Variant report

Variant	rs28502289
Chromosome Location	chr15:44040532-44040533
allele	C/T
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	HCFC1	chr15:44040527-44041060	Hela-S3	cervix:	n/a	n/a
2	POLR2A	chr15:44040513-44040937	GM12878	blood:	n/a	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr15:44038791..44041212-chr15:44089540..44091517,2	MCF-7	breast:
2	chr15:44037743..44040701-chr15:44068299..44070156,3	MCF-7	breast:

Variant related genes	Relation type
CATSPER2P1	TF binding region
ENSG00000128886	Chromatin interaction
ENSG00000184716	Chromatin interaction
ENSG00000140264	Chromatin interaction

Extended variants
information (count: 92 )
Associated
traits (count: 12 )

rSNPs within LD-proxies of this variant (count:78)

rs_ID	r²[population]
rs10163054	0.80[AFR][1000 genomes];0.96[AMR][1000 genomes];0.92[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs10438303	0.88[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs11070407	0.92[AMR][1000 genomes];0.94[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs11070408	0.90[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs11070410	0.86[ASN][1000 genomes]
rs11852840	0.85[AMR][1000 genomes];0.89[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs11856184	0.80[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs11857661	0.83[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs12101756	0.81[AFR][1000 genomes];0.96[AMR][1000 genomes];0.92[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs12437808	0.91[AMR][1000 genomes];0.88[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12440573	0.83[AMR][1000 genomes]
rs12441127	0.88[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12441861	0.86[AMR][1000 genomes];0.89[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs12442129	0.82[AFR][1000 genomes];0.95[AMR][1000 genomes];0.89[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs12443102	0.89[EUR][1000 genomes]
rs12702	0.86[AMR][1000 genomes]
rs13380397	0.80[AFR][1000 genomes];0.90[AMR][1000 genomes];0.89[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs16950562	0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs16963953	0.91[AMR][1000 genomes];0.89[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs2228368	0.86[AMR][1000 genomes]
rs2277531	0.81[AFR][1000 genomes];0.83[ASN][1000 genomes]
rs2412810	0.87[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2447193	0.82[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs2447208	0.84[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs2447211	0.82[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs2447212	0.82[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs2467402	0.95[AMR][1000 genomes];0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2467426	0.88[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs2470121	0.84[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs2788	0.81[AFR][1000 genomes];0.93[AMR][1000 genomes];0.89[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs28433760	0.88[AMR][1000 genomes];0.94[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs28504496	0.88[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs28542007	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs28546844	0.86[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs28578041	0.86[AMR][1000 genomes];0.95[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs28578398	0.93[AMR][1000 genomes];0.89[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs28583806	0.86[AMR][1000 genomes]
rs28595038	0.82[AFR][1000 genomes];0.95[AMR][1000 genomes];0.95[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs28606452	0.89[EUR][1000 genomes]
rs28674750	0.86[AMR][1000 genomes]
rs28678901	0.91[AMR][1000 genomes];0.89[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs28684672	0.83[AMR][1000 genomes]
rs28718261	0.81[AFR][1000 genomes];0.96[AMR][1000 genomes];0.95[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs28891769	0.93[AMR][1000 genomes];0.89[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2915776	0.86[EUR][1000 genomes]
rs2915779	0.86[EUR][1000 genomes]
rs2915792	0.82[EUR][1000 genomes]
rs2920781	0.86[EUR][1000 genomes]
rs2927072	0.80[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs2927075	0.87[EUR][1000 genomes]
rs2957637	0.80[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs35457073	0.91[AFR][1000 genomes];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs3736180	0.85[AMR][1000 genomes]
rs3759791	0.86[AMR][1000 genomes]
rs3825783	0.85[AMR][1000 genomes]
rs4332723	0.97[ASN][1000 genomes]
rs4997480	0.92[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs56008017	0.81[AMR][1000 genomes]
rs57865312	0.89[EUR][1000 genomes]
rs60883262	0.80[AFR][1000 genomes];0.91[AMR][1000 genomes];0.89[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs62018952	0.85[ASN][1000 genomes]
rs7167976	0.84[AFR][1000 genomes]
rs7168158	0.82[AFR][1000 genomes];0.95[AMR][1000 genomes];0.92[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs7169988	0.81[AFR][1000 genomes];0.90[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs7170167	0.81[AFR][1000 genomes];0.90[AMR][1000 genomes];0.89[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs7171750	0.89[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7174208	0.80[AFR][1000 genomes];0.96[AMR][1000 genomes];0.92[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs7174732	0.90[ASN][1000 genomes]
rs7175032	0.81[AFR][1000 genomes];0.90[AMR][1000 genomes];0.89[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs7175129	0.97[ASN][1000 genomes]
rs7180818	0.83[ASN][1000 genomes]
rs72714307	0.81[AFR][1000 genomes];0.93[AMR][1000 genomes]
rs8023696	0.85[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs8029210	0.83[AFR][1000 genomes];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs8030169	0.82[AFR][1000 genomes];0.88[AMR][1000 genomes];0.93[ASN][1000 genomes]
rs8033846	0.88[ASN][1000 genomes]
rs8033995	0.88[AFR][1000 genomes];0.98[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs8042868	0.90[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:14 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv1846172	chr15:43632138-44116986	Bivalent Enhancer Weak transcription Genic enhancers Strong transcription Active TSS Enhancers Flanking Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	101 gene(s)	inside rSNPs	diseases
2	esv1846701	chr15:43759774-44116986	Strong transcription Weak transcription Active TSS Flanking Active TSS Enhancers Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	90 gene(s)	inside rSNPs	diseases
3	esv2758379	chr15:43823158-44148641	Strong transcription Enhancers Weak transcription Transcr. at gene 5' and 3' Flanking Active TSS Active TSS Bivalent/Poised TSS Genic enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	84 gene(s)	inside rSNPs	diseases
4	esv2760028	chr15:43823158-44148641	Genic enhancers Enhancers Active TSS Transcr. at gene 5' and 3' Weak transcription Strong transcription Flanking Active TSS ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	84 gene(s)	inside rSNPs	diseases
5	nsv427960	chr15:43823158-44148641	Flanking Active TSS Active TSS Strong transcription Weak transcription Transcr. at gene 5' and 3' ZNF genes & repeats Enhancers Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	84 gene(s)	inside rSNPs	diseases
6	esv2757598	chr15:43831923-44058634	Enhancers Weak transcription Flanking Active TSS Active TSS Strong transcription ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	31 gene(s)	inside rSNPs	diseases
7	nsv904150	chr15:43836478-44040965	Flanking Active TSS Enhancers Weak transcription Active TSS Strong transcription ZNF genes & repeats Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	31 gene(s)	inside rSNPs	diseases
8	nsv904158	chr15:43852043-44053617	Strong transcription Flanking Active TSS Active TSS Enhancers Weak transcription ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	31 gene(s)	inside rSNPs	diseases
9	nsv1037786	chr15:43888926-44318587	Weak transcription Flanking Active TSS Strong transcription Transcr. at gene 5' and 3' Enhancers Active TSS Genic enhancers Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	90 gene(s)	inside rSNPs	diseases
10	nsv542370	chr15:43888926-44318587	Weak transcription Genic enhancers Flanking Active TSS Active TSS Enhancers Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	90 gene(s)	inside rSNPs	diseases
11	nsv431387	chr15:43929378-44862930	Weak transcription Strong transcription Active TSS ZNF genes & repeats Enhancers Flanking Active TSS Bivalent/Poised TSS Bivalent Enhancer 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	158 gene(s)	inside rSNPs	diseases
12	nsv976928	chr15:43948866-44040886	Active TSS Enhancers Flanking Active TSS Bivalent Enhancer Weak transcription Transcr. at gene 5' and 3' Strong transcription Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	28 gene(s)	inside rSNPs	diseases
13	nsv931051	chr15:43988761-44833518	Strong transcription Enhancers Weak transcription Active TSS Flanking Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Genic enhancers Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	154 gene(s)	inside rSNPs	diseases
14	esv33661	chr15:44016519-44064420	Weak transcription Enhancers Strong transcription Flanking Active TSS Active TSS Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	19 gene(s)	inside rSNPs	diseases

mRNA abundance (count:12)

SNP	Gene	Cis/trans	Tissue	Source
rs28502289	CATSPER2	cis	Whole Blood	GTEx
rs28502289	ADAL	cis	lung	GTEx
rs28502289	ADAL	cis	Thyroid	GTEx
rs28502289	ADAL	cis	Esophagus Muscularis	GTEx
rs28502289	CKMT1A	cis	Skin Sun Exposed Lower leg	GTEx
rs28502289	CATSPER2	cis	Esophagus Mucosa	GTEx
rs28502289	AC011330.5	cis	Esophagus Mucosa	GTEx
rs28502289	ADAL	cis	Nerve Tibial	GTEx
rs28502289	ADAL	cis	Stomach	GTEx
rs28502289	ADAL	cis	Artery Tibial	GTEx
rs28502289	ELL3	Cis_1M	lymphoblastoid	RTeQTL
rs28502289	CKMT1A	cis	Esophagus Mucosa	GTEx

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:44037800-44040600	Active TSS	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
2	chr15:44037800-44040600	Active TSS	Psoas Muscle	Psoas
3	chr15:44037800-44040600	Active TSS	Stomach Smooth Muscle	stomach
4	chr15:44037800-44040600	Active TSS	HSMM	muscle
5	chr15:44037800-44041000	Active TSS	HUES6 Cell Line	embryonic stem cell
6	chr15:44037800-44041000	Active TSS	Brain Dorsolateral Prefrontal Cortex	brain
7	chr15:44037800-44041200	Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
8	chr15:44037800-44041800	Active TSS	Breast Myoepithelial Primary Cells	Breast
9	chr15:44037800-44042000	Active TSS	Colonic Mucosa	Colon
10	chr15:44037800-44042200	Active TSS	Foreskin Keratinocyte Primary Cells skin02	Skin
11	chr15:44038000-44040600	Active TSS	H9 Cell Line	embryonic stem cell
12	chr15:44038000-44040600	Active TSS	iPS-18 Cell Line	embryonic stem cell
13	chr15:44038000-44040600	Active TSS	iPS-20b Cell Line	embryonic stem cell
14	chr15:44038000-44040600	Active TSS	Foreskin Fibroblast Primary Cells skin02	Skin
15	chr15:44038000-44040600	Active TSS	Pancreatic Islets	Pancreatic Islet
16	chr15:44038000-44040600	Active TSS	A549	lung
17	chr15:44038000-44040600	Active TSS	NH-A	brain
18	chr15:44038000-44040600	Active TSS	NHDF-Ad	bronchial
19	chr15:44038000-44040800	Active TSS	Foreskin Melanocyte Primary Cells skin01	Skin
20	chr15:44038000-44041000	Active TSS	HUES48 Cell Line	embryonic stem cell
21	chr15:44038000-44041000	Active TSS	HUES64 Cell Line	embryonic stem cell
22	chr15:44038000-44041000	Active TSS	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
23	chr15:44038000-44041800	Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
24	chr15:44038000-44042000	Active TSS	NHLF	lung
25	chr15:44038200-44040600	Active TSS	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
26	chr15:44038200-44040600	Active TSS	Muscle Satellite Cultured Cells	--
27	chr15:44038200-44040600	Active TSS	K562	blood
28	chr15:44038200-44040800	Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
29	chr15:44038200-44041400	Active TSS	Foreskin Keratinocyte Primary Cells skin03	Skin
30	chr15:44038200-44041600	Active TSS	GM12878-XiMat	blood
31	chr15:44038800-44040600	Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
32	chr15:44038800-44041000	Active TSS	Right Atrium	heart
33	chr15:44039200-44040800	Flanking Active TSS	Monocytes-CD14+_RO01746	blood
34	chr15:44039200-44049400	Weak transcription	Spleen	Spleen
35	chr15:44039400-44040600	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
36	chr15:44039600-44040600	Active TSS	Skeletal Muscle Female	skeletal muscle
37	chr15:44039600-44041400	Weak transcription	Fetal Muscle Trunk	muscle
38	chr15:44039600-44041800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
39	chr15:44039600-44041800	Weak transcription	Gastric	stomach
40	chr15:44039600-44041800	Weak transcription	Lung	lung
41	chr15:44039600-44052000	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
42	chr15:44039600-44055400	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
43	chr15:44039800-44040800	Enhancers	Primary hematopoietic stem cells	blood
44	chr15:44039800-44040800	Enhancers	Primary mononuclear cells fromperipheralblood	Blood
45	chr15:44039800-44041200	Enhancers	Colon Smooth Muscle	Colon
46	chr15:44039800-44041800	Enhancers	Primary B cells from peripheral blood	blood
47	chr15:44039800-44042200	Enhancers	Primary monocytes fromperipheralblood	blood
48	chr15:44039800-44048800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
49	chr15:44040000-44040600	Flanking Active TSS	Adipose Nuclei	Adipose
50	chr15:44040000-44040600	Enhancers	Fetal Stomach	stomach

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