Variant report

Variant	rs2864840
Chromosome Location	chr15:77732001-77732002
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr15:77729375..77731568-chr15:77731785..77734606,3	K562	blood:
2	chr15:77710797..77713299-chr15:77731423..77733931,3	MCF-7	breast:
3	chr15:77731986..77734609-chr15:77750032..77751722,2	MCF-7	breast:
4	chr15:77726192..77730190-chr15:77730606..77733927,4	MCF-7	breast:
5	chr15:77725832..77728730-chr15:77730504..77732246,2	K562	blood:
6	chr15:77728521..77730875-chr15:77731785..77733809,2	K562	blood:

Variant related genes	Relation type
ENSG00000173517	Chromatin interaction
ENSG00000140382	Chromatin interaction

Extended variants
information (count: 66 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:62)

rs_ID	r²[population]
rs11853696	0.89[AMR][1000 genomes];0.88[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs11854466	0.80[ASN][1000 genomes]
rs11856084	1.00[CEU][hapmap];1.00[CHB][hapmap];0.88[JPT][hapmap];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs11857330	0.88[CHB][hapmap];0.94[JPT][hapmap]
rs11858844	0.91[AMR][1000 genomes];0.96[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs12324016	0.87[ASN][1000 genomes]
rs12324211	0.88[CHB][hapmap];0.83[JPT][hapmap];0.85[ASN][1000 genomes]
rs12324366	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs12324795	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12912084	0.89[ASN][1000 genomes]
rs13380202	0.89[AMR][1000 genomes];0.88[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs1493699	0.87[ASN][1000 genomes]
rs16968730	0.93[CHB][hapmap];1.00[JPT][hapmap]
rs16968799	0.87[ASN][1000 genomes]
rs16968897	0.90[CEU][hapmap];0.82[EUR][1000 genomes]
rs16968900	0.80[EUR][1000 genomes]
rs17384809	0.89[AMR][1000 genomes];0.82[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs17385059	0.89[AMR][1000 genomes];0.85[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs17385296	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[AMR][1000 genomes];0.86[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs17385352	0.89[AMR][1000 genomes];0.86[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs17470529	0.89[AMR][1000 genomes];0.88[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs17470952	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs17471252	0.88[ASN][1000 genomes]
rs17471431	0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs17471480	0.95[CEU][hapmap];1.00[CHB][hapmap];0.83[JPT][hapmap];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs17471697	1.00[CEU][hapmap];1.00[CHB][hapmap];0.87[JPT][hapmap];0.91[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs17471753	0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs17472200	0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2012740	0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2012756	0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2137977	0.80[ASN][1000 genomes]
rs2172587	0.87[ASN][1000 genomes]
rs2307141	1.00[CEU][hapmap];1.00[CHB][hapmap];0.89[JPT][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs28437977	0.89[AMR][1000 genomes];0.88[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs35651077	0.87[ASN][1000 genomes]
rs3784787	0.89[AMR][1000 genomes];0.88[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs3784788	1.00[CEU][hapmap];1.00[CHB][hapmap];0.89[JPT][hapmap];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs4592615	0.88[CHB][hapmap];0.94[JPT][hapmap]
rs4886857	0.80[ASN][1000 genomes]
rs4886863	0.89[ASN][1000 genomes]
rs4886864	0.89[AMR][1000 genomes];0.88[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4886865	0.89[AMR][1000 genomes];0.88[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs56097641	0.87[EUR][1000 genomes]
rs59204923	0.83[EUR][1000 genomes]
rs59362734	0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs59386622	0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs60079927	0.80[ASN][1000 genomes]
rs61306472	0.83[EUR][1000 genomes]
rs62007297	0.91[ASN][1000 genomes]
rs62010566	0.87[ASN][1000 genomes]
rs7182221	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.80[ASN][1000 genomes]
rs74025105	0.80[ASN][1000 genomes]
rs74026910	0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs74026912	0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs74026913	0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs74026918	0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs74026923	0.84[AMR][1000 genomes];0.96[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs74026925	0.94[EUR][1000 genomes]
rs74026926	0.80[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs8035526	0.89[AMR][1000 genomes];0.88[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs883627	0.83[JPT][hapmap]
rs907398	1.00[CEU][hapmap];1.00[CHB][hapmap];0.89[JPT][hapmap];1.00[AFR][1000 genomes];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.91[ASN][1000 genomes]

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	nsv1040852	chr15:77160237-78137541	Enhancers Flanking Active TSS Active TSS Strong transcription Weak transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	42 gene(s)	inside rSNPs	diseases
2	nsv1045376	chr15:77354671-77801487	Enhancers Weak transcription Flanking Active TSS ZNF genes & repeats Active TSS Strong transcription Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	23 gene(s)	inside rSNPs	diseases
3	nsv542443	chr15:77354671-77801487	Weak transcription Enhancers Genic enhancers Flanking Active TSS Active TSS ZNF genes & repeats Strong transcription 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	23 gene(s)	inside rSNPs	diseases
4	nsv916323	chr15:77485765-78121259	Enhancers Strong transcription Weak transcription Genic enhancers Bivalent Enhancer Active TSS Bivalent/Poised TSS Flanking Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	29 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs2864840	TSPAN3	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:49 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:77714000-77748600	Weak transcription	Placenta	Placenta
2	chr15:77714400-77732400	Weak transcription	HSMM	muscle
3	chr15:77714400-77732800	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
4	chr15:77714400-77739200	Weak transcription	Right Atrium	heart
5	chr15:77714400-77741600	Weak transcription	Fetal Thymus	thymus
6	chr15:77714600-77732800	Weak transcription	Rectal Mucosa Donor 31	rectum
7	chr15:77714600-77734400	Weak transcription	Primary hematopoietic stem cells short term culture	blood
8	chr15:77714800-77739200	Weak transcription	Fetal Intestine Small	intestine
9	chr15:77715000-77740600	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
10	chr15:77715400-77733800	Weak transcription	Primary hematopoietic stem cells	blood
11	chr15:77715400-77737800	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
12	chr15:77716000-77733800	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
13	chr15:77716400-77734200	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
14	chr15:77716400-77741400	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
15	chr15:77716800-77738000	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
16	chr15:77716800-77742600	Weak transcription	Hela-S3	cervix
17	chr15:77717000-77732800	Weak transcription	Sigmoid Colon	Sigmoid Colon
18	chr15:77717000-77754400	Weak transcription	K562	blood
19	chr15:77717200-77739400	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
20	chr15:77717800-77732600	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
21	chr15:77720000-77739400	Weak transcription	Primary T killer memory cells from peripheral blood	blood
22	chr15:77720200-77743000	Weak transcription	Primary B cells from cord blood	blood
23	chr15:77723200-77738000	Weak transcription	Right Ventricle	heart
24	chr15:77727200-77741200	Weak transcription	Fetal Stomach	stomach
25	chr15:77727400-77747800	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
26	chr15:77728000-77737600	Weak transcription	Left Ventricle	heart
27	chr15:77728200-77746200	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
28	chr15:77728400-77738000	Weak transcription	Brain Inferior Temporal Lobe	brain
29	chr15:77729200-77740600	Weak transcription	Fetal Muscle Leg	muscle
30	chr15:77729400-77747200	Weak transcription	Breast Myoepithelial Primary Cells	Breast
31	chr15:77729600-77733200	Weak transcription	Rectal Mucosa Donor 29	rectum
32	chr15:77729600-77748000	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
33	chr15:77729600-77749200	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
34	chr15:77729800-77732400	Weak transcription	Primary T helper cells PMA-I stimulated	--
35	chr15:77729800-77732600	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
36	chr15:77729800-77733400	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
37	chr15:77729800-77740600	Weak transcription	Primary B cells from peripheral blood	blood
38	chr15:77729800-77747200	Weak transcription	Primary T helper cells fromperipheralblood	blood
39	chr15:77730000-77732200	Weak transcription	Primary T helper naive cells from peripheral blood	blood
40	chr15:77730000-77732400	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
41	chr15:77730400-77733200	Weak transcription	Primary T cells from cord blood	blood
42	chr15:77730400-77748600	Weak transcription	Primary T cells fromperipheralblood	blood
43	chr15:77730600-77740200	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
44	chr15:77730600-77758800	Weak transcription	Lung	lung
45	chr15:77731800-77732600	Weak transcription	Muscle Satellite Cultured Cells	--
46	chr15:77732000-77732400	Weak transcription	Skeletal Muscle Male	skeletal muscle
47	chr15:77732000-77732400	Enhancers	GM12878-XiMat	blood
48	chr15:77732000-77733200	Enhancers	Foreskin Melanocyte Primary Cells skin01	Skin
49	chr15:77732000-77735000	Enhancers	Skeletal Muscle Female	skeletal muscle

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links