Variant report

Variant	rs12900110
Chromosome Location	chr15:77495564-77495565
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 53 )
Associated
traits (count: 1 )

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

rs_ID	r²[population]
rs1015813	0.86[ASN][1000 genomes]
rs10519158	0.83[ASN][1000 genomes]
rs11853625	0.90[ASN][1000 genomes]
rs11853633	0.86[ASN][1000 genomes]
rs11854182	0.86[ASN][1000 genomes]
rs11856513	0.88[ASN][1000 genomes]
rs11856538	0.81[EUR][1000 genomes]
rs11857330	0.82[AFR][1000 genomes];0.97[AMR][1000 genomes];0.92[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs12148274	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs12324366	0.83[ASN][1000 genomes]
rs12902106	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12902434	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12902446	0.90[AFR][1000 genomes];0.94[AMR][1000 genomes];0.86[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs12912963	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs13379686	0.83[ASN][1000 genomes]
rs13380152	0.83[ASN][1000 genomes]
rs1374201	0.89[ASN][1000 genomes]
rs1446313	0.88[ASN][1000 genomes]
rs16968730	0.89[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs17381821	0.83[ASN][1000 genomes]
rs17383078	0.88[ASN][1000 genomes]
rs17466480	0.85[EUR][1000 genomes]
rs17468413	0.84[ASN][1000 genomes]
rs1867780	0.83[ASN][1000 genomes]
rs2044453	0.86[AMR][1000 genomes];0.86[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2292594	0.90[ASN][1000 genomes]
rs2864079	0.86[ASN][1000 genomes]
rs34572155	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs4592615	0.98[AMR][1000 genomes];0.92[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs4638539	0.88[ASN][1000 genomes]
rs4886514	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4886852	0.83[ASN][1000 genomes]
rs55881066	0.90[ASN][1000 genomes]
rs55994208	0.84[ASN][1000 genomes]
rs56070388	0.83[ASN][1000 genomes]
rs58792939	0.83[ASN][1000 genomes]
rs59831220	0.86[ASN][1000 genomes]
rs60761381	0.86[ASN][1000 genomes]
rs60863150	0.90[ASN][1000 genomes]
rs7163620	0.98[AMR][1000 genomes];0.93[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs7173670	0.86[ASN][1000 genomes]
rs74025074	0.83[ASN][1000 genomes]
rs74025104	0.83[ASN][1000 genomes]
rs74027548	0.90[ASN][1000 genomes]
rs74027549	0.88[ASN][1000 genomes]
rs7496431	0.86[ASN][1000 genomes]
rs9806326	0.87[AMR][1000 genomes];0.84[EUR][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	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	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
3	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
4	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
5	esv1832234	chr15:77451350-77694607	Enhancers Strong transcription Weak transcription ZNF genes & repeats Flanking Active TSS Genic enhancers Active TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
6	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
rs12900110	TSPAN3	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:62 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:77461600-77496800	Weak transcription	Lung	lung
2	chr15:77469800-77499200	Weak transcription	Rectal Smooth Muscle	rectum
3	chr15:77471400-77505800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
4	chr15:77472400-77500800	Weak transcription	HSMMtube	muscle
5	chr15:77473600-77527800	Weak transcription	Placenta	Placenta
6	chr15:77480400-77528000	Weak transcription	Fetal Stomach	stomach
7	chr15:77482000-77506200	Weak transcription	Pancreas	Pancrea
8	chr15:77482200-77504800	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
9	chr15:77482200-77528000	Weak transcription	Spleen	Spleen
10	chr15:77484000-77518800	Weak transcription	Colon Smooth Muscle	Colon
11	chr15:77487400-77516800	Weak transcription	Fetal Heart	heart
12	chr15:77491000-77500000	Weak transcription	HUES6 Cell Line	embryonic stem cell
13	chr15:77491800-77510600	Weak transcription	Primary B cells from peripheral blood	blood
14	chr15:77492000-77500800	Weak transcription	HUVEC	blood vessel
15	chr15:77492000-77505600	Weak transcription	Fetal Intestine Large	intestine
16	chr15:77492000-77516600	Weak transcription	NH-A	brain
17	chr15:77492000-77517000	Weak transcription	Primary hematopoietic stem cells	blood
18	chr15:77492200-77495800	Weak transcription	Fetal Muscle Leg	muscle
19	chr15:77492200-77496600	Weak transcription	Sigmoid Colon	Sigmoid Colon
20	chr15:77492200-77499600	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
21	chr15:77492200-77499800	Weak transcription	Dnd41	blood
22	chr15:77492200-77500000	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
23	chr15:77492200-77505800	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
24	chr15:77492200-77507000	Weak transcription	Left Ventricle	heart
25	chr15:77492200-77509400	Weak transcription	Ovary	ovary
26	chr15:77492200-77515000	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
27	chr15:77492200-77516600	Weak transcription	Duodenum Mucosa	Duodenum
28	chr15:77492200-77516800	Weak transcription	Adipose Nuclei	Adipose
29	chr15:77492200-77516800	Weak transcription	NHLF	lung
30	chr15:77492200-77527400	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
31	chr15:77492200-77527800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
32	chr15:77492200-77527800	Weak transcription	Fetal Muscle Trunk	muscle
33	chr15:77492200-77528200	Weak transcription	Rectal Mucosa Donor 29	rectum
34	chr15:77492400-77496400	Weak transcription	Osteobl	bone
35	chr15:77492400-77499600	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
36	chr15:77492400-77500200	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
37	chr15:77492400-77500200	Weak transcription	HSMM	muscle
38	chr15:77492400-77500400	Weak transcription	Primary T helper cells fromperipheralblood	blood
39	chr15:77492400-77501000	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
40	chr15:77492400-77506000	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
41	chr15:77492400-77516600	Weak transcription	Fetal Intestine Small	intestine
42	chr15:77492400-77516800	Weak transcription	Primary neutrophils fromperipheralblood	blood
43	chr15:77492400-77516800	Weak transcription	Primary B cells from cord blood	blood
44	chr15:77492400-77544000	Weak transcription	Skeletal Muscle Female	skeletal muscle
45	chr15:77492600-77497600	Weak transcription	Liver	Liver
46	chr15:77492600-77499600	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
47	chr15:77492600-77499600	Weak transcription	Breast Myoepithelial Primary Cells	Breast
48	chr15:77492600-77499600	Weak transcription	NHDF-Ad	bronchial
49	chr15:77492600-77499800	Weak transcription	Fetal Lung	lung
50	chr15:77492600-77501400	Weak transcription	Primary T cells from cord blood	blood

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