Variant report

Variant	rs11856513
Chromosome Location	chr15:77471105-77471106
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 60 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:55)

rs_ID	r²[population]
rs1015813	0.89[AMR][1000 genomes];0.95[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs10519158	1.00[CEU][hapmap];1.00[CHB][hapmap];0.94[JPT][hapmap];0.93[AMR][1000 genomes];0.88[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs11853625	0.91[AMR][1000 genomes];0.96[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs11853633	0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11854182	0.97[AMR][1000 genomes];0.89[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11854466	0.86[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs11856538	0.96[CHD][hapmap];0.88[JPT][hapmap];0.88[ASN][1000 genomes]
rs11857330	0.93[CHB][hapmap];1.00[JPT][hapmap]
rs11857804	0.91[EUR][1000 genomes]
rs12148274	0.82[ASN][1000 genomes]
rs12324366	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[AMR][1000 genomes];0.94[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs12900110	0.88[ASN][1000 genomes]
rs12902106	0.85[ASN][1000 genomes]
rs12902434	0.85[ASN][1000 genomes]
rs12902446	0.93[CHB][hapmap];1.00[JPT][hapmap];0.87[ASN][1000 genomes]
rs12912963	0.82[ASN][1000 genomes]
rs13379686	0.96[AMR][1000 genomes];0.89[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs13380152	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[AMR][1000 genomes];0.89[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1374201	0.90[CEU][hapmap];1.00[CHB][hapmap];0.96[CHD][hapmap];0.97[GIH][hapmap];0.94[JPT][hapmap];0.97[TSI][hapmap];0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1446313	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs16968730	0.93[CHB][hapmap];1.00[JPT][hapmap];0.83[TSI][hapmap];0.82[ASN][1000 genomes]
rs17381652	0.85[CHB][hapmap];0.83[JPT][hapmap];0.87[ASN][1000 genomes]
rs17381821	0.95[CEU][hapmap];0.86[CHB][hapmap];0.94[JPT][hapmap];0.91[AFR][1000 genomes];0.96[AMR][1000 genomes];0.89[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs17383078	0.90[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs17385296	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs17466480	0.89[ASN][1000 genomes]
rs17468413	0.88[AMR][1000 genomes];0.94[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs1867780	0.95[CEU][hapmap];0.86[CHB][hapmap];0.94[JPT][hapmap];0.93[AMR][1000 genomes];0.89[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2044453	0.93[CHB][hapmap];0.94[JPT][hapmap];0.83[TSI][hapmap];0.87[ASN][1000 genomes]
rs2137977	0.88[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs2292594	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.91[AMR][1000 genomes];0.96[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2864079	0.91[AMR][1000 genomes];0.92[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs34572155	0.93[CHB][hapmap];1.00[JPT][hapmap];0.83[TSI][hapmap];0.83[ASN][1000 genomes]
rs35093280	0.87[ASN][1000 genomes]
rs4592615	0.93[CHB][hapmap];1.00[JPT][hapmap]
rs4638539	0.97[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4886514	0.85[ASN][1000 genomes]
rs4886852	1.00[CEU][hapmap];1.00[CHB][hapmap];0.94[JPT][hapmap];0.96[AMR][1000 genomes];0.89[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4886857	0.86[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs55881066	0.91[AMR][1000 genomes];0.95[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs55994208	0.90[AMR][1000 genomes];0.94[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs56070388	0.86[AMR][1000 genomes];0.91[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs58792939	0.86[AMR][1000 genomes];0.94[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs59831220	0.97[AMR][1000 genomes];0.92[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs60079927	0.86[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs60761381	0.89[AMR][1000 genomes];0.95[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs60863150	0.91[AMR][1000 genomes];0.96[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs7173670	0.82[AFR][1000 genomes];1.00[AMR][1000 genomes];0.89[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7182221	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.86[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs74025074	0.96[AMR][1000 genomes];0.89[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs74025104	0.84[AMR][1000 genomes];0.90[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs74025105	0.86[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs74027548	0.91[AMR][1000 genomes];0.96[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs74027549	0.91[AMR][1000 genomes];0.93[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs7496431	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.97[AMR][1000 genomes];0.89[EUR][1000 genomes];0.98[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	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

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs11856513	TSPAN3	Cis_1M	lymphoblastoid	RTeQTL
rs11856513	PSTPIP1	cis	multi-tissue	Pritchard
rs11856513	HMG20A	cis	parietal	SCAN
rs11856513	CRABP1	cis	parietal	SCAN

Chromatin state (count:86 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:77437000-77471200	Weak transcription	Skeletal Muscle Male	skeletal muscle
2	chr15:77450400-77471200	Weak transcription	Fetal Muscle Leg	muscle
3	chr15:77450600-77471200	Weak transcription	Muscle Satellite Cultured Cells	--
4	chr15:77450800-77471200	Weak transcription	Fetal Muscle Trunk	muscle
5	chr15:77451000-77471200	Weak transcription	HSMM	muscle
6	chr15:77451000-77478800	Weak transcription	Brain Cingulate Gyrus	brain
7	chr15:77451200-77471800	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
8	chr15:77451200-77491800	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
9	chr15:77451400-77471200	Weak transcription	NHDF-Ad	bronchial
10	chr15:77454000-77471200	Weak transcription	NHLF	lung
11	chr15:77454000-77472400	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
12	chr15:77454200-77471200	Weak transcription	Placenta	Placenta
13	chr15:77454800-77471200	Weak transcription	Primary T cells fromperipheralblood	blood
14	chr15:77456400-77471800	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
15	chr15:77456600-77471400	Weak transcription	Primary hematopoietic stem cells	blood
16	chr15:77456600-77471600	Weak transcription	Primary hematopoietic stem cells short term culture	blood
17	chr15:77457200-77471600	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
18	chr15:77457200-77475200	Weak transcription	iPS-20b Cell Line	embryonic stem cell
19	chr15:77457200-77475400	Weak transcription	HUES48 Cell Line	embryonic stem cell
20	chr15:77457800-77471200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
21	chr15:77458200-77471200	Weak transcription	Spleen	Spleen
22	chr15:77460800-77471200	Weak transcription	Fetal Lung	lung
23	chr15:77460800-77479200	Weak transcription	Skeletal Muscle Female	skeletal muscle
24	chr15:77461200-77471200	Weak transcription	Right Ventricle	heart
25	chr15:77461400-77471200	Weak transcription	Fetal Stomach	stomach
26	chr15:77461600-77471200	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
27	chr15:77461600-77471200	Weak transcription	Aorta	Aorta
28	chr15:77461600-77471200	Weak transcription	Left Ventricle	heart
29	chr15:77461600-77471800	Weak transcription	HSMMtube	muscle
30	chr15:77461600-77496800	Weak transcription	Lung	lung
31	chr15:77461800-77472400	Weak transcription	NH-A	brain
32	chr15:77465200-77477000	Weak transcription	Gastric	stomach
33	chr15:77465400-77471200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
34	chr15:77465400-77488200	Weak transcription	Psoas Muscle	Psoas
35	chr15:77466200-77471200	Weak transcription	Sigmoid Colon	Sigmoid Colon
36	chr15:77466200-77479000	Weak transcription	Brain Anterior Caudate	brain
37	chr15:77466200-77479400	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
38	chr15:77466400-77472000	Weak transcription	Brain Substantia Nigra	brain
39	chr15:77466600-77472000	Weak transcription	Stomach Mucosa	stomach
40	chr15:77466800-77471200	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
41	chr15:77466800-77471200	Weak transcription	HepG2	liver
42	chr15:77467200-77491400	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
43	chr15:77468600-77473400	Strong transcription	Osteobl	bone
44	chr15:77468600-77474800	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
45	chr15:77468600-77475400	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
46	chr15:77468800-77473800	Weak transcription	Brain Inferior Temporal Lobe	brain
47	chr15:77469000-77474400	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
48	chr15:77469000-77480200	Weak transcription	iPS-18 Cell Line	embryonic stem cell
49	chr15:77469200-77471200	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
50	chr15:77469400-77471200	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin

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