Variant report

Variant	rs17471431
Chromosome Location	chr15:77749068-77749069
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr15:77744071..77746416-chr15:77748090..77750023,2	MCF-7	breast:

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]
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]
rs59386622	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[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
rs17471431	TSPAN3	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:109 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:77717000-77754400	Weak transcription	K562	blood
2	chr15:77729600-77749200	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
3	chr15:77730600-77758800	Weak transcription	Lung	lung
4	chr15:77733200-77749200	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
5	chr15:77733200-77750200	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
6	chr15:77736800-77749400	Weak transcription	Gastric	stomach
7	chr15:77736800-77750800	Weak transcription	H1 Cell Line	embryonic stem cell
8	chr15:77737200-77749400	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
9	chr15:77737800-77749200	Weak transcription	HUES48 Cell Line	embryonic stem cell
10	chr15:77738200-77749400	Weak transcription	Primary hematopoietic stem cells short term culture	blood
11	chr15:77738400-77749200	Weak transcription	iPS-20b Cell Line	embryonic stem cell
12	chr15:77738400-77749400	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
13	chr15:77738600-77750600	Weak transcription	Monocytes-CD14+_RO01746	blood
14	chr15:77739000-77750800	Weak transcription	Primary monocytes fromperipheralblood	blood
15	chr15:77739800-77749600	Weak transcription	Brain Anterior Caudate	brain
16	chr15:77739800-77749800	Weak transcription	HepG2	liver
17	chr15:77739800-77750800	Weak transcription	Liver	Liver
18	chr15:77739800-77751800	Weak transcription	Brain Inferior Temporal Lobe	brain
19	chr15:77739800-77755600	Weak transcription	A549	lung
20	chr15:77740000-77750600	Weak transcription	Fetal Muscle Trunk	muscle
21	chr15:77740200-77751800	Weak transcription	Brain Angular Gyrus	brain
22	chr15:77741000-77756000	Weak transcription	Colonic Mucosa	Colon
23	chr15:77741600-77749200	Weak transcription	Duodenum Mucosa	Duodenum
24	chr15:77741800-77749600	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
25	chr15:77742400-77749400	Weak transcription	Fetal Thymus	thymus
26	chr15:77742400-77750800	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
27	chr15:77742600-77749200	Weak transcription	HUES64 Cell Line	embryonic stem cell
28	chr15:77743200-77749600	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
29	chr15:77743200-77750800	Weak transcription	Rectal Mucosa Donor 29	rectum
30	chr15:77743200-77751400	Weak transcription	Hela-S3	cervix
31	chr15:77743200-77763200	Weak transcription	Brain Germinal Matrix	brain
32	chr15:77743400-77749200	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
33	chr15:77743400-77749400	Weak transcription	HUES6 Cell Line	embryonic stem cell
34	chr15:77743400-77749400	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
35	chr15:77743400-77750600	Weak transcription	Primary B cells from cord blood	blood
36	chr15:77743600-77749600	Weak transcription	Primary B cells from peripheral blood	blood
37	chr15:77743800-77749400	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
38	chr15:77743800-77750000	Weak transcription	Primary hematopoietic stem cells	blood
39	chr15:77744000-77749200	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
40	chr15:77744000-77749400	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
41	chr15:77744000-77750600	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
42	chr15:77744000-77750800	Weak transcription	Cortex derived primary cultured neurospheres	brain
43	chr15:77745000-77750000	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
44	chr15:77745600-77750000	Enhancers	Muscle Satellite Cultured Cells	--
45	chr15:77746000-77751000	Enhancers	Foreskin Fibroblast Primary Cells skin02	Skin
46	chr15:77746200-77750400	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
47	chr15:77746200-77751000	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
48	chr15:77746400-77750200	Enhancers	Skeletal Muscle Male	skeletal muscle
49	chr15:77746400-77750600	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
50	chr15:77746600-77751200	Enhancers	Fetal Lung	lung

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