Variant report

Variant	rs28758627
Chromosome Location	chr15:43642328-43642329
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr15:43641400..43644347-chr15:43658323..43660227,2	K562	blood:
2	chr15:43621200..43623287-chr15:43640681..43643730,3	MCF-7	breast:

Variant related genes	Relation type
ENSG00000168806	Chromatin interaction
ENSG00000168803	Chromatin interaction

Extended variants
information (count: 73 )
Associated
traits (count: 12 )

rSNPs within LD-proxies of this variant (count:68)

rs_ID	r²[population]
rs1095386	0.86[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs1123947	0.89[AMR][1000 genomes]
rs11858152	0.88[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs12101673	0.89[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs12323999	0.83[AMR][1000 genomes]
rs12324572	0.92[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs12324584	0.84[AMR][1000 genomes]
rs12440854	0.86[EUR][1000 genomes]
rs1549523	0.88[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs1549525	0.88[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs16957627	0.95[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs16957630	0.95[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs16957632	0.95[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs2243434	0.83[AMR][1000 genomes]
rs2256764	0.84[AMR][1000 genomes]
rs2278858	0.87[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs2278859	0.89[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs2278860	0.89[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs2412778	0.90[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs2412779	0.89[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs2412780	0.89[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs2412782	0.81[AMR][1000 genomes]
rs2439841	0.84[AMR][1000 genomes]
rs2584702	0.83[AMR][1000 genomes]
rs2601014	0.80[AMR][1000 genomes]
rs28415933	0.92[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs28461955	0.89[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs28578454	0.90[AMR][1000 genomes];0.87[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs28594657	0.82[EUR][1000 genomes]
rs28729853	0.89[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs2899082	0.89[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs3213990	0.90[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs3213991	0.89[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs3742969	0.88[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs3742971	0.88[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs3809481	0.90[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4075674	0.90[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs45585139	0.84[AMR][1000 genomes];0.81[ASN][1000 genomes]
rs4583210	0.89[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs471229	0.82[AMR][1000 genomes]
rs478104	0.88[AMR][1000 genomes]
rs484029	0.91[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs484846	0.89[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs488756	0.84[AMR][1000 genomes]
rs491648	0.86[AMR][1000 genomes];0.83[ASN][1000 genomes]
rs498837	0.86[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs511673	0.86[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs527921	0.81[AMR][1000 genomes]
rs528517	0.85[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs540031	0.86[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs6493081	0.94[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs6493082	0.94[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs6493085	0.90[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs6493087	0.89[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs6493088	0.90[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs7163245	0.87[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs7165471	0.94[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs7168940	0.89[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs7170489	0.95[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs7175434	0.88[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs8033714	0.90[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs8039638	0.92[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs8041132	0.94[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs825739	0.88[AMR][1000 genomes]
rs825740	0.89[AMR][1000 genomes]
rs933941	0.94[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs935901	0.97[EUR][1000 genomes]
rs956391	0.86[AMR][1000 genomes];0.80[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:5 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1044522	chr15:43115348-43658417	Strong transcription Weak transcription Flanking Active TSS Transcr. at gene 5' and 3' Enhancers Active TSS Genic enhancers Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	47 gene(s)	inside rSNPs	diseases
2	nsv1044508	chr15:43270637-43658417	Weak transcription Genic enhancers Strong transcription Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Active TSS Active TSS Enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	43 gene(s)	inside rSNPs	diseases
3	nsv534649	chr15:43591116-43851142	Flanking Active TSS Weak transcription Active TSS Transcr. at gene 5' and 3' Strong transcription Enhancers Genic enhancers Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	45 gene(s)	inside rSNPs	diseases
4	nsv1512	chr15:43616834-43661646	Strong transcription Flanking Active TSS Weak transcription ZNF genes & repeats Genic enhancers Enhancers Transcr. at gene 5' and 3' Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	21 gene(s)	inside rSNPs	diseases
5	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

mRNA abundance (count:12)

SNP	Gene	Cis/trans	Tissue	Source
rs28758627	ADAL	cis	Esophagus Muscularis	GTEx
rs28758627	ADAL	cis	Adipose Subcutaneous	GTEx
rs28758627	CKMT1A	cis	Esophagus Mucosa	GTEx
rs28758627	ELL3	Cis_1M	lymphoblastoid	RTeQTL
rs28758627	ADAL	cis	Thyroid	GTEx
rs28758627	ADAL	cis	Stomach	GTEx
rs28758627	CATSPER2	cis	Esophagus Mucosa	GTEx
rs28758627	ADAL	cis	Artery Tibial	GTEx
rs28758627	ADAL	cis	Artery Aorta	GTEx
rs28758627	ADAL	cis	lung	GTEx
rs28758627	ADAL	cis	Skin Sun Exposed Lower leg	GTEx
rs28758627	ADAL	cis	Nerve Tibial	GTEx

Chromatin state (count:119 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:43623200-43651000	Weak transcription	Placenta Amnion	Placenta Amnion
2	chr15:43623200-43651600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
3	chr15:43623200-43651600	Weak transcription	Pancreas	Pancrea
4	chr15:43623400-43644000	Weak transcription	Fetal Thymus	thymus
5	chr15:43623400-43649200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
6	chr15:43623400-43650400	Weak transcription	Fetal Brain Male	brain
7	chr15:43623400-43651000	Weak transcription	Gastric	stomach
8	chr15:43623400-43651000	Weak transcription	Small Intestine	intestine
9	chr15:43623400-43653200	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
10	chr15:43623600-43642600	Weak transcription	Primary hematopoietic stem cells short term culture	blood
11	chr15:43623600-43642600	Weak transcription	Rectal Smooth Muscle	rectum
12	chr15:43623600-43643200	Weak transcription	Primary monocytes fromperipheralblood	blood
13	chr15:43623600-43644000	Weak transcription	Brain Germinal Matrix	brain
14	chr15:43623600-43644200	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
15	chr15:43623600-43646000	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
16	chr15:43623600-43646200	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
17	chr15:43623600-43646600	Weak transcription	Primary T killer memory cells from peripheral blood	blood
18	chr15:43623600-43646800	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
19	chr15:43623600-43650400	Weak transcription	NH-A	brain
20	chr15:43623600-43650800	Weak transcription	HMEC	breast
21	chr15:43623600-43650800	Weak transcription	NHLF	lung
22	chr15:43623600-43651000	Weak transcription	H9 Cell Line	embryonic stem cell
23	chr15:43623600-43651000	Weak transcription	A549	lung
24	chr15:43623600-43653000	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
25	chr15:43623800-43645800	Weak transcription	Primary T helper naive cells from peripheral blood	blood
26	chr15:43623800-43646000	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
27	chr15:43624000-43647000	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
28	chr15:43624600-43644600	Weak transcription	Fetal Heart	heart
29	chr15:43625600-43647200	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
30	chr15:43628400-43650400	Weak transcription	Primary B cells from cord blood	blood
31	chr15:43629000-43646000	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
32	chr15:43629200-43651000	Weak transcription	NHDF-Ad	bronchial
33	chr15:43630200-43650200	Weak transcription	Primary B cells from peripheral blood	blood
34	chr15:43630400-43650400	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
35	chr15:43630800-43650600	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
36	chr15:43631200-43644000	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
37	chr15:43631600-43650400	Weak transcription	H1 Cell Line	embryonic stem cell
38	chr15:43631800-43642800	Weak transcription	Lung	lung
39	chr15:43631800-43643200	Weak transcription	Spleen	Spleen
40	chr15:43631800-43651000	Weak transcription	Esophagus	oesophagus
41	chr15:43632600-43644600	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
42	chr15:43633200-43650600	Weak transcription	Stomach Smooth Muscle	stomach
43	chr15:43633400-43642800	Weak transcription	Ovary	ovary
44	chr15:43633600-43642600	Weak transcription	Fetal Lung	lung
45	chr15:43633600-43642800	Weak transcription	Monocytes-CD14+_RO01746	blood
46	chr15:43633800-43642800	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
47	chr15:43633800-43650800	Weak transcription	Osteobl	bone
48	chr15:43634000-43651000	Weak transcription	Aorta	Aorta
49	chr15:43635200-43646600	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
50	chr15:43635400-43645000	Strong transcription	HUES64 Cell Line	embryonic stem cell

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