Variant report

Variant	rs1142468
Chromosome Location	chr15:40978726-40978727
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 59 )
Associated
traits (count: 6 )

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

rs_ID	r²[population]
rs10467972	0.91[CEU][hapmap]
rs10744948	0.82[EUR][1000 genomes]
rs11070284	0.84[EUR][1000 genomes]
rs11070292	0.91[CEU][hapmap];0.91[CHB][hapmap];1.00[CHD][hapmap];0.95[JPT][hapmap];1.00[MEX][hapmap];0.80[TSI][hapmap];0.86[AMR][1000 genomes];0.88[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs11633367	0.90[AMR][1000 genomes];0.97[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs11638204	0.87[AFR][1000 genomes];0.90[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs11854763	0.84[EUR][1000 genomes]
rs12438182	0.83[AMR][1000 genomes];0.90[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs12438955	0.84[EUR][1000 genomes]
rs12708401	0.84[EUR][1000 genomes]
rs12906095	0.81[EUR][1000 genomes]
rs12911738	1.00[CEU][hapmap];0.84[EUR][1000 genomes]
rs12912058	1.00[CEU][hapmap];0.84[EUR][1000 genomes]
rs12912339	0.84[EUR][1000 genomes]
rs12915109	0.86[EUR][1000 genomes]
rs12916082	0.86[EUR][1000 genomes]
rs17747351	1.00[CEU][hapmap]
rs2278888	1.00[CEU][hapmap]
rs2304580	1.00[CEU][hapmap];0.85[LWK][hapmap];0.86[TSI][hapmap];0.86[EUR][1000 genomes]
rs2412541	1.00[CEU][hapmap];0.84[EUR][1000 genomes]
rs2619681	1.00[CEU][hapmap];0.86[TSI][hapmap];0.89[EUR][1000 genomes]
rs3092978	1.00[CEU][hapmap];0.84[EUR][1000 genomes]
rs34285050	0.89[EUR][1000 genomes]
rs4417527	1.00[CEU][hapmap];0.89[EUR][1000 genomes]
rs4420508	0.84[EUR][1000 genomes]
rs45457497	0.85[EUR][1000 genomes]
rs4924484	0.83[EUR][1000 genomes]
rs4924487	0.91[CEU][hapmap];0.84[EUR][1000 genomes]
rs4924488	1.00[CEU][hapmap];0.84[EUR][1000 genomes]
rs4924490	0.89[AFR][1000 genomes];0.89[AMR][1000 genomes];0.90[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs4924491	0.88[EUR][1000 genomes]
rs4924500	1.00[CEU][hapmap];0.89[EUR][1000 genomes]
rs6492957	0.86[AFR][1000 genomes];0.89[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs6492958	1.00[CEU][hapmap];0.82[AFR][1000 genomes];0.81[AMR][1000 genomes];0.89[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs7161938	1.00[CEU][hapmap];0.81[CHB][hapmap];0.88[CHD][hapmap];0.87[JPT][hapmap];0.91[MEX][hapmap];0.89[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs7167417	1.00[CEU][hapmap];0.84[EUR][1000 genomes]
rs7168873	0.80[EUR][1000 genomes]
rs7171260	1.00[CEU][hapmap];0.84[EUR][1000 genomes]
rs7175361	0.83[EUR][1000 genomes]
rs7176974	0.84[EUR][1000 genomes]
rs7177192	1.00[CEU][hapmap];0.84[EUR][1000 genomes]
rs7178486	0.84[EUR][1000 genomes]
rs8025008	0.84[EUR][1000 genomes]
rs8028999	1.00[CEU][hapmap]
rs8031057	0.82[EUR][1000 genomes]
rs8035775	1.00[CEU][hapmap];0.84[EUR][1000 genomes]
rs8037804	1.00[CEU][hapmap];0.84[EUR][1000 genomes]
rs8040502	1.00[CEU][hapmap];0.84[EUR][1000 genomes]
rs8042729	0.91[CEU][hapmap]
rs896796	1.00[CEU][hapmap];0.85[CHB][hapmap];0.86[JPT][hapmap]
rs9806221	0.83[EUR][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	nsv832984	chr15:40794391-40998535	Weak transcription Active TSS ZNF genes & repeats Flanking Active TSS Strong transcription Enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Genic enhancers Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	46 gene(s)	inside rSNPs	diseases
2	esv2758378	chr15:40832545-40995111	Active TSS Flanking Active TSS Strong transcription Enhancers Genic enhancers Weak transcription Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	44 gene(s)	inside rSNPs	diseases
3	esv2760026	chr15:40832545-40995111	Weak transcription Flanking Active TSS Strong transcription Active TSS Enhancers Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	44 gene(s)	inside rSNPs	diseases
4	nsv1053173	chr15:40933163-41094127	Flanking Active TSS Genic enhancers Strong transcription Flanking Bivalent TSS/Enh Enhancers Weak transcription ZNF genes & repeats Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	57 gene(s)	inside rSNPs	diseases
5	nsv542363	chr15:40933163-41094127	Flanking Active TSS Enhancers Weak transcription Genic enhancers Active TSS Strong transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	57 gene(s)	inside rSNPs	diseases
6	nsv904099	chr15:40949526-41041875	Genic enhancers Enhancers Weak transcription Strong transcription Bivalent/Poised TSS Active TSS Flanking Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	26 gene(s)	inside rSNPs	diseases
7	nsv529030	chr15:40956471-41012695	Active TSS Flanking Active TSS Strong transcription Enhancers Weak transcription Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	26 gene(s)	inside rSNPs	diseases
8	nsv904100	chr15:40959624-40994706	Weak transcription Flanking Active TSS Strong transcription Active TSS Enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	25 gene(s)	inside rSNPs	diseases

mRNA abundance (count:6)

SNP	Gene	Cis/trans	Tissue	Source
rs1142468	FAM82A2	cis	parietal	SCAN
rs1142468	TGFBR3	trans	lymphoblastoid	seeQTL
rs1142468	RMDN3	cis	Muscle Skeletal	GTEx
rs1142468	RMDN3	cis	Heart Left Ventricle	GTEx
rs1142468	INO80	cis	cerebellum	SCAN
rs1142468	ZFYVE19	cis	cerebellum	SCAN

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:40913800-40986000	Weak transcription	A549	lung
2	chr15:40945000-40984200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
3	chr15:40950000-40981200	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
4	chr15:40955200-40983200	Weak transcription	Fetal Intestine Small	intestine
5	chr15:40958600-40981000	Weak transcription	Thymus	Thymus
6	chr15:40971200-40985800	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
7	chr15:40971400-40981000	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
8	chr15:40971600-40984000	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
9	chr15:40971600-40984200	Weak transcription	Primary T helper cells fromperipheralblood	blood
10	chr15:40971600-40985600	Weak transcription	Dnd41	blood
11	chr15:40971600-40985800	Weak transcription	Primary T killer memory cells from peripheral blood	blood
12	chr15:40971800-40982400	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
13	chr15:40971800-40983800	Weak transcription	Primary T cells fromperipheralblood	blood
14	chr15:40971800-40984000	Weak transcription	Brain Hippocampus Middle	brain
15	chr15:40971800-40984200	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
16	chr15:40971800-40985800	Weak transcription	Brain Angular Gyrus	brain
17	chr15:40972400-40984600	Weak transcription	Placenta	Placenta
18	chr15:40972600-40984200	Weak transcription	Spleen	Spleen
19	chr15:40972800-40984000	Weak transcription	HepG2	liver
20	chr15:40973200-40985600	Weak transcription	Primary B cells from cord blood	blood
21	chr15:40973400-40985800	Weak transcription	GM12878-XiMat	blood
22	chr15:40973600-40984000	Weak transcription	Primary B cells from peripheral blood	blood
23	chr15:40976200-40982800	Weak transcription	Fetal Stomach	stomach
24	chr15:40976200-40984000	Weak transcription	Primary T cells from cord blood	blood
25	chr15:40976400-40984000	Weak transcription	Brain Anterior Caudate	brain
26	chr15:40977000-40985800	Weak transcription	Cortex derived primary cultured neurospheres	brain
27	chr15:40977200-40981200	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
28	chr15:40977200-40981200	Weak transcription	HMEC	breast
29	chr15:40977200-40981200	Weak transcription	NHEK	skin
30	chr15:40977200-40985800	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
31	chr15:40977400-40985800	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
32	chr15:40977400-40986200	Weak transcription	Esophagus	oesophagus
33	chr15:40977800-40981000	Weak transcription	Fetal Muscle Leg	muscle
34	chr15:40977800-40984200	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
35	chr15:40978000-40984000	Weak transcription	Liver	Liver
36	chr15:40978000-40984200	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
37	chr15:40978000-40985800	Weak transcription	Gastric	stomach
38	chr15:40978000-40986000	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
39	chr15:40978200-40981200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
40	chr15:40978200-40983600	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
41	chr15:40978200-40984000	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
42	chr15:40978200-40984000	Weak transcription	Rectal Mucosa Donor 29	rectum
43	chr15:40978200-40984200	Weak transcription	Stomach Smooth Muscle	stomach
44	chr15:40978200-40985800	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
45	chr15:40978200-40986000	Weak transcription	HSMMtube	muscle
46	chr15:40978400-40978800	Weak transcription	iPS-20b Cell Line	embryonic stem cell
47	chr15:40978400-40980000	Weak transcription	Breast Myoepithelial Primary Cells	Breast
48	chr15:40978400-40984400	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
49	chr15:40978600-40986000	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
50	chr15:40978600-40986000	Weak transcription	Sigmoid Colon	Sigmoid Colon

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