapmap];0.84[CHD][hapmap];0.94[JPT][hapmap];0.91[MKK][hapmap];0.82[ASN][1000 genomes]
rs6795301	0.88[CHB][hapmap];0.82[CHD][hapmap];0.94[JPT][hapmap];0.82[ASN][1000 genomes]
rs6795500	0.82[ASN][1000 genomes]
rs7426584	1.00[ASW][hapmap];0.92[CEU][hapmap];0.94[CHB][hapmap];0.82[CHD][hapmap];0.88[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs7611705	1.00[CEU][hapmap];0.94[CHB][hapmap];1.00[JPT][hapmap];1.00[AFR][1000 genomes];0.95[AMR][1000 genomes];0.95[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs7619506	0.88[CHB][hapmap];0.87[JPT][hapmap]
rs7644383	0.83[MKK][hapmap]
rs9289641	0.82[CHB][hapmap];0.94[JPT][hapmap];0.91[MKK][hapmap]
rs963396	0.88[CHB][hapmap];0.84[CHD][hapmap];0.87[JPT][hapmap];0.91[MKK][hapmap]
rs9810193	0.83[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs9863685	0.82[ASN][1000 genomes]
rs9865777	0.81[CHB][hapmap];0.82[GIH][hapmap];0.94[JPT][hapmap]
rs9880805	0.82[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:9 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv949709	chr3:141295050-142178144	Weak transcription Strong transcription Flanking Active TSS Enhancers Genic enhancers Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	61 gene(s)	inside rSNPs	diseases
2	nsv1013352	chr3:141541105-141870293	Weak transcription Enhancers Strong transcription Genic enhancers Flanking Active TSS ZNF genes & repeats Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	27 gene(s)	inside rSNPs	diseases
3	nsv1002446	chr3:141719169-142070290	Enhancers Strong transcription Weak transcription Flanking Active TSS Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	25 gene(s)	inside rSNPs	diseases
4	esv2757892	chr3:141728870-142129836	Weak transcription Active TSS Strong transcription Genic enhancers ZNF genes & repeats Enhancers Flanking Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	26 gene(s)	inside rSNPs	diseases
5	esv2759182	chr3:141728870-142129836	Enhancers Strong transcription Flanking Active TSS Weak transcription ZNF genes & repeats Genic enhancers Active TSS Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	26 gene(s)	inside rSNPs	diseases
6	esv2757013	chr3:141756541-142094631	Weak transcription Strong transcription Enhancers ZNF genes & repeats Active TSS Flanking Active TSS Genic enhancers 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 target site	22 gene(s)	inside rSNPs	diseases
7	nsv1002123	chr3:141789746-141956778	Weak transcription Strong transcription Genic enhancers Active TSS Enhancers ZNF genes & repeats Flanking Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	20 gene(s)	inside rSNPs	diseases
8	nsv536733	chr3:141789746-141956778	Enhancers Strong transcription Weak transcription Active TSS Flanking Active TSS ZNF genes & repeats Bivalent/Poised TSS Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	20 gene(s)	inside rSNPs	diseases
9	nsv1004784	chr3:141789746-142070290	Enhancers Flanking Active TSS Strong transcription Weak transcription ZNF genes & repeats Active TSS Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	21 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs347684	PLSCR1	cis	parietal	SCAN

Chromatin state (count:41 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:141761000-141807800	Weak transcription	Fetal Lung	lung
2	chr3:141761800-141819600	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
3	chr3:141763000-141820000	Weak transcription	Pancreas	Pancrea
4	chr3:141763000-141824200	Weak transcription	Aorta	Aorta
5	chr3:141764000-141825600	Weak transcription	Primary T cells from cord blood	blood
6	chr3:141765000-141818800	Weak transcription	Primary B cells from cord blood	blood
7	chr3:141767600-141807200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
8	chr3:141795400-141835800	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
9	chr3:141795800-141811000	Weak transcription	Esophagus	oesophagus
10	chr3:141796000-141807400	Weak transcription	Liver	Liver
11	chr3:141797200-141813000	Weak transcription	Fetal Stomach	stomach
12	chr3:141797400-141807400	Weak transcription	Lung	lung
13	chr3:141797600-141819600	Weak transcription	Fetal Muscle Leg	muscle
14	chr3:141797600-141823600	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
15	chr3:141797800-141807200	Weak transcription	Adipose Nuclei	Adipose
16	chr3:141799600-141814600	Weak transcription	Primary hematopoietic stem cells	blood
17	chr3:141801000-141807600	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
18	chr3:141801000-141808000	Weak transcription	Ovary	ovary
19	chr3:141801200-141808800	Weak transcription	Dnd41	blood
20	chr3:141801200-141809000	Strong transcription	Fetal Thymus	thymus
21	chr3:141803600-141814200	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
22	chr3:141804000-141819200	Weak transcription	Breast Myoepithelial Primary Cells	Breast
23	chr3:141804000-141820800	Weak transcription	Left Ventricle	heart
24	chr3:141804400-141807000	Enhancers	Fetal Intestine Large	intestine
25	chr3:141804600-141806800	Weak transcription	Hela-S3	cervix
26	chr3:141804600-141807000	Enhancers	Fetal Intestine Small	intestine
27	chr3:141805000-141807800	Strong transcription	Thymus	Thymus
28	chr3:141805000-141808200	Enhancers	HepG2	liver
29	chr3:141805400-141807200	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
30	chr3:141805400-141807600	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
31	chr3:141805400-141808200	Enhancers	HMEC	breast
32	chr3:141805600-141808000	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
33	chr3:141805600-141808200	Enhancers	NHEK	skin
34	chr3:141806000-141807000	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
35	chr3:141806000-141807000	Enhancers	NHDF-Ad	bronchial
36	chr3:141806000-141807000	Enhancers	NHLF	lung
37	chr3:141806200-141807200	Enhancers	Duodenum Mucosa	Duodenum
38	chr3:141806200-141818600	Weak transcription	Rectal Mucosa Donor 29	rectum
39	chr3:141806400-141806800	Enhancers	Placenta	Placenta
40	chr3:141806400-141806800	Enhancers	Osteobl	bone
41	chr3:141806600-141807000	Enhancers	NH-A	brain

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