Variant report

Variant	rs2404733
Chromosome Location	chr15:76954064-76954065
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 128 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:97)

rs_ID	r²[population]
rs10444858	0.87[AMR][1000 genomes];0.94[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs1116535	0.84[AMR][1000 genomes];0.90[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs12148452	0.85[AMR][1000 genomes];0.90[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs12148877	0.85[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs12437627	0.82[ASN][1000 genomes]
rs12437733	0.80[ASN][1000 genomes]
rs12438077	0.80[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs12438186	0.84[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs12438540	0.87[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs12440151	0.85[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs12440835	0.82[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs12441484	0.80[ASN][1000 genomes]
rs12441550	0.82[ASN][1000 genomes]
rs12591660	0.80[ASN][1000 genomes]
rs12593871	0.81[AMR][1000 genomes];0.82[ASN][1000 genomes]
rs12595313	0.85[AFR][1000 genomes];0.87[AMR][1000 genomes];0.93[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs12900494	0.85[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs12902174	0.80[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs12902452	0.85[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs12903553	0.81[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs12904198	0.80[ASN][1000 genomes]
rs12908421	0.81[ASN][1000 genomes]
rs12910293	0.80[ASN][1000 genomes]
rs12910382	0.81[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs12910734	0.80[ASN][1000 genomes]
rs12911174	0.80[ASN][1000 genomes]
rs12911902	0.81[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs12911987	0.85[AFR][1000 genomes];0.82[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1471780	0.83[AMR][1000 genomes];0.86[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs1838048	0.86[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs1838050	0.85[ASN][1000 genomes]
rs1867197	0.85[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs1874944	0.80[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs1946650	0.82[ASN][1000 genomes]
rs2083762	0.83[ASN][1000 genomes]
rs2120108	0.80[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs2304920	0.85[AMR][1000 genomes];0.92[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2404736	0.80[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs2404737	0.80[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs34049670	0.80[ASN][1000 genomes]
rs34060246	0.95[AFR][1000 genomes];0.87[AMR][1000 genomes];0.93[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs34181263	0.82[ASN][1000 genomes]
rs34272342	0.84[AMR][1000 genomes];0.92[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs34287706	0.87[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs34478400	0.85[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs34639578	0.98[ASN][1000 genomes]
rs34707035	0.93[ASN][1000 genomes]
rs34924128	0.85[AFR][1000 genomes];0.87[AMR][1000 genomes];0.94[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs35077207	0.86[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs35138393	0.87[AMR][1000 genomes];0.93[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs35170561	0.80[ASN][1000 genomes]
rs35195096	0.86[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs35395069	0.87[AMR][1000 genomes];0.93[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs35498563	0.85[AFR][1000 genomes];0.87[AMR][1000 genomes];0.94[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs35561811	0.80[ASN][1000 genomes]
rs36070630	0.88[AFR][1000 genomes];0.87[AMR][1000 genomes];0.93[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs3816266	0.81[AFR][1000 genomes];0.85[AMR][1000 genomes];0.92[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs4383105	0.81[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs4442773	0.81[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs4525456	0.85[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs4641709	0.81[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs4886503	0.82[ASN][1000 genomes]
rs4886817	0.80[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs4886822	0.81[AMR][1000 genomes];0.89[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs4886824	0.85[AMR][1000 genomes];0.92[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs4886825	0.93[ASN][1000 genomes]
rs4886829	0.80[ASN][1000 genomes]
rs55676827	0.85[AFR][1000 genomes];0.87[AMR][1000 genomes];0.94[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs55864032	0.80[ASN][1000 genomes]
rs56193230	0.86[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs57178708	0.85[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs58361452	0.85[AFR][1000 genomes];0.87[AMR][1000 genomes];0.93[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs58973160	0.81[AFR][1000 genomes];0.85[AMR][1000 genomes];0.91[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs59088060	0.80[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs60658665	0.81[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs60912217	0.92[ASN][1000 genomes]
rs66866130	0.80[ASN][1000 genomes]
rs67010831	0.87[AMR][1000 genomes];0.94[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs67204011	0.82[ASN][1000 genomes]
rs67570291	0.83[AMR][1000 genomes];0.85[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs71405222	0.92[AMR][1000 genomes];0.83[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs71405223	0.83[AMR][1000 genomes];0.89[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs71405225	0.81[ASN][1000 genomes]
rs7163397	0.86[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7167613	0.80[ASN][1000 genomes]
rs7169394	0.85[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs7174673	0.80[ASN][1000 genomes]
rs7174953	0.85[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs72738889	0.85[AMR][1000 genomes];0.92[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7342603	0.85[AFR][1000 genomes];0.87[AMR][1000 genomes];0.93[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7350777	0.87[AMR][1000 genomes];0.93[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7495566	0.83[AMR][1000 genomes];0.83[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs8024476	0.85[AMR][1000 genomes];0.93[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs8028294	0.80[ASN][1000 genomes]
rs8036703	0.86[AMR][1000 genomes];0.94[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs8037005	0.88[AFR][1000 genomes];0.87[AMR][1000 genomes];0.94[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs8043474	0.83[AFR][1000 genomes];0.87[AMR][1000 genomes];0.93[EUR][1000 genomes];0.93[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:31 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv542439	chr15:76762161-77196336	Enhancers Weak transcription Strong transcription ZNF genes & repeats Flanking Active TSS Active TSS Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA	9 gene(s)	inside rSNPs	diseases
2	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
3	nsv904400	chr15:76772062-77085283	Strong transcription Weak transcription Genic enhancers ZNF genes & repeats Enhancers Active TSS Flanking Active TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA	4 gene(s)	inside rSNPs	diseases
4	nsv1053924	chr15:76803849-77089079	Enhancers Strong transcription Flanking Active TSS ZNF genes & repeats Weak transcription Active TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA	4 gene(s)	inside rSNPs	diseases
5	nsv471254	chr15:76811390-76978139	Enhancers Strong transcription Weak transcription ZNF genes & repeats Flanking Active TSS Active TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA	2 gene(s)	inside rSNPs	diseases
6	nsv570021	chr15:76813920-76978139	Enhancers Weak transcription Flanking Active TSS ZNF genes & repeats Strong transcription Active TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA	2 gene(s)	inside rSNPs	diseases
7	nsv570022	chr15:76816015-76978139	ZNF genes & repeats Strong transcription Weak transcription Enhancers Genic enhancers Flanking Active TSS Active TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA	2 gene(s)	inside rSNPs	diseases
8	nsv904401	chr15:76816015-77085283	Strong transcription Enhancers ZNF genes & repeats Weak transcription Flanking Active TSS Genic enhancers Active TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA	4 gene(s)	inside rSNPs	diseases
9	nsv1042089	chr15:76855098-77016127	Weak transcription Enhancers ZNF genes & repeats Genic enhancers Strong transcription Flanking Active TSS Active TSS	TF binding region CpG island Chromatin interactive region miRNA	2 gene(s)	inside rSNPs	diseases
10	esv2830013	chr15:76863023-77176158	Weak transcription ZNF genes & repeats Strong transcription Enhancers Flanking Active TSS Genic enhancers Active TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA	4 gene(s)	inside rSNPs	diseases
11	nsv1042623	chr15:76863437-76999030	Weak transcription Enhancers Strong transcription ZNF genes & repeats Flanking Active TSS Active TSS Genic enhancers	TF binding region CpG island Chromatin interactive region miRNA	2 gene(s)	inside rSNPs	diseases
12	nsv1039269	chr15:76863437-77057021	Weak transcription Strong transcription Enhancers ZNF genes & repeats Flanking Active TSS Genic enhancers Active TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA	4 gene(s)	inside rSNPs	diseases
13	nsv904404	chr15:76869929-77033934	Strong transcription ZNF genes & repeats Weak transcription Enhancers Flanking Active TSS Genic enhancers Active TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA	3 gene(s)	inside rSNPs	diseases
14	nsv904405	chr15:76869929-77047915	Weak transcription Enhancers Strong transcription ZNF genes & repeats Genic enhancers Active TSS Flanking Active TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA	4 gene(s)	inside rSNPs	diseases
15	nsv904406	chr15:76869929-77085283	Weak transcription Strong transcription ZNF genes & repeats Enhancers Genic enhancers Flanking Active TSS Active TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA	4 gene(s)	inside rSNPs	diseases
16	nsv904407	chr15:76869929-77121196	Weak transcription Strong transcription Active TSS ZNF genes & repeats Enhancers Flanking Active TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA	4 gene(s)	inside rSNPs	diseases
17	nsv1052133	chr15:76878362-76962756	Weak transcription Enhancers ZNF genes & repeats Strong transcription Active TSS Genic enhancers Flanking Active TSS	TF binding region CpG island Chromatin interactive region miRNA	2 gene(s)	inside rSNPs	diseases
18	nsv570023	chr15:76884127-76978139	Weak transcription Enhancers Strong transcription ZNF genes & repeats Genic enhancers Active TSS Flanking Active TSS	TF binding region CpG island Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
19	nsv904408	chr15:76884127-77085283	Enhancers Weak transcription Strong transcription ZNF genes & repeats Genic enhancers Flanking Active TSS Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
20	nsv1046858	chr15:76892097-77020971	Weak transcription Strong transcription ZNF genes & repeats Enhancers Flanking Active TSS Genic enhancers Active TSS	TF binding region CpG island Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
21	nsv542440	chr15:76892097-77020971	Weak transcription ZNF genes & repeats Strong transcription Enhancers Genic enhancers Active TSS Flanking Active TSS	TF binding region CpG island Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
22	nsv1043066	chr15:76892097-77057021	Weak transcription ZNF genes & repeats Strong transcription Enhancers Flanking Active TSS Active TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
23	nsv542441	chr15:76892097-77057021	Weak transcription ZNF genes & repeats Strong transcription Enhancers Genic enhancers Flanking Active TSS Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
24	nsv1046137	chr15:76892097-77196336	ZNF genes & repeats Strong transcription Weak transcription Enhancers Flanking Active TSS Genic enhancers Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
25	nsv542442	chr15:76892097-77196336	ZNF genes & repeats Strong transcription Weak transcription Enhancers Genic enhancers Flanking Active TSS Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
26	nsv904409	chr15:76893186-77033934	Strong transcription ZNF genes & repeats Weak transcription Enhancers Genic enhancers Active TSS Flanking Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
27	nsv904410	chr15:76893186-77047915	ZNF genes & repeats Enhancers Strong transcription Active TSS Genic enhancers Weak transcription Flanking Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
28	nsv904411	chr15:76893186-77085283	Weak transcription ZNF genes & repeats Strong transcription Enhancers Genic enhancers Active TSS Flanking Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
29	nsv570109	chr15:76907376-76978139	Weak transcription Enhancers ZNF genes & repeats Strong transcription Active TSS Genic enhancers Flanking Active TSS	TF binding region Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
30	nsv904412	chr15:76910031-77085283	Weak transcription ZNF genes & repeats Strong transcription Enhancers Genic enhancers Flanking Active TSS Active TSS	TF binding region Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
31	nsv904413	chr15:76923917-76995150	ZNF genes & repeats Strong transcription Weak transcription Enhancers Genic enhancers Flanking Active TSS Active TSS	TF binding region Chromatin interactive region	1 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs2404733	SCAPER	cis	lung	GTEx
rs2404733	SCAPER	Cis_1M	lymphoblastoid	RTeQTL
rs2404733	SCAPER	cis	Artery Tibial	GTEx

Chromatin state (count:60 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:76882200-76991400	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
2	chr15:76898400-76981000	Weak transcription	Pancreas	Pancrea
3	chr15:76902600-76992000	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
4	chr15:76910000-76964200	Weak transcription	Brain Hippocampus Middle	brain
5	chr15:76910200-76959400	Weak transcription	Brain Substantia Nigra	brain
6	chr15:76911400-76990800	Weak transcription	Placenta	Placenta
7	chr15:76926200-76962000	Weak transcription	Gastric	stomach
8	chr15:76926600-76974600	Weak transcription	Esophagus	oesophagus
9	chr15:76929200-76954200	Weak transcription	Adipose Nuclei	Adipose
10	chr15:76929200-76955800	Weak transcription	Psoas Muscle	Psoas
11	chr15:76929200-76959200	Weak transcription	Monocytes-CD14+_RO01746	blood
12	chr15:76933200-76974800	Weak transcription	Thymus	Thymus
13	chr15:76933800-76961800	Weak transcription	Rectal Mucosa Donor 29	rectum
14	chr15:76934200-76954800	Weak transcription	Brain Germinal Matrix	brain
15	chr15:76936600-76991800	Weak transcription	Skeletal Muscle Male	skeletal muscle
16	chr15:76937400-76958000	Weak transcription	Fetal Lung	lung
17	chr15:76938800-76959000	Weak transcription	Duodenum Mucosa	Duodenum
18	chr15:76939000-76967800	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
19	chr15:76940000-76970800	Weak transcription	Placenta Amnion	Placenta Amnion
20	chr15:76940200-76960400	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
21	chr15:76940200-76991800	Weak transcription	Left Ventricle	heart
22	chr15:76941400-76959000	Weak transcription	Brain Inferior Temporal Lobe	brain
23	chr15:76941400-76991600	Weak transcription	Stomach Smooth Muscle	stomach
24	chr15:76941600-76955600	Weak transcription	Fetal Intestine Large	intestine
25	chr15:76941800-76954400	Weak transcription	Primary hematopoietic stem cells short term culture	blood
26	chr15:76941800-76956600	Weak transcription	Aorta	Aorta
27	chr15:76941800-76956800	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
28	chr15:76941800-76974200	Weak transcription	Fetal Stomach	stomach
29	chr15:76941800-76976200	Weak transcription	Fetal Muscle Leg	muscle
30	chr15:76942400-76991800	Weak transcription	Duodenum Smooth Muscle	Duodenum
31	chr15:76944400-76954400	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
32	chr15:76944400-76960400	Weak transcription	Skeletal Muscle Female	skeletal muscle
33	chr15:76944600-76956400	Weak transcription	Breast Myoepithelial Primary Cells	Breast
34	chr15:76944600-76973800	Weak transcription	Fetal Intestine Small	intestine
35	chr15:76946400-76959000	Weak transcription	Brain Anterior Caudate	brain
36	chr15:76946400-76961800	Weak transcription	Rectal Mucosa Donor 31	rectum
37	chr15:76947400-76959200	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
38	chr15:76947400-76959400	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
39	chr15:76947400-76962000	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
40	chr15:76947400-76991600	Weak transcription	Primary T cells fromperipheralblood	blood
41	chr15:76947400-76991600	Weak transcription	Sigmoid Colon	Sigmoid Colon
42	chr15:76947600-76957200	Weak transcription	Dnd41	blood
43	chr15:76947600-76962000	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
44	chr15:76948000-76958800	Weak transcription	Primary T helper cells fromperipheralblood	blood
45	chr15:76948200-76971000	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
46	chr15:76948400-76958200	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
47	chr15:76948600-76958800	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
48	chr15:76949000-76956400	Weak transcription	Fetal Heart	heart
49	chr15:76952000-76974600	Weak transcription	Right Ventricle	heart
50	chr15:76952400-76956200	Weak transcription	Primary T helper naive cells from peripheral blood	blood

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