Variant report

Variant	rs1705619
Chromosome Location	chr3:141786073-141786074
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 55 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:47)

rs_ID	r²[population]
rs11569198	0.83[CHB][hapmap];0.87[JPT][hapmap]
rs11569216	0.87[JPT][hapmap]
rs1397763	0.90[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs1543064	0.83[CHB][hapmap];0.90[GIH][hapmap];0.94[JPT][hapmap];0.91[MKK][hapmap];0.80[AMR][1000 genomes]
rs1704990	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1705612	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.90[MKK][hapmap];1.00[TSI][hapmap];0.90[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1705613	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.87[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1705615	0.90[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs1705628	0.90[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2063453	0.83[CHB][hapmap];0.87[JPT][hapmap];0.91[MKK][hapmap]
rs2063454	0.83[CHB][hapmap];0.87[JPT][hapmap];0.91[MKK][hapmap]
rs2271386	0.83[CHB][hapmap];0.87[JPT][hapmap];0.91[MKK][hapmap]
rs2862123	0.85[ASN][1000 genomes]
rs2862124	0.82[AMR][1000 genomes];0.85[ASN][1000 genomes]
rs2862126	1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs347680	0.90[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs347681	0.90[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs347682	0.90[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs347684	0.90[AMR][1000 genomes];0.97[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs347688	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs347689	0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs347690	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs3811708	0.87[JPT][hapmap]
rs3817176	0.83[CHB][hapmap];0.87[JPT][hapmap];0.91[MKK][hapmap]
rs4683666	0.93[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs4683668	0.90[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs62284561	0.84[ASN][1000 genomes]
rs62284562	0.94[ASN][1000 genomes]
rs62284573	0.81[ASN][1000 genomes]
rs6440062	0.90[AMR][1000 genomes];0.96[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs6766782	0.94[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs6773343	0.82[JPT][hapmap]
rs6773377	0.90[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs6778085	0.83[CHB][hapmap];0.90[GIH][hapmap];0.94[JPT][hapmap];0.91[MKK][hapmap];0.80[AMR][1000 genomes]
rs6784390	0.81[ASN][1000 genomes]
rs6795301	0.83[CHB][hapmap];0.90[GIH][hapmap];0.94[JPT][hapmap];0.80[AMR][1000 genomes]
rs6795500	0.80[AMR][1000 genomes]
rs7426584	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];0.90[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7611705	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.85[AMR][1000 genomes];0.93[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs7619506	0.82[CHB][hapmap];0.87[JPT][hapmap]
rs7644383	0.83[MKK][hapmap]
rs9289641	0.89[CHB][hapmap];0.83[CHD][hapmap];0.90[GIH][hapmap];0.94[JPT][hapmap];0.91[MKK][hapmap];0.82[AMR][1000 genomes];0.85[ASN][1000 genomes]
rs963396	0.83[CHB][hapmap];0.87[JPT][hapmap];0.91[MKK][hapmap]
rs9810193	0.92[AMR][1000 genomes];0.92[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs9863685	0.80[AMR][1000 genomes]
rs9865777	0.88[CHB][hapmap];0.85[CHD][hapmap];0.94[JPT][hapmap];0.80[AMR][1000 genomes];0.85[ASN][1000 genomes]
rs9880805	0.80[AMR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:8 , 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	nsv877553	chr3:141732321-141786073	Weak transcription ZNF genes & repeats Enhancers Genic enhancers Strong transcription Flanking Active TSS Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region	6 gene(s)	inside rSNPs	diseases
7	nsv877555	chr3:141740076-141791408	Enhancers Flanking Active TSS Active TSS Weak transcription Genic enhancers Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region	6 gene(s)	inside rSNPs	diseases
8	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

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs1705619	PLSCR1	cis	parietal	SCAN

Chromatin state (count:34 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:141760600-141800800	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
2	chr3:141761000-141807800	Weak transcription	Fetal Lung	lung
3	chr3:141761800-141819600	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
4	chr3:141763000-141820000	Weak transcription	Pancreas	Pancrea
5	chr3:141763000-141824200	Weak transcription	Aorta	Aorta
6	chr3:141764000-141825600	Weak transcription	Primary T cells from cord blood	blood
7	chr3:141765000-141818800	Weak transcription	Primary B cells from cord blood	blood
8	chr3:141767000-141798000	Weak transcription	Primary hematopoietic stem cells short term culture	blood
9	chr3:141767600-141807200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
10	chr3:141769600-141790200	Strong transcription	Fetal Thymus	thymus
11	chr3:141770400-141795800	Weak transcription	Fetal Stomach	stomach
12	chr3:141771000-141789200	Weak transcription	Rectal Mucosa Donor 31	rectum
13	chr3:141774400-141798800	Weak transcription	Primary hematopoietic stem cells	blood
14	chr3:141776000-141805400	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
15	chr3:141776400-141795800	Weak transcription	Ovary	ovary
16	chr3:141780600-141787200	Weak transcription	Fetal Intestine Small	intestine
17	chr3:141780600-141791400	Weak transcription	Thymus	Thymus
18	chr3:141780600-141796400	Weak transcription	Breast Myoepithelial Primary Cells	Breast
19	chr3:141780800-141796400	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
20	chr3:141781800-141790400	Weak transcription	Dnd41	blood
21	chr3:141783000-141795800	Weak transcription	Psoas Muscle	Psoas
22	chr3:141783800-141790600	Weak transcription	Rectal Mucosa Donor 29	rectum
23	chr3:141784000-141796000	Weak transcription	Lung	lung
24	chr3:141784600-141796000	Weak transcription	Fetal Muscle Leg	muscle
25	chr3:141785000-141790000	Weak transcription	Small Intestine	intestine
26	chr3:141785200-141796600	Weak transcription	Duodenum Smooth Muscle	Duodenum
27	chr3:141785400-141786600	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
28	chr3:141785600-141786400	Weak transcription	HUES48 Cell Line	embryonic stem cell
29	chr3:141785600-141786600	Weak transcription	HUES6 Cell Line	embryonic stem cell
30	chr3:141785600-141791800	Weak transcription	ES-I3 Cell Line	embryonic stem cell
31	chr3:141785800-141791200	Weak transcription	iPS-18 Cell Line	embryonic stem cell
32	chr3:141785800-141791400	Weak transcription	HUES64 Cell Line	embryonic stem cell
33	chr3:141785800-141791600	Weak transcription	iPS-20b Cell Line	embryonic stem cell
34	chr3:141785800-141796200	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived

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