Variant report

Variant	rs1867780
Chromosome Location	chr15:77407114-77407115
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr15:77397830..77402873-chr15:77403837..77409871,6	K562	blood:

Extended variants
information (count: 56 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:51)

rs_ID	r²[population]
rs1015813	0.90[AFR][1000 genomes];0.84[AMR][1000 genomes];0.86[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs10162742	0.85[YRI][hapmap]
rs10519158	0.95[CEU][hapmap];0.86[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs11853625	0.90[AFR][1000 genomes];0.87[AMR][1000 genomes];0.87[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs11853633	0.95[AFR][1000 genomes];0.93[AMR][1000 genomes];0.91[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs11854182	0.90[AFR][1000 genomes];0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs11854466	0.90[AFR][1000 genomes];0.85[EUR][1000 genomes]
rs11856513	0.95[CEU][hapmap];0.86[CHB][hapmap];0.94[JPT][hapmap];0.93[AMR][1000 genomes];0.89[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs11856538	0.93[CHB][hapmap];0.94[JPT][hapmap];0.92[ASN][1000 genomes]
rs11857330	0.88[JPT][hapmap]
rs11857804	0.87[AFR][1000 genomes];0.85[EUR][1000 genomes]
rs12324366	0.95[CEU][hapmap];0.86[CHB][hapmap];0.94[JPT][hapmap];1.00[YRI][hapmap];0.90[AFR][1000 genomes];0.85[EUR][1000 genomes]
rs12900110	0.83[ASN][1000 genomes]
rs12902446	0.88[JPT][hapmap];0.89[ASN][1000 genomes]
rs13379686	0.95[AFR][1000 genomes];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs13380152	0.95[CEU][hapmap];0.86[CHB][hapmap];0.94[JPT][hapmap];0.87[YRI][hapmap];0.95[AFR][1000 genomes];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1374201	0.85[CEU][hapmap];0.86[CHB][hapmap];0.88[JPT][hapmap];0.95[AFR][1000 genomes];0.87[AMR][1000 genomes];0.89[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs1446313	0.95[CEU][hapmap];0.86[CHB][hapmap];0.94[JPT][hapmap];1.00[YRI][hapmap];0.95[AFR][1000 genomes];0.87[AMR][1000 genomes];0.89[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs16968730	0.80[CHB][hapmap];0.94[JPT][hapmap]
rs17381652	1.00[CHB][hapmap];0.83[JPT][hapmap];0.93[ASN][1000 genomes]
rs17381821	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17383078	0.95[AFR][1000 genomes];0.86[AMR][1000 genomes];0.88[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs17466480	0.97[ASN][1000 genomes]
rs17468413	0.82[AMR][1000 genomes];0.85[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs2044453	0.80[CHB][hapmap];1.00[JPT][hapmap];0.89[ASN][1000 genomes]
rs2137977	0.82[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs2292594	0.95[CEU][hapmap];0.86[CHB][hapmap];0.94[JPT][hapmap];1.00[YRI][hapmap];0.92[AFR][1000 genomes];0.87[AMR][1000 genomes];0.87[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2864079	0.87[AMR][1000 genomes];0.84[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs34572155	0.80[CHB][hapmap];0.94[JPT][hapmap]
rs35093280	0.93[ASN][1000 genomes]
rs4592615	0.88[JPT][hapmap]
rs4638539	0.95[AFR][1000 genomes];0.93[AMR][1000 genomes];0.87[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs4886514	0.80[ASN][1000 genomes]
rs4886852	0.95[CEU][hapmap];0.86[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.95[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4886857	0.85[AFR][1000 genomes];0.85[EUR][1000 genomes]
rs55881066	0.90[AFR][1000 genomes];0.87[AMR][1000 genomes];0.86[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs55994208	0.90[AFR][1000 genomes];0.86[AMR][1000 genomes];0.86[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs56070388	0.85[AFR][1000 genomes];0.85[EUR][1000 genomes]
rs58792939	0.92[AFR][1000 genomes];0.85[EUR][1000 genomes]
rs59831220	0.95[AFR][1000 genomes];0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs60079927	0.90[AFR][1000 genomes];0.84[EUR][1000 genomes]
rs60761381	0.87[AFR][1000 genomes];0.84[AMR][1000 genomes];0.86[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs60863150	0.86[AFR][1000 genomes];0.87[AMR][1000 genomes];0.87[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs7173670	0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7182221	0.95[CEU][hapmap];0.86[CHB][hapmap];0.94[JPT][hapmap];0.84[EUR][1000 genomes]
rs74025074	0.97[AFR][1000 genomes];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs74025104	0.90[AFR][1000 genomes];0.85[EUR][1000 genomes]
rs74025105	0.85[AFR][1000 genomes];0.84[EUR][1000 genomes]
rs74027548	0.92[AFR][1000 genomes];0.87[AMR][1000 genomes];0.87[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs74027549	0.92[AFR][1000 genomes];0.87[AMR][1000 genomes];0.85[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs7496431	0.95[CEU][hapmap];0.86[CHB][hapmap];0.93[JPT][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:5 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv3440794	chr15:76764595-77571114	Weak transcription Enhancers Strong transcription Active TSS Flanking Active TSS Genic enhancers ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	25 gene(s)	inside rSNPs	diseases
2	esv3367577	chr15:77015618-77442634	Genic enhancers Weak transcription Strong transcription Enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Flanking Active TSS Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	20 gene(s)	inside rSNPs	diseases
3	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
4	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
5	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

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs1867780	TSPAN3	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:102 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:77394600-77413400	Weak transcription	iPS-20b Cell Line	embryonic stem cell
2	chr15:77397600-77411200	Weak transcription	HUVEC	blood vessel
3	chr15:77397800-77411400	Weak transcription	Fetal Thymus	thymus
4	chr15:77398000-77411600	Weak transcription	Fetal Brain Female	brain
5	chr15:77400000-77411400	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
6	chr15:77400200-77411400	Weak transcription	Stomach Mucosa	stomach
7	chr15:77400200-77424200	Weak transcription	Esophagus	oesophagus
8	chr15:77400200-77427200	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
9	chr15:77400200-77429000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
10	chr15:77400400-77411400	Weak transcription	HUES48 Cell Line	embryonic stem cell
11	chr15:77400400-77413000	Weak transcription	HUES6 Cell Line	embryonic stem cell
12	chr15:77400400-77428600	Weak transcription	Primary hematopoietic stem cells	blood
13	chr15:77400600-77411400	Weak transcription	ES-I3 Cell Line	embryonic stem cell
14	chr15:77400600-77411400	Weak transcription	Brain Substantia Nigra	brain
15	chr15:77400600-77411400	Weak transcription	Small Intestine	intestine
16	chr15:77400600-77425400	Weak transcription	Rectal Smooth Muscle	rectum
17	chr15:77401000-77411600	Weak transcription	Fetal Kidney	kidney
18	chr15:77401600-77449600	Weak transcription	Colonic Mucosa	Colon
19	chr15:77401800-77411400	Weak transcription	NH-A	brain
20	chr15:77402000-77407600	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
21	chr15:77402800-77412600	Weak transcription	iPS-18 Cell Line	embryonic stem cell
22	chr15:77403000-77407600	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
23	chr15:77403800-77407400	Strong transcription	Duodenum Mucosa	Duodenum
24	chr15:77404200-77407400	Strong transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
25	chr15:77404200-77407400	Strong transcription	Foreskin Melanocyte Primary Cells skin01	Skin
26	chr15:77404200-77407600	Strong transcription	Cortex derived primary cultured neurospheres	brain
27	chr15:77404200-77407600	Strong transcription	Fetal Stomach	stomach
28	chr15:77404200-77407800	Strong transcription	Primary neutrophils fromperipheralblood	blood
29	chr15:77404200-77408200	Strong transcription	Breast Myoepithelial Primary Cells	Breast
30	chr15:77404200-77430800	Weak transcription	Thymus	Thymus
31	chr15:77404400-77409000	Weak transcription	K562	blood
32	chr15:77404600-77411600	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
33	chr15:77404600-77419200	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
34	chr15:77404600-77435600	Weak transcription	HMEC	breast
35	chr15:77404800-77407400	Strong transcription	HepG2	liver
36	chr15:77405000-77407400	Strong transcription	Muscle Satellite Cultured Cells	--
37	chr15:77405000-77407800	Strong transcription	Primary B cells from cord blood	blood
38	chr15:77405000-77411400	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
39	chr15:77405000-77411400	Weak transcription	GM12878-XiMat	blood
40	chr15:77405200-77407600	Strong transcription	Brain Cingulate Gyrus	brain
41	chr15:77405200-77407600	Strong transcription	Spleen	Spleen
42	chr15:77405200-77411400	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
43	chr15:77405400-77407200	Strong transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
44	chr15:77405400-77407400	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
45	chr15:77405400-77407400	Strong transcription	Foreskin Fibroblast Primary Cells skin02	Skin
46	chr15:77405400-77407400	Strong transcription	Aorta	Aorta
47	chr15:77405400-77407400	Strong transcription	NHLF	lung
48	chr15:77405400-77407600	Strong transcription	Ganglion Eminence derived primary cultured neurospheres	brain
49	chr15:77405600-77407200	Strong transcription	Dnd41	blood
50	chr15:77405600-77407400	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell

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