Variant report

Variant	rs2486274
Chromosome Location	chr15:45666228-45666229
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 78 )
Associated
traits (count: 14 )

rSNPs within LD-proxies of this variant (count:72)

rs_ID	r²[population]
rs1049518	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10519018	1.00[CHB][hapmap]
rs1060896	1.00[CHB][hapmap]
rs1145076	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1145077	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1145080	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1145084	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1145086	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1145089	1.00[CHB][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1145093	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1145097	0.98[AMR][1000 genomes];0.91[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs1153845	0.85[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs1153855	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1153857	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1153860	0.85[AFR][1000 genomes];0.98[AMR][1000 genomes];0.91[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1153862	0.82[AFR][1000 genomes];0.98[AMR][1000 genomes];0.91[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs11632752	1.00[CHB][hapmap]
rs11632778	1.00[CHB][hapmap]
rs11632920	1.00[CHB][hapmap]
rs11636114	0.88[AMR][1000 genomes]
rs11637838	1.00[CHB][hapmap]
rs11637920	1.00[CHB][hapmap]
rs11639420	1.00[CHB][hapmap]
rs11855414	0.90[AMR][1000 genomes]
rs12904150	1.00[CHB][hapmap]
rs12908818	1.00[CHB][hapmap]
rs12909409	0.90[AMR][1000 genomes]
rs12910764	0.90[AMR][1000 genomes]
rs12911186	1.00[CHB][hapmap]
rs12915314	1.00[CHB][hapmap]
rs1346267	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1426932	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1547487	0.85[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs1617634	0.98[AMR][1000 genomes];0.87[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs1617984	1.00[CHB][hapmap];0.98[AMR][1000 genomes];0.88[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs1706770	1.00[CHB][hapmap]
rs1719231	1.00[CHB][hapmap]
rs1719245	0.98[AMR][1000 genomes];0.88[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs1719246	1.00[CEU][hapmap];0.98[AMR][1000 genomes];0.91[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs1719250	0.91[CEU][hapmap];1.00[CHB][hapmap]
rs17536527	1.00[CHB][hapmap]
rs2002035	0.86[AMR][1000 genomes];0.82[ASN][1000 genomes]
rs2015295	0.85[AMR][1000 genomes];0.82[ASN][1000 genomes]
rs2413768	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs2413772	1.00[CHB][hapmap]
rs2413774	1.00[CHB][hapmap]
rs2433601	0.85[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2433616	0.85[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs2453533	0.85[AFR][1000 genomes];0.98[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2461700	0.85[AFR][1000 genomes];0.98[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2461705	1.00[CHB][hapmap]
rs2467853	1.00[CEU][hapmap];0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2467858	0.89[YRI][hapmap]
rs2467862	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2467865	0.85[AFR][1000 genomes];0.98[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2486288	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2899375	0.88[AMR][1000 genomes]
rs35861938	0.85[AFR][1000 genomes];0.98[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6493143	1.00[CHB][hapmap]
rs6493144	1.00[CHB][hapmap]
rs6493145	1.00[CHB][hapmap]
rs7165039	1.00[CHB][hapmap]
rs7166580	1.00[CHB][hapmap]
rs7167146	1.00[CHB][hapmap]
rs7171312	1.00[CHB][hapmap]
rs8024620	1.00[CHB][hapmap]
rs8039138	1.00[CHB][hapmap]
rs8039352	1.00[CHB][hapmap]
rs8039354	1.00[CHB][hapmap]
rs8039540	1.00[CHB][hapmap]
rs872192	1.00[CEU][hapmap];1.00[CHB][hapmap];0.98[AMR][1000 genomes];0.85[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs9921008	0.86[AMR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:6 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv916374	chr15:45058112-45769052	Enhancers Active TSS Flanking Active TSS Bivalent/Poised TSS Strong transcription ZNF genes & repeats Weak transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	104 gene(s)	inside rSNPs	diseases
2	nsv932147	chr15:45319178-45872076	Bivalent/Poised TSS Enhancers Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh Weak transcription Strong transcription ZNF genes & repeats Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	87 gene(s)	inside rSNPs	diseases
3	nsv869616	chr15:45401411-45736209	Active TSS Enhancers Weak transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS Flanking Active TSS Strong transcription Bivalent Enhancer Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	76 gene(s)	inside rSNPs	diseases
4	nsv569315	chr15:45446156-45772448	Flanking Active TSS Weak transcription Active TSS Enhancers Flanking Bivalent TSS/Enh Strong transcription ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	75 gene(s)	inside rSNPs	diseases
5	nsv469721	chr15:45608881-45788002	Strong transcription Enhancers Bivalent Enhancer Weak transcription Flanking Active TSS Genic enhancers Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	54 gene(s)	inside rSNPs	diseases
6	nsv482380	chr15:45608881-45788002	Weak transcription Enhancers Active TSS Bivalent Enhancer Strong transcription Flanking Active TSS ZNF genes & repeats Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	54 gene(s)	inside rSNPs	diseases

mRNA abundance (count:14)

SNP	Gene	Cis/trans	Tissue	Source
rs2486274	CTD-2651B20.3	cis	lung	GTEx
rs2486274	CTD-2651B20.3	cis	Thyroid	GTEx
rs2486274	SPATA5L1	Cis_1M	lymphoblastoid	RTeQTL
rs2486274	CTD-2651B20.4	cis	Skin Sun Exposed Lower leg	GTEx
rs2486274	CTD-2651B20.3	cis	Esophagus Muscularis	GTEx
rs2486274	CTD-2651B20.3	cis	Artery Tibial	GTEx
rs2486274	CTD-2651B20.3	cis	Nerve Tibial	GTEx
rs2486274	CTD-2651B20.4	cis	Artery Tibial	GTEx
rs2486274	CTD-2651B20.3	cis	Adipose Subcutaneous	GTEx
rs2486274	CTD-2651B20.3	cis	Skin Sun Exposed Lower leg	GTEx
rs2486274	CTD-2651B20.3	cis	Muscle Skeletal	GTEx
rs2486274	CTD-2651B20.3	cis	Artery Aorta	GTEx
rs2486274	CTD-2651B20.3	cis	Heart Left Ventricle	GTEx
rs2486274	CTD-2651B20.4	cis	Nerve Tibial	GTEx

Chromatin state (count:58 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:45648200-45668600	Weak transcription	Colonic Mucosa	Colon
2	chr15:45650600-45668000	Weak transcription	Right Ventricle	heart
3	chr15:45652600-45668800	Weak transcription	Spleen	Spleen
4	chr15:45652800-45669800	Weak transcription	Lung	lung
5	chr15:45653000-45667000	Weak transcription	Placenta	Placenta
6	chr15:45654200-45668800	Weak transcription	Primary hematopoietic stem cells short term culture	blood
7	chr15:45655200-45668000	Weak transcription	Fetal Brain Male	brain
8	chr15:45656400-45668400	Weak transcription	Psoas Muscle	Psoas
9	chr15:45658400-45667600	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
10	chr15:45658400-45668000	Weak transcription	Esophagus	oesophagus
11	chr15:45658400-45668000	Weak transcription	Gastric	stomach
12	chr15:45658400-45669600	Weak transcription	Aorta	Aorta
13	chr15:45658600-45668600	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
14	chr15:45659000-45667400	Weak transcription	Adipose Nuclei	Adipose
15	chr15:45659000-45668200	Weak transcription	Breast Myoepithelial Primary Cells	Breast
16	chr15:45660400-45667800	Weak transcription	Skeletal Muscle Male	skeletal muscle
17	chr15:45660800-45667000	Weak transcription	Fetal Stomach	stomach
18	chr15:45660800-45668600	Weak transcription	Left Ventricle	heart
19	chr15:45661000-45668600	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
20	chr15:45661600-45668400	Weak transcription	Primary B cells from peripheral blood	blood
21	chr15:45662000-45667200	Weak transcription	Stomach Smooth Muscle	stomach
22	chr15:45662200-45667600	Weak transcription	Fetal Muscle Leg	muscle
23	chr15:45662400-45667600	Weak transcription	Ovary	ovary
24	chr15:45662800-45668400	Weak transcription	GM12878-XiMat	blood
25	chr15:45663200-45666400	Enhancers	Cortex derived primary cultured neurospheres	brain
26	chr15:45663200-45666800	Weak transcription	Pancreas	Pancrea
27	chr15:45663600-45666600	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
28	chr15:45663600-45666800	Enhancers	Fetal Intestine Large	intestine
29	chr15:45663600-45667000	Enhancers	Fetal Intestine Small	intestine
30	chr15:45664000-45666800	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
31	chr15:45664000-45666800	Weak transcription	Fetal Muscle Trunk	muscle
32	chr15:45664200-45666400	Enhancers	Stomach Mucosa	stomach
33	chr15:45664400-45667800	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
34	chr15:45664400-45669600	Weak transcription	Small Intestine	intestine
35	chr15:45664400-45669800	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
36	chr15:45664600-45668200	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
37	chr15:45665000-45667600	Weak transcription	Rectal Smooth Muscle	rectum
38	chr15:45665000-45668000	Weak transcription	Rectal Mucosa Donor 31	rectum
39	chr15:45665000-45668200	Weak transcription	Rectal Mucosa Donor 29	rectum
40	chr15:45665000-45668200	Weak transcription	HSMMtube	muscle
41	chr15:45665000-45668400	Weak transcription	Sigmoid Colon	Sigmoid Colon
42	chr15:45665200-45667000	Enhancers	Brain Cingulate Gyrus	brain
43	chr15:45665200-45667800	Weak transcription	HSMM	muscle
44	chr15:45665200-45668000	Weak transcription	Brain Germinal Matrix	brain
45	chr15:45665200-45668000	Enhancers	Brain Inferior Temporal Lobe	brain
46	chr15:45665200-45668000	Weak transcription	Fetal Brain Female	brain
47	chr15:45665400-45667800	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
48	chr15:45665800-45666400	Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
49	chr15:45665800-45666400	Flanking Active TSS	Brain Anterior Caudate	brain
50	chr15:45666000-45666400	Genic enhancers	Skeletal Muscle Female	skeletal muscle

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