Variant report

Variant	rs59386622
Chromosome Location	chr15:77752693-77752694
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

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

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

rs_ID	r²[population]
rs11853696	0.88[AFR][1000 genomes];0.91[AMR][1000 genomes];0.86[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs11856084	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11858844	0.97[AFR][1000 genomes];0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs12324016	0.83[ASN][1000 genomes]
rs12324211	0.90[ASN][1000 genomes]
rs12324795	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12912084	0.84[ASN][1000 genomes]
rs13380202	0.88[AFR][1000 genomes];0.91[AMR][1000 genomes];0.86[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs1493699	0.83[ASN][1000 genomes]
rs16968799	0.83[ASN][1000 genomes]
rs16968897	0.81[AFR][1000 genomes];0.82[EUR][1000 genomes]
rs16968900	0.80[EUR][1000 genomes]
rs17384809	0.91[AMR][1000 genomes];0.81[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs17385059	0.85[AFR][1000 genomes];0.91[AMR][1000 genomes];0.83[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs17385296	0.87[AMR][1000 genomes];0.84[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs17385352	0.85[AFR][1000 genomes];0.91[AMR][1000 genomes];0.84[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs17470529	0.88[AFR][1000 genomes];0.91[AMR][1000 genomes];0.86[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs17470952	0.97[AMR][1000 genomes];0.95[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs17471252	0.87[ASN][1000 genomes]
rs17471431	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17471480	0.97[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17471697	0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs17471753	0.97[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs17472200	0.97[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2012740	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2012756	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2172587	0.83[ASN][1000 genomes]
rs2307141	0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28437977	0.88[AFR][1000 genomes];0.91[AMR][1000 genomes];0.86[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2864840	0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs35651077	0.83[ASN][1000 genomes]
rs3784787	0.88[AFR][1000 genomes];0.91[AMR][1000 genomes];0.86[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs3784788	0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4886863	0.84[ASN][1000 genomes]
rs4886864	0.85[AFR][1000 genomes];0.91[AMR][1000 genomes];0.86[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs4886865	0.92[AFR][1000 genomes];0.91[AMR][1000 genomes];0.86[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs56097641	0.82[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs59204923	0.83[AFR][1000 genomes];0.83[EUR][1000 genomes]
rs59362734	1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs61306472	0.81[AFR][1000 genomes];0.83[EUR][1000 genomes]
rs62007297	0.86[ASN][1000 genomes]
rs62010566	0.83[ASN][1000 genomes]
rs74026910	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs74026912	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs74026913	0.87[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs74026918	0.97[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs74026923	0.87[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs74026925	0.95[EUR][1000 genomes]
rs74026926	0.85[AFR][1000 genomes];0.83[AMR][1000 genomes];0.88[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs8035526	0.92[AFR][1000 genomes];0.91[AMR][1000 genomes];0.86[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs907398	0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[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	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
5	nsv1043284	chr15:77740632-77884026	Weak transcription Strong transcription Genic enhancers Enhancers Bivalent Enhancer Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	11 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs59386622	TSPAN3	Cis_1M	lymphoblastoid	RTeQTL

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:77717000-77754400	Weak transcription	K562	blood
2	chr15:77730600-77758800	Weak transcription	Lung	lung
3	chr15:77739800-77755600	Weak transcription	A549	lung
4	chr15:77741000-77756000	Weak transcription	Colonic Mucosa	Colon
5	chr15:77743200-77763200	Weak transcription	Brain Germinal Matrix	brain
6	chr15:77748200-77766800	Weak transcription	Aorta	Aorta
7	chr15:77748400-77770600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
8	chr15:77749000-77757400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
9	chr15:77749000-77770400	Weak transcription	Spleen	Spleen
10	chr15:77749400-77757000	Weak transcription	Fetal Intestine Small	intestine
11	chr15:77749600-77763400	Weak transcription	Fetal Brain Male	brain
12	chr15:77749800-77758800	Weak transcription	ES-I3 Cell Line	embryonic stem cell
13	chr15:77750000-77758000	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
14	chr15:77750000-77758800	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
15	chr15:77750000-77760600	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
16	chr15:77750000-77763400	Weak transcription	Primary T killer memory cells from peripheral blood	blood
17	chr15:77750000-77766400	Weak transcription	Psoas Muscle	Psoas
18	chr15:77750000-77770400	Weak transcription	H9 Cell Line	embryonic stem cell
19	chr15:77750200-77754800	Weak transcription	Skeletal Muscle Male	skeletal muscle
20	chr15:77750200-77756600	Weak transcription	Pancreas	Pancrea
21	chr15:77750200-77757000	Weak transcription	Sigmoid Colon	Sigmoid Colon
22	chr15:77750200-77759000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
23	chr15:77750200-77759000	Weak transcription	Ovary	ovary
24	chr15:77750200-77763400	Weak transcription	Rectal Smooth Muscle	rectum
25	chr15:77750200-77763800	Weak transcription	Right Ventricle	heart
26	chr15:77750200-77767000	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
27	chr15:77750400-77753600	Strong transcription	Primary T cells fromperipheralblood	blood
28	chr15:77750400-77755600	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
29	chr15:77750400-77755800	Weak transcription	Brain Hippocampus Middle	brain
30	chr15:77750400-77756400	Weak transcription	Brain Anterior Caudate	brain
31	chr15:77750400-77759400	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
32	chr15:77750400-77777800	Strong transcription	Primary B cells from peripheral blood	blood
33	chr15:77750600-77753000	Strong transcription	Ganglion Eminence derived primary cultured neurospheres	brain
34	chr15:77750600-77754000	Strong transcription	Primary B cells from cord blood	blood
35	chr15:77750600-77754000	Strong transcription	Fetal Muscle Trunk	muscle
36	chr15:77750600-77755800	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
37	chr15:77750600-77758000	Weak transcription	Primary T helper naive cells from peripheral blood	blood
38	chr15:77750600-77759000	Weak transcription	HMEC	breast
39	chr15:77750600-77759200	Weak transcription	Colon Smooth Muscle	Colon
40	chr15:77750600-77759400	Weak transcription	NHEK	skin
41	chr15:77750600-77777800	Strong transcription	Monocytes-CD14+_RO01746	blood
42	chr15:77750600-77779200	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
43	chr15:77750600-77779600	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
44	chr15:77750800-77752800	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
45	chr15:77750800-77752800	Strong transcription	Primary monocytes fromperipheralblood	blood
46	chr15:77750800-77752800	Strong transcription	Placenta	Placenta
47	chr15:77750800-77752800	Strong transcription	GM12878-XiMat	blood
48	chr15:77750800-77753000	Strong transcription	iPS-18 Cell Line	embryonic stem cell
49	chr15:77750800-77753000	Strong transcription	Dnd41	blood
50	chr15:77750800-77753400	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin

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