Variant report

Variant	rs28729853
Chromosome Location	chr15:43673680-43673681
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr15:43667336..43672122-chr15:43673183..43677434,8	K562	blood:

Variant related genes	Relation type
ENSG00000137822	Chromatin interaction

Extended variants
information (count: 167 )
Associated
traits (count: 12 )

rSNPs within LD-proxies of this variant (count:165)

rs_ID	r²[population]
rs101094	0.81[AMR][1000 genomes]
rs1095386	0.88[AMR][1000 genomes];0.88[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs11070399	0.95[ASN][1000 genomes]
rs1123947	0.91[AMR][1000 genomes];0.86[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs1133395	0.95[ASN][1000 genomes]
rs11637572	0.81[ASN][1000 genomes]
rs11858152	0.91[AFR][1000 genomes];0.92[AMR][1000 genomes];0.88[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs11858640	0.84[AMR][1000 genomes]
rs12101673	0.91[AMR][1000 genomes];0.88[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs12102205	0.95[ASN][1000 genomes]
rs12148735	0.83[ASN][1000 genomes]
rs12323999	0.87[AFR][1000 genomes];0.94[AMR][1000 genomes];0.86[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs12324572	0.91[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs12324584	0.92[AMR][1000 genomes];0.86[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs12905772	0.95[ASN][1000 genomes]
rs1549523	0.88[AFR][1000 genomes];0.92[AMR][1000 genomes];0.88[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs1549525	0.90[AFR][1000 genomes];0.92[AMR][1000 genomes];0.88[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs16957627	0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs16957630	0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs16957632	0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs1814538	0.83[AMR][1000 genomes]
rs1837959	0.82[AFR][1000 genomes];0.88[ASN][1000 genomes]
rs1837960	0.87[AFR][1000 genomes];0.88[ASN][1000 genomes]
rs2012467	0.92[ASN][1000 genomes]
rs2242068	0.86[ASN][1000 genomes]
rs2242069	0.81[AMR][1000 genomes]
rs2243434	0.80[AFR][1000 genomes];0.94[AMR][1000 genomes];0.86[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2244746	0.88[ASN][1000 genomes]
rs2245054	0.84[AMR][1000 genomes]
rs2245176	0.84[AMR][1000 genomes]
rs2245664	0.87[AMR][1000 genomes]
rs2245780	0.84[AMR][1000 genomes]
rs2245785	0.83[AMR][1000 genomes]
rs2245790	0.84[AMR][1000 genomes]
rs2245908	0.87[AMR][1000 genomes]
rs2251538	0.83[AMR][1000 genomes]
rs2253708	0.83[AMR][1000 genomes]
rs2254321	0.89[AMR][1000 genomes]
rs2254325	0.89[AMR][1000 genomes]
rs2255383	0.84[AMR][1000 genomes]
rs2256764	0.83[AMR][1000 genomes]
rs2264049	0.83[AMR][1000 genomes]
rs2264239	0.84[AMR][1000 genomes]
rs2264876	0.84[AMR][1000 genomes]
rs2278856	0.95[ASN][1000 genomes]
rs2278857	0.95[ASN][1000 genomes]
rs2278859	0.91[AMR][1000 genomes];0.88[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2278860	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2412778	0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2412779	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2412780	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2412781	0.99[ASN][1000 genomes]
rs2412782	0.89[AMR][1000 genomes];0.85[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2439831	0.80[AFR][1000 genomes];0.84[AMR][1000 genomes]
rs2439836	0.83[AMR][1000 genomes]
rs2439841	0.89[AMR][1000 genomes]
rs2439848	0.84[AMR][1000 genomes]
rs2439850	0.83[AMR][1000 genomes]
rs2444028	0.87[AMR][1000 genomes]
rs2444029	0.87[AMR][1000 genomes]
rs2444032	0.84[AMR][1000 genomes]
rs2444036	0.89[AFR][1000 genomes];0.91[ASN][1000 genomes]
rs2444247	0.87[AMR][1000 genomes]
rs2444249	0.84[AMR][1000 genomes]
rs2444250	0.83[AMR][1000 genomes]
rs2467733	0.88[AFR][1000 genomes];0.91[ASN][1000 genomes]
rs2467736	0.83[AMR][1000 genomes]
rs2467739	0.86[AMR][1000 genomes]
rs2467740	0.84[AMR][1000 genomes]
rs2467743	0.84[AMR][1000 genomes]
rs2467746	0.83[AMR][1000 genomes]
rs2584694	0.82[AMR][1000 genomes]
rs2584700	0.85[ASN][1000 genomes]
rs2584701	0.94[ASN][1000 genomes]
rs2584702	0.90[AFR][1000 genomes];0.94[AMR][1000 genomes];0.86[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2584703	0.88[ASN][1000 genomes]
rs2584706	0.83[AMR][1000 genomes]
rs2584726	0.87[AMR][1000 genomes]
rs28415933	0.91[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs28461955	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs28653441	0.83[AMR][1000 genomes];0.82[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs28666488	0.84[AMR][1000 genomes]
rs28702649	0.95[ASN][1000 genomes]
rs28758627	0.89[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs2899082	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs3213990	0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs3213991	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs3742969	0.88[AFR][1000 genomes];0.92[AMR][1000 genomes];0.88[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs3742971	0.88[AFR][1000 genomes];0.92[AMR][1000 genomes];0.88[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs3809481	0.92[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs3809482	0.95[ASN][1000 genomes]
rs4075674	0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs4296223	0.94[ASN][1000 genomes]
rs4401024	0.94[ASN][1000 genomes]
rs4547312	0.95[ASN][1000 genomes]
rs45585139	0.83[AMR][1000 genomes]
rs4583210	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs471229	0.87[AMR][1000 genomes]
rs478028	0.93[ASN][1000 genomes]
rs478104	0.89[AMR][1000 genomes];0.86[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs483724	0.86[AMR][1000 genomes]
rs484029	0.89[AMR][1000 genomes];0.88[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs484846	0.88[AMR][1000 genomes];0.88[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs488756	0.82[AMR][1000 genomes];0.93[ASN][1000 genomes]
rs491800	0.81[ASN][1000 genomes]
rs498837	0.88[AMR][1000 genomes];0.88[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs499035	0.89[ASN][1000 genomes]
rs507178	0.93[ASN][1000 genomes]
rs510108	0.89[ASN][1000 genomes]
rs511673	0.88[AMR][1000 genomes];0.88[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs512628	0.94[ASN][1000 genomes]
rs526083	0.81[AMR][1000 genomes]
rs528517	0.86[AMR][1000 genomes];0.88[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs537115	0.86[AMR][1000 genomes]
rs540031	0.88[AMR][1000 genomes];0.88[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs550239	0.87[AMR][1000 genomes]
rs552701	0.93[ASN][1000 genomes]
rs558656	0.89[AMR][1000 genomes]
rs561863	0.83[AMR][1000 genomes]
rs565007	0.87[AMR][1000 genomes]
rs573615	0.93[ASN][1000 genomes]
rs576557	0.85[ASN][1000 genomes]
rs6493081	0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs6493082	0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs6493083	0.95[ASN][1000 genomes]
rs6493084	0.95[ASN][1000 genomes]
rs6493085	0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs6493086	0.95[ASN][1000 genomes]
rs6493087	0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs6493088	0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs689596	0.83[AMR][1000 genomes]
rs689616	0.83[AMR][1000 genomes]
rs689647	0.82[AMR][1000 genomes]
rs689826	0.84[AMR][1000 genomes]
rs689835	0.86[AMR][1000 genomes]
rs690002	0.84[AMR][1000 genomes]
rs690038	0.89[AMR][1000 genomes]
rs690263	0.87[AMR][1000 genomes]
rs690316	0.87[AMR][1000 genomes]
rs690436	0.84[AMR][1000 genomes]
rs690466	0.81[AMR][1000 genomes]
rs7163245	0.97[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7165471	0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7166812	0.95[ASN][1000 genomes]
rs7167882	0.94[ASN][1000 genomes]
rs7168940	0.91[AMR][1000 genomes];0.88[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7169790	0.90[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs7170152	0.94[ASN][1000 genomes]
rs7170489	0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7172374	0.88[ASN][1000 genomes]
rs7175434	0.90[AFR][1000 genomes];0.92[AMR][1000 genomes];0.88[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7176849	0.94[ASN][1000 genomes]
rs8033714	0.95[AMR][1000 genomes];0.89[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs8039638	0.91[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs8041132	0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs8042688	0.95[ASN][1000 genomes]
rs825739	0.89[AMR][1000 genomes];0.86[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs825740	0.88[AMR][1000 genomes];0.86[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs884704	0.92[AFR][1000 genomes];0.92[ASN][1000 genomes]
rs933941	0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs935901	0.87[EUR][1000 genomes]
rs956391	0.84[AMR][1000 genomes];0.87[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs9920879	0.95[ASN][1000 genomes]
rs999026	0.92[ASN][1000 genomes]
rs999047	0.93[AFR][1000 genomes];0.92[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:2 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	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
2	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
rs28729853	ADAL	cis	Artery Aorta	GTEx
rs28729853	ADAL	cis	Adipose Subcutaneous	GTEx
rs28729853	ADAL	cis	multi-tissue	Pritchard
rs28729853	ELL3	Cis_1M	lymphoblastoid	RTeQTL
rs28729853	ADAL	cis	Esophagus Muscularis	GTEx
rs28729853	ADAL	cis	lung	GTEx
rs28729853	ADAL	cis	Thyroid	GTEx
rs28729853	ADAL	cis	Nerve Tibial	GTEx
rs28729853	ADAL	cis	Artery Tibial	GTEx
rs28729853	ADAL	cis	Stomach	GTEx
rs28729853	CKMT1A	cis	Esophagus Mucosa	GTEx
rs28729853	ADAL	cis	Skin Sun Exposed Lower leg	GTEx

Chromatin state (count:124 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:43664000-43677200	Weak transcription	Aorta	Aorta
2	chr15:43664000-43692600	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
3	chr15:43664200-43678000	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
4	chr15:43664400-43675200	Weak transcription	NHDF-Ad	bronchial
5	chr15:43664400-43675400	Weak transcription	Psoas Muscle	Psoas
6	chr15:43664400-43676400	Weak transcription	Placenta Amnion	Placenta Amnion
7	chr15:43664400-43677200	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
8	chr15:43664600-43675400	Weak transcription	Muscle Satellite Cultured Cells	--
9	chr15:43664600-43675400	Weak transcription	Rectal Smooth Muscle	rectum
10	chr15:43664600-43687800	Weak transcription	iPS-15b Cell Line	embryonic stem cell
11	chr15:43664600-43688000	Weak transcription	Stomach Mucosa	stomach
12	chr15:43664600-43695600	Weak transcription	Fetal Heart	heart
13	chr15:43664800-43675400	Weak transcription	Small Intestine	intestine
14	chr15:43665000-43677600	Weak transcription	Fetal Brain Male	brain
15	chr15:43665000-43687800	Weak transcription	Pancreatic Islets	Pancreatic Islet
16	chr15:43665000-43730000	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
17	chr15:43665200-43675400	Weak transcription	Primary T helper naive cells from peripheral blood	blood
18	chr15:43665200-43676000	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
19	chr15:43665200-43676200	Weak transcription	Colon Smooth Muscle	Colon
20	chr15:43665200-43686600	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
21	chr15:43667400-43681600	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
22	chr15:43667600-43681600	Strong transcription	Hela-S3	cervix
23	chr15:43668000-43717800	Strong transcription	Primary hematopoietic stem cells short term culture	blood
24	chr15:43668200-43674200	Strong transcription	Skeletal Muscle Female	skeletal muscle
25	chr15:43668200-43680400	Strong transcription	Fetal Stomach	stomach
26	chr15:43668200-43680600	Strong transcription	Fetal Muscle Leg	muscle
27	chr15:43668200-43680800	Strong transcription	Breast Myoepithelial Primary Cells	Breast
28	chr15:43668200-43681400	Strong transcription	Duodenum Mucosa	Duodenum
29	chr15:43668200-43681800	Strong transcription	Dnd41	blood
30	chr15:43668200-43683800	Strong transcription	Liver	Liver
31	chr15:43668200-43702200	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
32	chr15:43668200-43732800	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
33	chr15:43668400-43679600	Strong transcription	Rectal Mucosa Donor 31	rectum
34	chr15:43668400-43680600	Strong transcription	Fetal Muscle Trunk	muscle
35	chr15:43668400-43680800	Strong transcription	Rectal Mucosa Donor 29	rectum
36	chr15:43668400-43683800	Strong transcription	Primary T cells from cord blood	blood
37	chr15:43668600-43674200	Strong transcription	Ganglion Eminence derived primary cultured neurospheres	brain
38	chr15:43668600-43674400	Strong transcription	Foreskin Fibroblast Primary Cells skin01	Skin
39	chr15:43668600-43677000	Strong transcription	Brain Hippocampus Middle	brain
40	chr15:43668600-43679600	Strong transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
41	chr15:43668600-43680800	Strong transcription	iPS-20b Cell Line	embryonic stem cell
42	chr15:43668600-43680800	Strong transcription	Sigmoid Colon	Sigmoid Colon
43	chr15:43668600-43681200	Strong transcription	HUES64 Cell Line	embryonic stem cell
44	chr15:43668600-43681400	Strong transcription	Primary hematopoietic stem cells	blood
45	chr15:43668600-43681400	Strong transcription	Fetal Thymus	thymus
46	chr15:43668600-43681600	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
47	chr15:43668600-43681800	Strong transcription	HUES6 Cell Line	embryonic stem cell
48	chr15:43668600-43681800	Strong transcription	HepG2	liver
49	chr15:43668600-43682000	Strong transcription	HUES48 Cell Line	embryonic stem cell
50	chr15:43668600-43682000	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--

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