Variant report

Variant	rs347689
Chromosome Location	chr3:141781890-141781891
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr3:141776813..141779383-chr3:141780587..141782430,2	K562	blood:
2	chr1:202085934..202088826-chr3:141779136..141781977,2	K562	blood:

Extended variants
information (count: 63 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:54)

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	0.87[AMR][1000 genomes];0.96[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs1543064	0.88[CHB][hapmap];0.87[CHD][hapmap];0.90[GIH][hapmap];0.94[JPT][hapmap];0.91[MKK][hapmap];0.82[ASN][1000 genomes]
rs1704990	0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs1705612	1.00[ASW][hapmap];1.00[CEU][hapmap];0.94[CHB][hapmap];0.85[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.90[MKK][hapmap];1.00[TSI][hapmap];0.87[AMR][1000 genomes];0.96[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs1705613	1.00[CEU][hapmap];0.94[CHB][hapmap];1.00[JPT][hapmap];0.85[AMR][1000 genomes];0.96[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs1705615	0.87[AMR][1000 genomes];0.96[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs1705619	0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs1705628	1.00[AFR][1000 genomes];0.87[AMR][1000 genomes];0.96[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs1820941	0.82[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]
rs2862122	0.81[ASN][1000 genomes]
rs2862126	0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs347680	1.00[AFR][1000 genomes];0.87[AMR][1000 genomes];0.96[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs347681	0.87[AMR][1000 genomes];0.96[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs347682	0.87[AMR][1000 genomes];0.96[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs347684	0.87[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs347688	0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs347690	1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[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]
rs4683417	0.81[ASN][1000 genomes]
rs4683666	0.92[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs4683668	0.87[AMR][1000 genomes];0.96[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs62284561	0.93[ASN][1000 genomes]
rs62284562	0.84[ASN][1000 genomes]
rs62284565	0.81[ASN][1000 genomes]
rs62284573	0.90[ASN][1000 genomes]
rs6440062	0.87[AMR][1000 genomes];0.95[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs6764833	0.84[ASN][1000 genomes]
rs6766782	0.93[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs6773343	0.82[JPT][hapmap]
rs6773377	0.89[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs6778085	0.88[CHB][hapmap];0.87[CHD][hapmap];0.90[GIH][hapmap];0.94[JPT][hapmap];0.91[MKK][hapmap];0.84[ASN][1000 genomes]
rs6795301	0.88[CHB][hapmap];0.84[CHD][hapmap];0.90[GIH][hapmap];0.94[JPT][hapmap];0.84[ASN][1000 genomes]
rs6795500	0.84[ASN][1000 genomes]
rs6803884	0.81[ASN][1000 genomes]
rs6806443	0.81[ASN][1000 genomes]
rs7426584	1.00[ASW][hapmap];1.00[CEU][hapmap];0.94[CHB][hapmap];0.85[CHD][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];0.87[AMR][1000 genomes];0.96[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs7611705	0.92[CEU][hapmap];0.94[CHB][hapmap];1.00[JPT][hapmap];0.83[AMR][1000 genomes];0.92[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs7619506	0.88[CHB][hapmap];0.87[JPT][hapmap];0.81[ASN][1000 genomes]
rs7633321	0.81[ASN][1000 genomes]
rs7644383	0.83[MKK][hapmap]
rs907293	0.81[ASN][1000 genomes]
rs9289641	0.82[CHB][hapmap];0.90[GIH][hapmap];0.94[JPT][hapmap];0.91[MKK][hapmap]
rs963396	0.88[CHB][hapmap];0.87[CHD][hapmap];0.87[JPT][hapmap];0.91[MKK][hapmap];0.81[ASN][1000 genomes]
rs9810193	0.90[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs9863685	0.84[ASN][1000 genomes]
rs9865777	0.81[CHB][hapmap];0.94[JPT][hapmap]
rs9880805	0.84[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	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	nsv877554	chr3:141735532-141781890	Enhancers Strong transcription Flanking Active TSS Weak transcription Genic enhancers Active TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region	6 gene(s)	inside rSNPs	diseases
8	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
9	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
rs347689	PLSCR1	cis	parietal	SCAN

Chromatin state (count:30 , 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	chr3:141762800-141782800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
5	chr3:141763000-141820000	Weak transcription	Pancreas	Pancrea
6	chr3:141763000-141824200	Weak transcription	Aorta	Aorta
7	chr3:141764000-141825600	Weak transcription	Primary T cells from cord blood	blood
8	chr3:141765000-141818800	Weak transcription	Primary B cells from cord blood	blood
9	chr3:141767000-141798000	Weak transcription	Primary hematopoietic stem cells short term culture	blood
10	chr3:141767600-141807200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
11	chr3:141769600-141790200	Strong transcription	Fetal Thymus	thymus
12	chr3:141770400-141795800	Weak transcription	Fetal Stomach	stomach
13	chr3:141771000-141789200	Weak transcription	Rectal Mucosa Donor 31	rectum
14	chr3:141774400-141783000	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
15	chr3:141774400-141798800	Weak transcription	Primary hematopoietic stem cells	blood
16	chr3:141776000-141805400	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
17	chr3:141776400-141795800	Weak transcription	Ovary	ovary
18	chr3:141777800-141784000	Weak transcription	Fetal Muscle Leg	muscle
19	chr3:141780600-141782800	Weak transcription	H9 Cell Line	embryonic stem cell
20	chr3:141780600-141783000	Weak transcription	H1 Cell Line	embryonic stem cell
21	chr3:141780600-141787200	Weak transcription	Fetal Intestine Small	intestine
22	chr3:141780600-141791400	Weak transcription	Thymus	Thymus
23	chr3:141780600-141796400	Weak transcription	Breast Myoepithelial Primary Cells	Breast
24	chr3:141780800-141782800	Weak transcription	HUES6 Cell Line	embryonic stem cell
25	chr3:141780800-141783000	Weak transcription	HUES48 Cell Line	embryonic stem cell
26	chr3:141780800-141783000	Weak transcription	iPS-20b Cell Line	embryonic stem cell
27	chr3:141780800-141796400	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
28	chr3:141781200-141782800	Weak transcription	ES-I3 Cell Line	embryonic stem cell
29	chr3:141781200-141782800	Weak transcription	iPS-18 Cell Line	embryonic stem cell
30	chr3:141781800-141790400	Weak transcription	Dnd41	blood

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links