Variant report

Variant	rs2461701
Chromosome Location	chr15:45703391-45703392
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr15:45693480..45696046-chr15:45703264..45708561,5	K562	blood:

Variant related genes	Relation type
ENSG00000171766	Chromatin interaction
ENSG00000171763	Chromatin interaction

Extended variants
information (count: 132 )
Associated
traits (count: 14 )

rSNPs within LD-proxies of this variant (count:126)

rs_ID	r²[population]
rs10444821	0.81[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1049503	0.82[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1049508	1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs10519021	0.82[AMR][1000 genomes];0.87[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs10519022	0.81[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs11070453	0.81[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs11070454	0.82[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs11070456	0.82[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs11070457	0.82[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1145074	0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1145078	1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1145079	1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1145081	1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1145085	1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1145091	1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1153847	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1153849	1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1153854	0.96[AMR][1000 genomes];0.93[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs1153858	1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs11852800	0.82[AMR][1000 genomes];0.87[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs11855527	0.84[AMR][1000 genomes]
rs11858495	0.82[AMR][1000 genomes];0.87[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs12101539	0.81[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12437840	0.82[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12437887	0.82[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12439274	0.82[AMR][1000 genomes];0.87[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs12439575	0.82[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12440038	0.82[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12441971	0.82[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12591058	0.82[AMR][1000 genomes];0.87[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs12593230	0.94[EUR][1000 genomes]
rs12593370	0.82[EUR][1000 genomes]
rs12593371	0.86[EUR][1000 genomes]
rs12593402	0.82[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs12594857	0.82[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12595087	0.82[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12595153	0.82[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1288775	1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12909158	0.82[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs1346266	0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1346268	0.82[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1554521	0.82[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1613559	0.92[AMR][1000 genomes];0.82[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs1618874	0.92[AMR][1000 genomes];0.82[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs16942000	0.82[AMR][1000 genomes];0.87[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs16942568	0.82[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs16943246	0.90[EUR][1000 genomes]
rs1719247	0.92[AMR][1000 genomes];0.80[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs1820518	0.82[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1890565	0.82[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1974981	0.88[EUR][1000 genomes]
rs1980288	0.82[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs2056493	0.81[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2066090	0.81[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2114501	0.81[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2172874	0.81[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2433611	1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2453541	1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2467853	0.80[AFR][1000 genomes]
rs2467854	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2467858	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2467864	0.98[AMR][1000 genomes];0.87[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2486272	0.99[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs2486288	0.80[AFR][1000 genomes]
rs2668747	0.96[AMR][1000 genomes];0.82[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs28569043	0.88[EUR][1000 genomes]
rs28605551	0.85[EUR][1000 genomes]
rs28679834	0.81[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs3759899	0.82[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs3809472	0.82[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4271549	0.82[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4395020	0.82[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4534782	0.82[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4572329	0.80[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4625670	0.82[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4627277	0.82[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4774577	0.81[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4774578	0.81[AMR][1000 genomes];0.94[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4774579	0.82[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4774580	0.81[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4775895	0.82[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs4775906	0.81[AMR][1000 genomes];0.87[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs4775907	0.82[AMR][1000 genomes];0.87[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs4775909	0.84[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4775911	0.81[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4775937	0.82[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs55885762	0.87[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs56669689	0.82[AMR][1000 genomes];0.87[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs56806728	0.82[AMR][1000 genomes];0.87[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs56850226	0.84[EUR][1000 genomes]
rs59889118	0.82[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs60476496	0.82[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs61365925	0.80[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs61524473	0.89[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs66528868	0.82[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs66714503	0.81[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs66939267	0.82[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs67045941	0.82[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs67461176	0.82[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs67744121	0.82[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs67831559	0.81[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs68087211	0.96[ASN][1000 genomes]
rs7163720	0.82[AMR][1000 genomes];0.87[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs7164139	0.82[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7164602	0.82[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7167900	0.82[AMR][1000 genomes];0.87[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs7168414	0.86[EUR][1000 genomes]
rs7169587	0.82[AMR][1000 genomes];0.87[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs7169818	0.98[AMR][1000 genomes];0.87[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs7171163	0.81[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs7171577	0.81[AMR][1000 genomes];0.87[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs7179743	0.82[AMR][1000 genomes];0.87[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs7181167	0.82[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7182300	0.82[AMR][1000 genomes];0.87[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs7182723	0.82[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7183946	0.82[AMR][1000 genomes];0.87[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs72623915	0.81[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7402632	0.81[AMR][1000 genomes];0.99[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7402650	0.81[AMR][1000 genomes];0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7494956	0.82[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs8032904	0.82[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs8038342	0.82[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs8039476	0.83[AMR][1000 genomes]
rs8042786	0.82[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9783731	0.84[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs9788780	0.82[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][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
rs2461701	GATM	cis	Muscle Skeletal	GTEx
rs2461701	CTD-2651B20.4	cis	Artery Tibial	GTEx
rs2461701	SPATA5L1	cis	Whole Blood	GTEx
rs2461701	SPATA5L1	Cis_1M	lymphoblastoid	RTeQTL
rs2461701	CTD-2651B20.3	cis	lung	GTEx
rs2461701	SPATA5L1	cis	Thyroid	GTEx
rs2461701	CTD-2651B20.3	cis	Adipose Subcutaneous	GTEx
rs2461701	CTD-2651B20.3	cis	Thyroid	GTEx
rs2461701	CTD-2651B20.3	cis	Muscle Skeletal	GTEx
rs2461701	CTD-2651B20.3	cis	Nerve Tibial	GTEx
rs2461701	CTD-2651B20.3	cis	Artery Tibial	GTEx
rs2461701	CTD-2651B20.4	cis	Nerve Tibial	GTEx
rs2461701	SPATA5L1	cis	Adipose Subcutaneous	GTEx
rs2461701	CTD-2651B20.3	cis	Esophagus Muscularis	GTEx

Chromatin state (count:126 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:45696200-45703600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
2	chr15:45696200-45707400	Weak transcription	Small Intestine	intestine
3	chr15:45696200-45712800	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
4	chr15:45696400-45703400	Weak transcription	Aorta	Aorta
5	chr15:45696600-45711000	Weak transcription	Stomach Mucosa	stomach
6	chr15:45696600-45715000	Strong transcription	iPS-20b Cell Line	embryonic stem cell
7	chr15:45696600-45718400	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
8	chr15:45696800-45706000	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
9	chr15:45696800-45714800	Strong transcription	HUES64 Cell Line	embryonic stem cell
10	chr15:45697000-45711000	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
11	chr15:45697000-45722200	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
12	chr15:45697200-45703400	Strong transcription	HSMM	muscle
13	chr15:45697200-45706000	Strong transcription	Brain Substantia Nigra	brain
14	chr15:45697200-45706400	Strong transcription	Skeletal Muscle Male	skeletal muscle
15	chr15:45697200-45712400	Strong transcription	Placenta	Placenta
16	chr15:45697200-45713800	Strong transcription	H1 Cell Line	embryonic stem cell
17	chr15:45697200-45714200	Strong transcription	Osteobl	bone
18	chr15:45697200-45715200	Strong transcription	HUES48 Cell Line	embryonic stem cell
19	chr15:45697200-45715200	Strong transcription	HUES6 Cell Line	embryonic stem cell
20	chr15:45697400-45703400	Weak transcription	Pancreatic Islets	Pancreatic Islet
21	chr15:45697400-45704800	Strong transcription	Primary hematopoietic stem cells short term culture	blood
22	chr15:45697400-45705800	Strong transcription	Fetal Intestine Large	intestine
23	chr15:45697400-45712000	Strong transcription	Foreskin Fibroblast Primary Cells skin01	Skin
24	chr15:45697400-45713400	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
25	chr15:45697400-45713600	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
26	chr15:45697400-45714600	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
27	chr15:45697400-45714800	Strong transcription	Skeletal Muscle Female	skeletal muscle
28	chr15:45697400-45715200	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
29	chr15:45697400-45715200	Strong transcription	Adipose Nuclei	Adipose
30	chr15:45697400-45716000	Strong transcription	Primary neutrophils fromperipheralblood	blood
31	chr15:45697400-45716200	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
32	chr15:45697400-45716400	Strong transcription	Rectal Mucosa Donor 29	rectum
33	chr15:45697600-45703600	Strong transcription	Muscle Satellite Cultured Cells	--
34	chr15:45697600-45703800	Strong transcription	Colon Smooth Muscle	Colon
35	chr15:45697600-45704800	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
36	chr15:45697600-45704800	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
37	chr15:45697600-45706000	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
38	chr15:45697600-45706000	Strong transcription	Rectal Mucosa Donor 31	rectum
39	chr15:45697600-45710000	Strong transcription	Primary hematopoietic stem cells	blood
40	chr15:45697600-45712800	Strong transcription	Brain Cingulate Gyrus	brain
41	chr15:45697600-45713400	Strong transcription	Fetal Muscle Trunk	muscle
42	chr15:45697600-45714800	Strong transcription	iPS-18 Cell Line	embryonic stem cell
43	chr15:45697600-45715200	Strong transcription	Primary B cells from peripheral blood	blood
44	chr15:45697600-45715200	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
45	chr15:45697600-45715200	Strong transcription	Duodenum Smooth Muscle	Duodenum
46	chr15:45697600-45715200	Strong transcription	Fetal Thymus	thymus
47	chr15:45697600-45715800	Strong transcription	Monocytes-CD14+_RO01746	blood
48	chr15:45697800-45705000	Strong transcription	Liver	Liver
49	chr15:45697800-45705400	Strong transcription	Breast Myoepithelial Primary Cells	Breast
50	chr15:45697800-45707000	Strong transcription	Fetal Lung	lung

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