Variant report

Variant	rs12324016
Chromosome Location	chr15:77627567-77627568
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	chr15:77619982..77622270-chr15:77624523..77628155,3	K562	blood:
2	chr15:77603476..77605050-chr15:77627091..77629724,2	K562	blood:

Extended variants
information (count: 71 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:60)

rs_ID	r²[population]
rs10162778	0.96[AFR][1000 genomes];0.99[AMR][1000 genomes];0.96[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs11853696	0.88[ASN][1000 genomes]
rs11856084	0.93[CHB][hapmap];0.88[JPT][hapmap];0.83[ASN][1000 genomes]
rs11856513	0.93[CHB][hapmap];1.00[JPT][hapmap]
rs11857330	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.83[ASN][1000 genomes]
rs12324211	1.00[CEU][hapmap];1.00[CHB][hapmap];0.89[JPT][hapmap];0.88[YRI][hapmap];0.82[AFR][1000 genomes];0.90[AMR][1000 genomes];0.83[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs12324366	0.86[CHB][hapmap];0.94[JPT][hapmap]
rs12324795	0.86[CHB][hapmap];0.94[JPT][hapmap];0.85[ASN][1000 genomes]
rs12902446	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[YRI][hapmap]
rs12912084	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];0.94[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs13380152	0.86[CHB][hapmap];0.94[JPT][hapmap]
rs13380202	0.92[ASN][1000 genomes]
rs1374201	0.93[CHB][hapmap];0.94[JPT][hapmap]
rs1446313	0.86[CHB][hapmap];0.94[JPT][hapmap]
rs1493699	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs16968730	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap]
rs16968799	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17384809	0.92[ASN][1000 genomes]
rs17385059	0.92[ASN][1000 genomes]
rs17385296	0.86[CHB][hapmap];0.94[JPT][hapmap];0.92[ASN][1000 genomes]
rs17385352	0.92[ASN][1000 genomes]
rs17470529	0.90[ASN][1000 genomes]
rs17470952	0.86[ASN][1000 genomes]
rs17471252	0.83[AFR][1000 genomes];0.93[AMR][1000 genomes];0.85[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs17471431	0.83[ASN][1000 genomes]
rs17471480	0.93[CHB][hapmap];0.83[JPT][hapmap];0.83[ASN][1000 genomes]
rs17471697	0.93[CHB][hapmap];0.87[JPT][hapmap];0.81[ASN][1000 genomes]
rs17471753	0.81[ASN][1000 genomes]
rs2012740	0.83[ASN][1000 genomes]
rs2012756	0.83[ASN][1000 genomes]
rs2172587	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2292594	0.93[CHB][hapmap];1.00[JPT][hapmap]
rs2307141	0.86[CHB][hapmap];0.83[JPT][hapmap];0.83[ASN][1000 genomes]
rs28437977	0.90[ASN][1000 genomes]
rs2864840	0.86[CHB][hapmap];0.94[JPT][hapmap];0.87[ASN][1000 genomes]
rs34572155	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap]
rs35651077	0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3784787	0.90[ASN][1000 genomes]
rs3784788	0.86[CHB][hapmap];0.83[JPT][hapmap];0.81[ASN][1000 genomes]
rs4592615	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.83[ASN][1000 genomes]
rs4886863	0.97[AMR][1000 genomes];0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4886864	0.90[ASN][1000 genomes]
rs4886865	0.90[ASN][1000 genomes]
rs59362734	0.82[ASN][1000 genomes]
rs59386622	0.83[ASN][1000 genomes]
rs62007297	0.88[AFR][1000 genomes];0.93[AMR][1000 genomes];0.85[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs62010566	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7163620	0.83[ASN][1000 genomes]
rs7182221	0.93[CHB][hapmap];1.00[JPT][hapmap]
rs74026910	0.84[ASN][1000 genomes]
rs74026912	0.86[ASN][1000 genomes]
rs74026913	0.87[ASN][1000 genomes]
rs74026918	0.81[ASN][1000 genomes]
rs74026926	0.80[ASN][1000 genomes]
rs7496431	0.92[CHB][hapmap];1.00[JPT][hapmap]
rs8029163	0.90[AMR][1000 genomes];0.91[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs8035526	0.90[ASN][1000 genomes]
rs883627	0.96[CEU][hapmap];0.81[CHB][hapmap];0.83[JPT][hapmap];0.88[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs907398	0.86[CHB][hapmap];0.83[JPT][hapmap]
rs9806326	0.82[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:11 , 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	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
5	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
6	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
7	nsv1051744	chr15:77511489-77679160	Enhancers Weak transcription ZNF genes & repeats Strong transcription Flanking Active TSS Genic enhancers Active TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
8	esv1830237	chr15:77535785-77694607	Enhancers Weak transcription ZNF genes & repeats Strong transcription Genic enhancers Flanking Active TSS Active TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
9	nsv482689	chr15:77576396-77731559	Weak transcription Enhancers Active TSS Genic enhancers ZNF genes & repeats Flanking Active TSS Strong transcription Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	12 gene(s)	inside rSNPs	diseases
10	nsv1040430	chr15:77584375-77676957	Enhancers Weak transcription Genic enhancers Strong transcription ZNF genes & repeats Flanking Active TSS Bivalent Enhancer Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
11	esv1836778	chr15:77608747-77694607	Weak transcription Enhancers Strong transcription Genic enhancers Flanking Active TSS ZNF genes & repeats Bivalent Enhancer Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs12324016	TSPAN3	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:34 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:77603400-77633400	Weak transcription	Primary B cells from cord blood	blood
2	chr15:77606000-77627800	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
3	chr15:77619000-77630200	Weak transcription	Brain Angular Gyrus	brain
4	chr15:77620000-77645200	Weak transcription	Muscle Satellite Cultured Cells	--
5	chr15:77620800-77639200	Weak transcription	Osteobl	bone
6	chr15:77621800-77628200	Weak transcription	Ovary	ovary
7	chr15:77622000-77627600	Weak transcription	NHLF	lung
8	chr15:77622000-77627800	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
9	chr15:77622000-77627800	Weak transcription	Right Ventricle	heart
10	chr15:77622000-77636800	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
11	chr15:77622000-77645200	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
12	chr15:77623000-77628000	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
13	chr15:77623200-77627800	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
14	chr15:77623200-77628000	Weak transcription	NHDF-Ad	bronchial
15	chr15:77625600-77630400	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
16	chr15:77625600-77633000	Weak transcription	Primary hematopoietic stem cells	blood
17	chr15:77625600-77633800	Weak transcription	Primary T cells from cord blood	blood
18	chr15:77626400-77634000	Weak transcription	Dnd41	blood
19	chr15:77626800-77628200	Enhancers	Fetal Adrenal Gland	Adrenal Gland
20	chr15:77627000-77628000	Enhancers	Brain Anterior Caudate	brain
21	chr15:77627000-77628800	Enhancers	Brain Hippocampus Middle	brain
22	chr15:77627200-77628800	Enhancers	Left Ventricle	heart
23	chr15:77627200-77629200	Enhancers	Foreskin Melanocyte Primary Cells skin01	Skin
24	chr15:77627200-77630600	Enhancers	Breast Myoepithelial Primary Cells	Breast
25	chr15:77627400-77628200	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
26	chr15:77627400-77628200	Enhancers	Adipose Nuclei	Adipose
27	chr15:77627400-77628200	Enhancers	Fetal Lung	lung
28	chr15:77627400-77628400	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
29	chr15:77627400-77628800	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
30	chr15:77627400-77628800	Enhancers	Brain Inferior Temporal Lobe	brain
31	chr15:77627400-77629000	Enhancers	Brain Substantia Nigra	brain
32	chr15:77627400-77629000	Enhancers	Fetal Heart	heart
33	chr15:77627400-77629200	Enhancers	Brain Cingulate Gyrus	brain
34	chr15:77627400-77657400	Weak transcription	Aorta	Aorta

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