Variant report

Variant	rs28781888
Chromosome Location	chr15:44112006-44112007
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr15:44082965..44094882-chr15:44108427..44121402,26	K562	blood:
2	chr15:44109520..44111190-chr15:44111853..44114212,2	K562	blood:

Variant related genes	Relation type
ENSG00000184716	Chromatin interaction
ENSG00000242028	Chromatin interaction
ENSG00000140264	Chromatin interaction
ENSG00000221792	Chromatin interaction

Extended variants
information (count: 111 )
Associated
traits (count: 6 )

rSNPs within LD-proxies of this variant (count:100)

rs_ID	r²[population]
rs10163054	0.83[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs10438303	0.81[EUR][1000 genomes]
rs11070408	0.81[EUR][1000 genomes]
rs11070410	0.83[ASN][1000 genomes]
rs11852767	0.88[EUR][1000 genomes]
rs11852840	0.87[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs11856495	0.88[AMR][1000 genomes];0.93[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs11856795	0.93[AMR][1000 genomes];0.87[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs12101756	0.83[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs12440573	0.91[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs12441127	0.81[EUR][1000 genomes]
rs12441861	0.87[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs12441984	0.82[AFR][1000 genomes];0.98[AMR][1000 genomes];0.93[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs12442129	0.81[AMR][1000 genomes];0.87[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs12442297	0.80[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs12702	0.89[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs13329084	0.92[EUR][1000 genomes]
rs13380397	0.83[AMR][1000 genomes];0.87[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs16950562	0.81[EUR][1000 genomes]
rs16963953	0.84[AMR][1000 genomes];0.87[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs16965120	0.85[AMR][1000 genomes];1.00[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs16977724	0.93[AMR][1000 genomes];0.93[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs16977798	0.95[AMR][1000 genomes];0.93[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs1965794	0.91[AMR][1000 genomes];0.89[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs1965795	0.91[AMR][1000 genomes];0.87[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2228368	0.92[AFR][1000 genomes];0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2277531	0.83[ASN][1000 genomes]
rs2412810	0.81[EUR][1000 genomes]
rs2788	0.86[AMR][1000 genomes];0.87[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs28377539	0.83[ASN][1000 genomes]
rs28413704	0.96[AMR][1000 genomes];0.93[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs28413881	0.91[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs28476182	0.90[AMR][1000 genomes];0.92[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs28509275	1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs28513374	0.96[AMR][1000 genomes];0.92[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs28519630	0.91[AMR][1000 genomes];0.93[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs28524541	0.95[AMR][1000 genomes];0.93[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs28531819	0.95[AMR][1000 genomes];0.93[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs28542007	0.81[EUR][1000 genomes]
rs28546844	0.87[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs28564774	0.96[AMR][1000 genomes];0.93[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs28578398	0.86[AMR][1000 genomes];0.87[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs28583806	0.89[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs28590651	0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs28595038	0.81[AMR][1000 genomes];0.81[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs28636829	0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs28674750	0.90[AFR][1000 genomes];0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs28678901	0.84[AMR][1000 genomes];0.87[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs28679673	0.90[AMR][1000 genomes];0.93[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs28684672	0.94[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs28687459	0.82[AFR][1000 genomes];0.98[AMR][1000 genomes];0.93[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs28696802	0.90[AMR][1000 genomes];0.93[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs28699233	0.92[EUR][1000 genomes]
rs28707214	0.96[AMR][1000 genomes];0.93[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs28718261	0.83[AMR][1000 genomes];0.81[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs28780699	0.90[AMR][1000 genomes];0.93[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs28823973	0.90[AMR][1000 genomes];0.90[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs28858500	0.91[AMR][1000 genomes];0.90[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs28866846	0.86[AMR][1000 genomes];0.93[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs28891769	0.86[AMR][1000 genomes];0.87[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2955969	0.97[ASN][1000 genomes]
rs3736180	0.90[AFR][1000 genomes];0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs3742982	0.97[EUR][1000 genomes]
rs3759790	0.90[AMR][1000 genomes];0.93[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs3759791	0.90[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs3784275	0.98[EUR][1000 genomes]
rs3816792	0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs3825783	0.84[AFR][1000 genomes];0.91[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs4597285	0.86[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs4997480	0.81[EUR][1000 genomes]
rs56008017	0.96[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs56909447	0.88[AMR][1000 genomes];0.90[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs575082	0.95[ASN][1000 genomes]
rs60883262	0.84[AMR][1000 genomes];0.87[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs61390361	0.93[AMR][1000 genomes];0.90[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs62018952	0.90[ASN][1000 genomes]
rs67541383	0.88[EUR][1000 genomes]
rs68079546	0.90[AMR][1000 genomes];0.93[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs688009	0.86[ASN][1000 genomes]
rs693919	0.95[ASN][1000 genomes]
rs694461	0.95[ASN][1000 genomes]
rs7168158	0.81[AMR][1000 genomes];0.84[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs7169322	0.96[AMR][1000 genomes];0.93[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7169382	0.95[ASN][1000 genomes]
rs7169988	0.83[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs7170167	0.83[AMR][1000 genomes];0.87[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs7170751	0.91[AMR][1000 genomes];0.93[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs7171750	0.81[EUR][1000 genomes]
rs7174208	0.83[AMR][1000 genomes];0.84[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs7175032	0.83[AMR][1000 genomes];0.87[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs7179388	0.93[AMR][1000 genomes];0.93[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7180818	0.85[ASN][1000 genomes]
rs7181039	0.90[EUR][1000 genomes]
rs7183809	0.90[AMR][1000 genomes];0.93[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs8023508	0.80[ASN][1000 genomes]
rs8023696	0.81[EUR][1000 genomes]
rs8032649	0.96[AMR][1000 genomes];0.93[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs8040839	0.90[AMR][1000 genomes];0.86[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs9944216	0.91[AMR][1000 genomes];0.90[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs9989313	0.96[AMR][1000 genomes];0.93[EUR][1000 genomes];0.93[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:11 , 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	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
7	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
8	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
9	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
10	nsv1036318	chr15:44053617-44160773	Flanking Active TSS Strong transcription Genic enhancers Enhancers Weak transcription Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	68 gene(s)	inside rSNPs	diseases
11	nsv1050263	chr15:44093927-44204047	Strong transcription Flanking Active TSS Weak transcription Bivalent/Poised TSS Enhancers Active TSS Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	22 gene(s)	inside rSNPs	n/a

mRNA abundance (count:6)

SNP	Gene	Cis/trans	Tissue	Source
rs28781888	CKMT1A	cis	Esophagus Mucosa	GTEx
rs28781888	ADAL	cis	Esophagus Muscularis	GTEx
rs28781888	ADAL	cis	Nerve Tibial	GTEx
rs28781888	ADAL	cis	lung	GTEx
rs28781888	ADAL	cis	Artery Tibial	GTEx
rs28781888	ADAL	cis	Thyroid	GTEx

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:44093600-44116000	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
2	chr15:44093600-44116400	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
3	chr15:44093800-44112800	Strong transcription	Thymus	Thymus
4	chr15:44093800-44113800	Weak transcription	Stomach Mucosa	stomach
5	chr15:44093800-44115800	Weak transcription	Right Atrium	heart
6	chr15:44094000-44113200	Strong transcription	Fetal Muscle Leg	muscle
7	chr15:44094000-44113400	Strong transcription	Fetal Stomach	stomach
8	chr15:44094000-44114600	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
9	chr15:44094000-44114800	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
10	chr15:44094200-44113000	Strong transcription	Cortex derived primary cultured neurospheres	brain
11	chr15:44094200-44113200	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
12	chr15:44094400-44113200	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
13	chr15:44094400-44113200	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
14	chr15:44101000-44113200	Strong transcription	Fetal Intestine Small	intestine
15	chr15:44105000-44115800	Weak transcription	Psoas Muscle	Psoas
16	chr15:44106800-44112200	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
17	chr15:44106800-44113800	Weak transcription	Pancreatic Islets	Pancreatic Islet
18	chr15:44106800-44115600	Weak transcription	Right Ventricle	heart
19	chr15:44107200-44116000	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
20	chr15:44107400-44112800	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
21	chr15:44107400-44115600	Weak transcription	Fetal Heart	heart
22	chr15:44107600-44114200	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
23	chr15:44107600-44115400	Weak transcription	Aorta	Aorta
24	chr15:44107800-44112400	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
25	chr15:44107800-44113800	Weak transcription	Fetal Brain Male	brain
26	chr15:44107800-44114200	Weak transcription	Esophagus	oesophagus
27	chr15:44107800-44115800	Weak transcription	iPS-15b Cell Line	embryonic stem cell
28	chr15:44107800-44115800	Weak transcription	Gastric	stomach
29	chr15:44108000-44115800	Weak transcription	ES-I3 Cell Line	embryonic stem cell
30	chr15:44108200-44113000	Weak transcription	Small Intestine	intestine
31	chr15:44109400-44115400	Weak transcription	Placenta Amnion	Placenta Amnion
32	chr15:44109800-44114200	Weak transcription	Colon Smooth Muscle	Colon
33	chr15:44109800-44114600	Weak transcription	Lung	lung
34	chr15:44109800-44114600	Weak transcription	Ovary	ovary
35	chr15:44109800-44114800	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
36	chr15:44109800-44115600	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
37	chr15:44109800-44115800	Weak transcription	H1 Cell Line	embryonic stem cell
38	chr15:44109800-44115800	Weak transcription	HSMMtube	muscle
39	chr15:44109800-44116000	Weak transcription	H9 Cell Line	embryonic stem cell
40	chr15:44110000-44112400	Weak transcription	Fetal Brain Female	brain
41	chr15:44110000-44112400	Weak transcription	Dnd41	blood
42	chr15:44110000-44112400	Weak transcription	NHEK	skin
43	chr15:44110000-44112600	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
44	chr15:44110000-44113600	Weak transcription	Breast Myoepithelial Primary Cells	Breast
45	chr15:44110000-44113600	Weak transcription	Primary T killer memory cells from peripheral blood	blood
46	chr15:44110000-44113800	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
47	chr15:44110000-44113800	Weak transcription	Muscle Satellite Cultured Cells	--
48	chr15:44110000-44114000	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
49	chr15:44110000-44114000	Weak transcription	Primary B cells from cord blood	blood
50	chr15:44110000-44114000	Weak transcription	Fetal Lung	lung

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