Variant report

Variant	rs1153847
Chromosome Location	chr15:45696890-45696891
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	POLR2A	chr15:45696842-45697011	HepG2	liver:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr15:45471561..45475350-chr15:45693833..45697444,3	MCF-7	breast:
2	chr15:45695514..45697340-chr15:45717063..45718801,2	MCF-7	breast:
3	chr15:45696319..45698017-chr15:45701079..45702699,2	MCF-7	breast:
4	chr15:45694563..45696942-chr15:45878361..45881039,2	K562	blood:

Variant related genes	Relation type
GATM	TF binding region
SPATA5L1	TF binding region
ENSG00000260170	Chromatin interaction
ENSG00000138606	Chromatin interaction
ENSG00000171763	Chromatin interaction
ENSG00000104164	Chromatin interaction

Extended variants
information (count: 130 )
Associated
traits (count: 14 )

rSNPs within LD-proxies of this variant (count:124)

rs_ID	r²[population]
rs10444821	0.81[AMR][1000 genomes];0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs1049503	0.82[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs1049508	1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs10519021	0.82[AMR][1000 genomes];0.88[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs10519022	0.81[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs11070453	0.81[AMR][1000 genomes];0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs11070454	0.82[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs11070456	0.82[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs11070457	0.82[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1145074	0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1145078	1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1145079	1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1145081	1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1145085	1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs1145091	1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs1153849	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1153854	0.96[AMR][1000 genomes];0.93[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs1153858	1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs11852800	0.82[AMR][1000 genomes];0.87[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs11855527	0.84[AMR][1000 genomes]
rs11858495	0.82[AMR][1000 genomes];0.87[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs12101539	0.81[AMR][1000 genomes];0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs12437840	0.82[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs12437887	0.82[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs12439274	0.82[AMR][1000 genomes];0.87[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs12439575	0.82[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12440038	0.82[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12441971	0.82[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs12591058	0.82[AMR][1000 genomes];0.87[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs12593230	0.95[EUR][1000 genomes]
rs12593370	0.82[EUR][1000 genomes]
rs12593371	0.87[EUR][1000 genomes]
rs12593402	0.82[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs12594857	0.82[AMR][1000 genomes];0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs12595087	0.82[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs12595153	0.82[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs1288775	1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs12909158	0.83[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs1346266	0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1346268	0.82[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1554521	0.82[AMR][1000 genomes];0.97[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs1613559	0.92[AMR][1000 genomes];0.83[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs1618874	0.92[AMR][1000 genomes];0.83[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs16942000	0.82[AMR][1000 genomes];0.88[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs16942568	0.82[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs16943246	0.91[EUR][1000 genomes]
rs1719247	0.92[AMR][1000 genomes];0.81[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs1820518	0.82[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1890565	0.82[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs1974981	0.88[EUR][1000 genomes]
rs1980288	0.83[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs2056493	0.81[AMR][1000 genomes];0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2066090	0.81[AMR][1000 genomes];0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2114501	0.81[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2172874	0.81[AMR][1000 genomes];0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2433611	1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2453541	1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2461701	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2467854	0.88[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2467858	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2467864	0.98[AMR][1000 genomes];0.87[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2486272	0.99[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs2668747	0.96[AMR][1000 genomes];0.82[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs28569043	0.89[EUR][1000 genomes]
rs28605551	0.85[EUR][1000 genomes]
rs28679834	0.82[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs3759899	0.82[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs3809472	0.82[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4271549	0.82[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs4395020	0.82[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs4534782	0.82[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs4572329	0.80[AMR][1000 genomes];0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs4625670	0.82[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs4627277	0.82[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs4774577	0.81[AMR][1000 genomes];0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs4774578	0.81[AMR][1000 genomes];0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs4774579	0.82[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs4774580	0.81[AMR][1000 genomes];0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs4775895	0.83[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs4775906	0.81[AMR][1000 genomes];0.87[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs4775907	0.82[AMR][1000 genomes];0.87[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs4775909	0.84[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs4775911	0.81[AMR][1000 genomes];0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs4775937	0.82[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs55885762	0.87[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs56669689	0.82[AMR][1000 genomes];0.87[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs56806728	0.82[AMR][1000 genomes];0.87[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs56850226	0.85[EUR][1000 genomes]
rs59889118	0.83[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs60476496	0.82[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs61365925	0.80[AMR][1000 genomes];0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs61524473	0.90[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs66528868	0.82[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs66714503	0.81[AMR][1000 genomes];0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs66939267	0.82[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs67045941	0.82[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs67461176	0.82[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs67744121	0.82[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs67831559	0.81[AMR][1000 genomes];0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs68087211	0.95[ASN][1000 genomes]
rs7163720	0.82[AMR][1000 genomes];0.87[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs7164139	0.82[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7164602	0.82[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7167900	0.82[AMR][1000 genomes];0.87[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs7168414	0.87[EUR][1000 genomes]
rs7169587	0.82[AMR][1000 genomes];0.87[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs7169818	0.98[AMR][1000 genomes];0.87[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs7171163	0.81[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs7171577	0.81[AMR][1000 genomes];0.87[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs7179743	0.82[AMR][1000 genomes];0.87[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs7181167	0.82[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7182300	0.82[AMR][1000 genomes];0.88[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs7182723	0.82[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7183946	0.82[AMR][1000 genomes];0.88[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs72623915	0.81[AMR][1000 genomes];0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7402632	0.81[AMR][1000 genomes];0.98[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs7402650	0.81[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7494956	0.82[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs8032904	0.82[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs8038342	0.82[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs8039476	0.83[AMR][1000 genomes]
rs8042786	0.82[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs9783731	0.84[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs9788780	0.82[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[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
rs1153847	SPATA5L1	Cis_1M	lymphoblastoid	RTeQTL
rs1153847	CTD-2651B20.3	cis	Thyroid	GTEx
rs1153847	CTD-2651B20.3	cis	Artery Tibial	GTEx
rs1153847	SPATA5L1	cis	Adipose Subcutaneous	GTEx
rs1153847	CTD-2651B20.3	cis	Adipose Subcutaneous	GTEx
rs1153847	CTD-2651B20.3	cis	lung	GTEx
rs1153847	GATM	cis	Muscle Skeletal	GTEx
rs1153847	CTD-2651B20.4	cis	Nerve Tibial	GTEx
rs1153847	CTD-2651B20.4	cis	Artery Tibial	GTEx
rs1153847	SPATA5L1	cis	Thyroid	GTEx
rs1153847	CTD-2651B20.3	cis	Nerve Tibial	GTEx
rs1153847	SPATA5L1	cis	Whole Blood	GTEx
rs1153847	CTD-2651B20.3	cis	Esophagus Muscularis	GTEx
rs1153847	CTD-2651B20.3	cis	Muscle Skeletal	GTEx

Chromatin state (count:127 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:45693400-45697000	Active TSS	Fetal Intestine Large	intestine
2	chr15:45693400-45697600	Active TSS	GM12878-XiMat	blood
3	chr15:45693600-45697000	Active TSS	HUES6 Cell Line	embryonic stem cell
4	chr15:45693600-45697200	Active TSS	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
5	chr15:45695200-45697400	Active TSS	Foreskin Fibroblast Primary Cells skin02	Skin
6	chr15:45695600-45697000	Flanking Active TSS	H9 Derived Neuron Cultured Cells	ES cell derived
7	chr15:45695600-45697000	Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
8	chr15:45695600-45697000	Flanking Active TSS	Foreskin Melanocyte Primary Cells skin03	Skin
9	chr15:45695800-45697000	Flanking Active TSS	Cortex derived primary cultured neurospheres	brain
10	chr15:45695800-45697000	Flanking Active TSS	Brain Hippocampus Middle	brain
11	chr15:45695800-45697000	Enhancers	Spleen	Spleen
12	chr15:45696000-45697000	Flanking Active TSS	Muscle Satellite Cultured Cells	--
13	chr15:45696000-45699200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
14	chr15:45696000-45699200	Weak transcription	Esophagus	oesophagus
15	chr15:45696000-45699400	Weak transcription	Gastric	stomach
16	chr15:45696000-45703000	Weak transcription	Lung	lung
17	chr15:45696000-45703200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
18	chr15:45696000-45703200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
19	chr15:45696200-45697000	Flanking Active TSS	Breast Myoepithelial Primary Cells	Breast
20	chr15:45696200-45697000	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
21	chr15:45696200-45697000	Enhancers	Foreskin Melanocyte Primary Cells skin01	Skin
22	chr15:45696200-45697000	Flanking Active TSS	HMEC	breast
23	chr15:45696200-45697200	Enhancers	Primary B cells from peripheral blood	blood
24	chr15:45696200-45697200	Weak transcription	Placenta	Placenta
25	chr15:45696200-45697400	Enhancers	Primary monocytes fromperipheralblood	blood
26	chr15:45696200-45700800	Weak transcription	Placenta Amnion	Placenta Amnion
27	chr15:45696200-45703600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
28	chr15:45696200-45707400	Weak transcription	Small Intestine	intestine
29	chr15:45696200-45712800	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
30	chr15:45696400-45697000	Enhancers	Primary T cells fromperipheralblood	blood
31	chr15:45696400-45697000	Enhancers	Brain Dorsolateral Prefrontal Cortex	brain
32	chr15:45696400-45697000	Enhancers	Colonic Mucosa	Colon
33	chr15:45696400-45697000	Active TSS	Fetal Intestine Small	intestine
34	chr15:45696400-45697000	Enhancers	Fetal Muscle Trunk	muscle
35	chr15:45696400-45697000	Genic enhancers	Fetal Muscle Leg	muscle
36	chr15:45696400-45697000	Enhancers	Fetal Thymus	thymus
37	chr15:45696400-45697000	Enhancers	Thymus	Thymus
38	chr15:45696400-45697400	Enhancers	Primary hematopoietic stem cells	blood
39	chr15:45696400-45697800	Enhancers	Primary T helper 17 cells PMA-I stimulated	--
40	chr15:45696400-45699000	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
41	chr15:45696400-45699200	Weak transcription	Sigmoid Colon	Sigmoid Colon
42	chr15:45696400-45703400	Weak transcription	Aorta	Aorta
43	chr15:45696600-45697000	Active TSS	HUES48 Cell Line	embryonic stem cell
44	chr15:45696600-45697000	Enhancers	Adipose Nuclei	Adipose
45	chr15:45696600-45697000	Enhancers	Colon Smooth Muscle	Colon
46	chr15:45696600-45697000	Enhancers	Psoas Muscle	Psoas
47	chr15:45696600-45697000	Enhancers	Rectal Mucosa Donor 31	rectum
48	chr15:45696600-45697000	Enhancers	Right Atrium	heart
49	chr15:45696600-45697000	Enhancers	Skeletal Muscle Male	skeletal muscle
50	chr15:45696600-45697200	Weak transcription	H1 Cell Line	embryonic stem cell

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