Variant report

Variant	rs3759861
Chromosome Location	chr15:55473192-55473193
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr15:55473058..55474936-chr15:55475651..55479463,4	K562	blood:
2	chr15:55468427..55470541-chr15:55470610..55476298,5	K562	blood:
3	chr15:55468607..55473383-chr15:55473749..55481384,11	K562	blood:

Extended variants
information (count: 112 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:106)

rs_ID	r²[population]
rs10162819	0.91[ASN][1000 genomes]
rs10162843	0.91[ASN][1000 genomes]
rs1050931	0.95[CEU][hapmap];0.93[CHB][hapmap];0.92[CHD][hapmap];1.00[GIH][hapmap];0.85[TSI][hapmap];0.91[AMR][1000 genomes];0.92[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs10518804	0.86[CHB][hapmap];0.83[ASN][1000 genomes]
rs1061821	0.89[AMR][1000 genomes];0.90[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs1061822	0.91[AMR][1000 genomes];0.91[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs1061823	0.94[CEU][hapmap];0.93[CHB][hapmap];0.91[AMR][1000 genomes];0.91[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs1061824	0.95[CEU][hapmap];0.93[CHB][hapmap];0.92[CHD][hapmap];1.00[GIH][hapmap];0.85[TSI][hapmap];0.91[AMR][1000 genomes];0.91[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs1061870	0.95[CEU][hapmap];0.93[CHB][hapmap];0.96[CHD][hapmap];1.00[GIH][hapmap];1.00[MEX][hapmap];0.85[TSI][hapmap];0.91[AMR][1000 genomes];0.92[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs1061873	0.95[CEU][hapmap];0.93[CHB][hapmap];0.92[CHD][hapmap];1.00[GIH][hapmap];0.85[TSI][hapmap];0.91[AMR][1000 genomes];0.92[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs1061874	0.89[AMR][1000 genomes];0.91[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs1061875	0.89[AMR][1000 genomes];0.91[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs11852763	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];0.93[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs11855907	0.91[AMR][1000 genomes];0.92[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs11855973	0.91[AMR][1000 genomes];0.91[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs11855978	0.91[AMR][1000 genomes];0.89[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs11856010	0.91[AMR][1000 genomes];0.92[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs11857087	0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12385963	0.91[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12440420	0.86[CHB][hapmap]
rs13380400	0.91[AMR][1000 genomes];0.92[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs13733	0.91[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs16976036	0.93[CHB][hapmap];0.86[JPT][hapmap];0.82[ASN][1000 genomes]
rs16976039	0.93[CHB][hapmap];0.88[JPT][hapmap];0.82[ASN][1000 genomes]
rs16976065	0.89[ASN][1000 genomes]
rs16976083	0.86[ASN][1000 genomes]
rs16976094	0.93[ASN][1000 genomes]
rs16976116	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs16976149	0.93[CHB][hapmap];0.91[ASN][1000 genomes]
rs28433503	0.91[AMR][1000 genomes];0.92[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs28449712	0.91[AMR][1000 genomes];0.92[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs28489312	0.91[AMR][1000 genomes];0.92[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs28499113	0.86[AMR][1000 genomes];0.89[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs28508034	0.91[AMR][1000 genomes];0.92[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs28522816	0.82[AMR][1000 genomes];0.84[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs28526269	0.91[AMR][1000 genomes];0.92[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs28530662	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];0.90[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs28535372	0.91[AMR][1000 genomes];0.92[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs28541469	0.91[AMR][1000 genomes];0.92[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs28558576	0.93[ASN][1000 genomes]
rs28562431	0.91[ASN][1000 genomes]
rs28564077	0.91[AMR][1000 genomes];0.92[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs28589384	0.95[CEU][hapmap];0.93[CHB][hapmap];0.92[CHD][hapmap];1.00[GIH][hapmap];0.85[TSI][hapmap];0.91[AMR][1000 genomes];0.92[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs28589609	0.86[AMR][1000 genomes];0.89[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs28590021	0.82[ASN][1000 genomes]
rs28591259	0.91[AMR][1000 genomes];0.92[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs28592928	0.85[ASN][1000 genomes]
rs28600759	0.84[ASN][1000 genomes]
rs28630909	0.91[AMR][1000 genomes];0.92[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs28636526	0.83[ASN][1000 genomes]
rs28649719	0.91[AMR][1000 genomes];0.92[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs28673043	0.80[ASN][1000 genomes]
rs28699327	0.91[AMR][1000 genomes];0.92[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs28704109	0.91[AMR][1000 genomes];0.92[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs28706531	0.91[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs28708989	0.91[AMR][1000 genomes];0.92[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs28710976	0.99[ASN][1000 genomes]
rs28714578	0.91[AMR][1000 genomes];0.91[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs28784096	0.86[AMR][1000 genomes];0.89[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs28864456	0.86[AMR][1000 genomes];0.89[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs28889339	0.86[AMR][1000 genomes];0.89[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs2899580	0.93[CEU][hapmap];0.93[CHB][hapmap];0.91[AMR][1000 genomes];0.92[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2899581	0.91[AMR][1000 genomes];0.92[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2899582	0.95[CEU][hapmap];0.93[CHB][hapmap];0.91[AMR][1000 genomes];0.92[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs3179664	0.94[CEU][hapmap];0.93[CHB][hapmap];1.00[AMR][1000 genomes];0.93[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs3759862	0.95[CEU][hapmap];1.00[CHB][hapmap];0.88[JPT][hapmap];0.89[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs3809539	0.93[CHB][hapmap];0.87[ASN][1000 genomes]
rs3809540	0.95[CEU][hapmap];1.00[CHB][hapmap];0.96[CHD][hapmap];1.00[GIH][hapmap];0.88[TSI][hapmap];0.91[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4238316	0.93[ASN][1000 genomes]
rs4503734	1.00[ASN][1000 genomes]
rs4545742	0.91[ASN][1000 genomes]
rs56328329	0.86[AMR][1000 genomes];0.89[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs62020114	0.91[AMR][1000 genomes];0.92[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs62639732	0.84[AMR][1000 genomes]
rs6493767	0.87[CHB][hapmap]
rs6493768	0.94[CEU][hapmap];1.00[CHB][hapmap];0.88[JPT][hapmap];0.91[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6493769	0.91[AMR][1000 genomes];0.87[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs6493771	0.84[AMR][1000 genomes];0.83[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs7165491	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];0.93[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs7168472	1.00[CHB][hapmap];0.88[JPT][hapmap];0.99[ASN][1000 genomes]
rs7168737	0.95[CEU][hapmap];0.91[AMR][1000 genomes];0.92[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs7172108	0.91[AMR][1000 genomes];0.92[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs7172289	0.91[AMR][1000 genomes];0.90[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs7176676	0.81[ASN][1000 genomes]
rs7179365	0.91[ASN][1000 genomes]
rs7180594	0.91[ASN][1000 genomes]
rs7181237	0.86[CHB][hapmap]
rs73409851	0.86[AMR][1000 genomes];0.89[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs73409853	0.86[AMR][1000 genomes];0.90[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs8027098	0.95[CEU][hapmap];0.93[CHB][hapmap];0.91[AMR][1000 genomes];0.92[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs8027256	0.82[AMR][1000 genomes];0.80[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs8028525	0.84[ASN][1000 genomes]
rs8030981	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];0.93[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs8031949	0.94[CEU][hapmap];0.93[CHB][hapmap];0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];0.93[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs8033588	0.92[CHB][hapmap];0.88[JPT][hapmap];0.91[ASN][1000 genomes]
rs8034063	0.91[ASN][1000 genomes]
rs8034402	1.00[CHB][hapmap];0.87[CHD][hapmap];0.88[JPT][hapmap];0.99[ASN][1000 genomes]
rs8034853	0.91[ASN][1000 genomes]
rs8034882	1.00[CHB][hapmap];0.88[JPT][hapmap];0.91[ASN][1000 genomes]
rs8035625	1.00[CHB][hapmap];0.91[CHD][hapmap];0.88[JPT][hapmap];0.99[ASN][1000 genomes]
rs8043029	0.95[CEU][hapmap];1.00[CHB][hapmap];0.96[CHD][hapmap];1.00[GIH][hapmap];0.88[JPT][hapmap];0.94[TSI][hapmap];0.89[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs9300	1.00[CEU][hapmap];1.00[CHB][hapmap];0.96[CHD][hapmap];1.00[GIH][hapmap];0.88[MEX][hapmap];0.87[TSI][hapmap];0.91[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs9920136	0.86[AMR][1000 genomes];0.89[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs9920219	0.95[CEU][hapmap];0.86[AMR][1000 genomes];0.89[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs9920220	0.86[AMR][1000 genomes];0.89[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs9920737	0.84[CEU][hapmap];0.91[AFR][1000 genomes];0.89[AMR][1000 genomes];0.82[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:6 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1043176	chr15:55010228-55563000	Genic enhancers Active TSS Weak transcription Enhancers Transcr. at gene 5' and 3' Strong transcription Flanking Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	21 gene(s)	inside rSNPs	diseases
2	nsv1042741	chr15:55068022-55622497	Strong transcription Weak transcription Flanking Active TSS Enhancers Active TSS Genic enhancers ZNF genes & repeats 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	31 gene(s)	inside rSNPs	diseases
3	nsv1039471	chr15:55137606-55552555	Enhancers Strong transcription Weak transcription Active TSS Flanking Active TSS Genic enhancers Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	20 gene(s)	inside rSNPs	diseases
4	nsv917323	chr15:55290499-56041334	Genic enhancers Active TSS ZNF genes & repeats Weak transcription Strong transcription Enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	57 gene(s)	inside rSNPs	diseases
5	nsv1043789	chr15:55400872-56092454	Weak transcription Enhancers Genic enhancers Strong transcription Flanking Bivalent TSS/Enh Active TSS Bivalent Enhancer Bivalent/Poised TSS Flanking Active TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	55 gene(s)	inside rSNPs	diseases
6	nsv525768	chr15:55466155-55485494	Weak transcription Enhancers Strong transcription Genic enhancers Transcr. at gene 5' and 3' Flanking Active TSS Active TSS	Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs3759861	RAB27A	Cis_1M	lymphoblastoid	RTeQTL
rs3759861	PIGB	cis	Artery Tibial	GTEx

Chromatin state (count:123 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:55455800-55487200	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
2	chr15:55462600-55488600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
3	chr15:55463200-55474600	Weak transcription	ES-I3 Cell Line	embryonic stem cell
4	chr15:55464800-55488200	Weak transcription	Lung	lung
5	chr15:55465400-55476600	Weak transcription	Brain Anterior Caudate	brain
6	chr15:55466800-55474000	Weak transcription	Primary T killer memory cells from peripheral blood	blood
7	chr15:55466800-55474600	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
8	chr15:55466800-55486800	Weak transcription	Psoas Muscle	Psoas
9	chr15:55467800-55480600	Weak transcription	Fetal Stomach	stomach
10	chr15:55468000-55482000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
11	chr15:55468200-55481600	Weak transcription	Fetal Intestine Small	intestine
12	chr15:55468600-55474600	Weak transcription	Brain Substantia Nigra	brain
13	chr15:55468800-55487000	Weak transcription	Gastric	stomach
14	chr15:55469000-55474400	Weak transcription	Skeletal Muscle Male	skeletal muscle
15	chr15:55469000-55477200	Strong transcription	Primary T cells from cord blood	blood
16	chr15:55469000-55481800	Weak transcription	Spleen	Spleen
17	chr15:55469200-55477200	Strong transcription	Breast Myoepithelial Primary Cells	Breast
18	chr15:55469200-55484800	Strong transcription	Liver	Liver
19	chr15:55469200-55485000	Strong transcription	Primary T cells fromperipheralblood	blood
20	chr15:55469400-55478000	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
21	chr15:55469400-55485200	Strong transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
22	chr15:55469600-55473200	Strong transcription	Thymus	Thymus
23	chr15:55469600-55474000	Weak transcription	Colonic Mucosa	Colon
24	chr15:55469600-55479600	Strong transcription	Primary T helper cells fromperipheralblood	blood
25	chr15:55469600-55485000	Strong transcription	Primary hematopoietic stem cells short term culture	blood
26	chr15:55469600-55485200	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
27	chr15:55469600-55486000	Strong transcription	Primary B cells from cord blood	blood
28	chr15:55469800-55477400	Strong transcription	Duodenum Mucosa	Duodenum
29	chr15:55469800-55477400	Strong transcription	Fetal Intestine Large	intestine
30	chr15:55469800-55477800	Strong transcription	HSMM	muscle
31	chr15:55469800-55484800	Strong transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
32	chr15:55469800-55485000	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
33	chr15:55469800-55486400	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
34	chr15:55469800-55486600	Strong transcription	HUES64 Cell Line	embryonic stem cell
35	chr15:55470000-55477600	Strong transcription	Adipose Nuclei	Adipose
36	chr15:55470000-55484800	Strong transcription	Primary hematopoietic stem cells	blood
37	chr15:55470000-55484800	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
38	chr15:55470200-55474000	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
39	chr15:55470200-55475400	Weak transcription	NHEK	skin
40	chr15:55470200-55477800	Strong transcription	iPS-20b Cell Line	embryonic stem cell
41	chr15:55470200-55479800	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
42	chr15:55470200-55484000	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
43	chr15:55470200-55486600	Weak transcription	Small Intestine	intestine
44	chr15:55470400-55473200	Strong transcription	Fetal Muscle Trunk	muscle
45	chr15:55470400-55473400	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
46	chr15:55470400-55474800	Weak transcription	Fetal Brain Male	brain
47	chr15:55470400-55475800	Strong transcription	A549	lung
48	chr15:55470400-55477200	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
49	chr15:55470400-55477200	Strong transcription	Left Ventricle	heart
50	chr15:55470400-55477400	Strong transcription	GM12878-XiMat	blood

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links