Variant report

Variant	rs2864079
Chromosome Location	chr15:77499531-77499532
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 55 )
Associated
traits (count: 1 )

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

rs_ID	r²[population]
rs1015813	0.97[AMR][1000 genomes];0.95[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs10519158	0.87[AMR][1000 genomes];0.83[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs11853625	1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs11853633	0.94[AMR][1000 genomes];0.92[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs11854182	0.94[AMR][1000 genomes];0.84[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs11854466	0.91[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs11856513	0.91[AMR][1000 genomes];0.92[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs11857804	0.91[EUR][1000 genomes]
rs12148274	0.82[ASN][1000 genomes]
rs12324366	0.91[AMR][1000 genomes];0.94[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs12900110	0.86[ASN][1000 genomes]
rs12902106	0.85[ASN][1000 genomes]
rs12902434	0.85[ASN][1000 genomes]
rs12912963	0.82[ASN][1000 genomes]
rs13379686	0.93[AMR][1000 genomes];0.84[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs13380152	0.93[AMR][1000 genomes];0.84[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs1374201	1.00[AMR][1000 genomes];0.92[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs1446313	1.00[AMR][1000 genomes];0.92[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs16968730	0.82[ASN][1000 genomes]
rs17381821	0.87[AMR][1000 genomes];0.84[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs17383078	0.99[AMR][1000 genomes];0.92[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs17466480	0.80[ASN][1000 genomes]
rs17468413	0.91[AMR][1000 genomes];0.94[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs1867780	0.87[AMR][1000 genomes];0.84[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs2137977	0.91[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs2292594	1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs34572155	0.83[ASN][1000 genomes]
rs4638539	0.94[AMR][1000 genomes];0.89[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs4886514	0.85[ASN][1000 genomes]
rs4886852	0.90[AMR][1000 genomes];0.84[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs4886857	0.91[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs55881066	1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs55994208	0.99[AMR][1000 genomes];0.96[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs56070388	0.91[AMR][1000 genomes];0.91[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs58792939	0.91[AMR][1000 genomes];0.94[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs59831220	0.94[AMR][1000 genomes];0.88[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs60079927	0.91[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs60761381	0.97[AMR][1000 genomes];0.95[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs60863150	1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs7173670	0.91[AMR][1000 genomes];0.84[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs7182221	0.91[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs74025074	0.93[AMR][1000 genomes];0.84[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs74025104	0.90[AMR][1000 genomes];0.90[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs74025105	0.91[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs74027548	1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs74027549	1.00[AMR][1000 genomes];0.94[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs7496431	0.94[AMR][1000 genomes];0.84[EUR][1000 genomes];0.86[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:8 , 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
7	nsv974604	chr15:77496873-77500234	Weak transcription ZNF genes & repeats Enhancers Strong transcription	TF binding region lncRNA	1 gene(s)	inside rSNPs	n/a
8	nsv1041064	chr15:77497903-77631698	Strong transcription Enhancers Weak transcription ZNF genes & repeats Genic enhancers Flanking Active TSS Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs2864079	TSPAN3	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:59 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:77471400-77505800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
2	chr15:77472400-77500800	Weak transcription	HSMMtube	muscle
3	chr15:77473600-77527800	Weak transcription	Placenta	Placenta
4	chr15:77480400-77528000	Weak transcription	Fetal Stomach	stomach
5	chr15:77482000-77506200	Weak transcription	Pancreas	Pancrea
6	chr15:77482200-77504800	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
7	chr15:77482200-77528000	Weak transcription	Spleen	Spleen
8	chr15:77484000-77518800	Weak transcription	Colon Smooth Muscle	Colon
9	chr15:77487400-77516800	Weak transcription	Fetal Heart	heart
10	chr15:77491000-77500000	Weak transcription	HUES6 Cell Line	embryonic stem cell
11	chr15:77491800-77510600	Weak transcription	Primary B cells from peripheral blood	blood
12	chr15:77492000-77500800	Weak transcription	HUVEC	blood vessel
13	chr15:77492000-77505600	Weak transcription	Fetal Intestine Large	intestine
14	chr15:77492000-77516600	Weak transcription	NH-A	brain
15	chr15:77492000-77517000	Weak transcription	Primary hematopoietic stem cells	blood
16	chr15:77492200-77499600	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
17	chr15:77492200-77499800	Weak transcription	Dnd41	blood
18	chr15:77492200-77500000	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
19	chr15:77492200-77505800	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
20	chr15:77492200-77507000	Weak transcription	Left Ventricle	heart
21	chr15:77492200-77509400	Weak transcription	Ovary	ovary
22	chr15:77492200-77515000	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
23	chr15:77492200-77516600	Weak transcription	Duodenum Mucosa	Duodenum
24	chr15:77492200-77516800	Weak transcription	Adipose Nuclei	Adipose
25	chr15:77492200-77516800	Weak transcription	NHLF	lung
26	chr15:77492200-77527400	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
27	chr15:77492200-77527800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
28	chr15:77492200-77527800	Weak transcription	Fetal Muscle Trunk	muscle
29	chr15:77492200-77528200	Weak transcription	Rectal Mucosa Donor 29	rectum
30	chr15:77492400-77499600	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
31	chr15:77492400-77500200	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
32	chr15:77492400-77500200	Weak transcription	HSMM	muscle
33	chr15:77492400-77500400	Weak transcription	Primary T helper cells fromperipheralblood	blood
34	chr15:77492400-77501000	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
35	chr15:77492400-77506000	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
36	chr15:77492400-77516600	Weak transcription	Fetal Intestine Small	intestine
37	chr15:77492400-77516800	Weak transcription	Primary neutrophils fromperipheralblood	blood
38	chr15:77492400-77516800	Weak transcription	Primary B cells from cord blood	blood
39	chr15:77492400-77544000	Weak transcription	Skeletal Muscle Female	skeletal muscle
40	chr15:77492600-77499600	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
41	chr15:77492600-77499600	Weak transcription	Breast Myoepithelial Primary Cells	Breast
42	chr15:77492600-77499600	Weak transcription	NHDF-Ad	bronchial
43	chr15:77492600-77499800	Weak transcription	Fetal Lung	lung
44	chr15:77492600-77501400	Weak transcription	Primary T cells from cord blood	blood
45	chr15:77492600-77516600	Weak transcription	Rectal Mucosa Donor 31	rectum
46	chr15:77492600-77516800	Weak transcription	Aorta	Aorta
47	chr15:77492800-77516400	Weak transcription	Muscle Satellite Cultured Cells	--
48	chr15:77494600-77499600	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
49	chr15:77494600-77501000	Weak transcription	Brain Angular Gyrus	brain
50	chr15:77494600-77516600	Weak transcription	Brain Substantia Nigra	brain

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