Variant report

Variant	rs2468130
Chromosome Location	chr15:76796496-76796497
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 50 )
Associated
traits (count: 13 )

rSNPs within LD-proxies of this variant (count:46)

rs_ID	r²[population]
rs11072591	0.82[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs11072597	0.95[AFR][1000 genomes];0.84[AMR][1000 genomes];0.91[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs11072598	0.95[AFR][1000 genomes];0.84[AMR][1000 genomes];0.91[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs11629888	0.93[AFR][1000 genomes];0.81[AMR][1000 genomes];0.87[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs11632222	0.93[AFR][1000 genomes];0.81[AMR][1000 genomes];0.86[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs11635463	0.95[AFR][1000 genomes];0.84[AMR][1000 genomes];0.90[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs11637490	0.83[AMR][1000 genomes];0.89[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs11638767	0.82[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs11857015	0.90[AFR][1000 genomes];0.82[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs11857327	0.95[AFR][1000 genomes];0.84[AMR][1000 genomes];0.91[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs12900179	0.83[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs12903874	0.84[EUR][1000 genomes]
rs12906143	0.93[AFR][1000 genomes];0.81[AMR][1000 genomes];0.85[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs157783	0.86[ASN][1000 genomes]
rs1607015	0.93[AFR][1000 genomes];0.81[AMR][1000 genomes];0.85[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs2048856	1.00[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs206205	0.81[ASN][1000 genomes]
rs2280306	0.82[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs2436994	0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2436996	0.81[AFR][1000 genomes];0.83[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2454450	0.83[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2454454	0.80[AMR][1000 genomes];0.86[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2459361	0.81[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs2461871	0.83[AMR][1000 genomes];0.86[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2468131	1.00[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2469249	0.95[AFR][1000 genomes];0.94[ASN][1000 genomes]
rs283789	0.91[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs283793	0.93[ASN][1000 genomes]
rs283795	0.86[ASN][1000 genomes]
rs284899	0.86[ASN][1000 genomes]
rs284909	0.81[ASN][1000 genomes]
rs2957614	0.84[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs3765115	0.83[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs437131	0.85[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs4886493	0.83[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs4886495	0.81[AMR][1000 genomes];0.88[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs4886798	0.88[AFR][1000 genomes];0.84[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs4886800	0.86[AFR][1000 genomes];0.83[ASN][1000 genomes]
rs4886805	0.95[AFR][1000 genomes];0.82[AMR][1000 genomes];0.89[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs56246286	0.84[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs57682236	0.81[AFR][1000 genomes]
rs62028380	0.83[EUR][1000 genomes]
rs62028406	0.86[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs62028423	0.83[AMR][1000 genomes];0.89[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs62028434	0.85[AMR][1000 genomes];0.91[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs908817	0.80[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv542438	chr15:76697056-76892157	Weak transcription Strong transcription ZNF genes & repeats Enhancers Flanking Active TSS Genic enhancers Active TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA	3 gene(s)	inside rSNPs	diseases
2	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
3	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
4	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

mRNA abundance (count:13)

SNP	Gene	Cis/trans	Tissue	Source
rs2468130	SCAPER	cis	lung	GTEx
rs2468130	ISL2	Cis_1M	lymphoblastoid	RTeQTL
rs2468130	SCAPER	cis	Whole Blood	GTEx
rs2468130	SCAPER	cis	Artery Tibial	GTEx
rs2468130	SCAPER	cis	Thyroid	GTEx
rs2468130	SCAPER	cis	Skin Sun Exposed Lower leg	GTEx
rs2468130	SCAPER	cis	Nerve Tibial	GTEx
rs2468130	SCAPER	cis	Esophagus Mucosa	GTEx
rs2468130	SCAPER	cis	Esophagus Muscularis	GTEx
rs2468130	ISL2	cis	Whole Blood	GTEx
rs2468130	SCAPER	cis	Muscle Skeletal	GTEx
rs2468130	SCAPER	Cis_1M	lymphoblastoid	RTeQTL
rs2468130	SCAPER	cis	Adipose Subcutaneous	GTEx

Chromatin state (count:41 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:76725800-76812600	Weak transcription	Left Ventricle	heart
2	chr15:76785400-76799800	Weak transcription	Skeletal Muscle Female	skeletal muscle
3	chr15:76788000-76796600	Weak transcription	HSMM	muscle
4	chr15:76788200-76798400	Weak transcription	Dnd41	blood
5	chr15:76788400-76813600	Weak transcription	Primary T cells fromperipheralblood	blood
6	chr15:76789200-76796600	Weak transcription	Adipose Nuclei	Adipose
7	chr15:76790000-76802000	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
8	chr15:76791200-76806200	Weak transcription	Fetal Muscle Leg	muscle
9	chr15:76792600-76798600	Weak transcription	Monocytes-CD14+_RO01746	blood
10	chr15:76792600-76801800	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
11	chr15:76793800-76796600	Weak transcription	Ovary	ovary
12	chr15:76793800-76798600	Weak transcription	Placenta	Placenta
13	chr15:76793800-76799400	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
14	chr15:76794000-76810400	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
15	chr15:76794200-76798200	Weak transcription	Pancreas	Pancrea
16	chr15:76794200-76806400	Weak transcription	Gastric	stomach
17	chr15:76794400-76797200	Weak transcription	Lung	lung
18	chr15:76794600-76796600	Weak transcription	Primary B cells from peripheral blood	blood
19	chr15:76794800-76797200	Weak transcription	Thymus	Thymus
20	chr15:76794800-76801200	Weak transcription	Right Ventricle	heart
21	chr15:76795000-76797200	Strong transcription	Primary T cells from cord blood	blood
22	chr15:76795200-76796800	Strong transcription	Primary T helper naive cells fromperipheralblood	blood
23	chr15:76795200-76797600	Weak transcription	Fetal Muscle Trunk	muscle
24	chr15:76795200-76798400	Weak transcription	Brain Angular Gyrus	brain
25	chr15:76795200-76806800	Weak transcription	Brain Inferior Temporal Lobe	brain
26	chr15:76795400-76798200	Weak transcription	Esophagus	oesophagus
27	chr15:76795800-76810600	Weak transcription	Sigmoid Colon	Sigmoid Colon
28	chr15:76796200-76796600	Weak transcription	Fetal Stomach	stomach
29	chr15:76796200-76796800	Strong transcription	Breast Myoepithelial Primary Cells	Breast
30	chr15:76796200-76797000	Strong transcription	Primary hematopoietic stem cells	blood
31	chr15:76796200-76797200	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
32	chr15:76796200-76797200	Strong transcription	Liver	Liver
33	chr15:76796200-76797400	Strong transcription	Primary T helper cells fromperipheralblood	blood
34	chr15:76796200-76799400	Weak transcription	Duodenum Mucosa	Duodenum
35	chr15:76796400-76796800	Genic enhancers	Fetal Intestine Small	intestine
36	chr15:76796400-76797000	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
37	chr15:76796400-76797000	Strong transcription	Fetal Thymus	thymus
38	chr15:76796400-76797000	Strong transcription	Rectal Mucosa Donor 29	rectum
39	chr15:76796400-76797000	Strong transcription	Stomach Smooth Muscle	stomach
40	chr15:76796400-76797400	Strong transcription	Primary B cells from cord blood	blood
41	chr15:76796400-76805200	Weak transcription	Fetal Intestine Large	intestine

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