Variant report

Variant	rs28461955
Chromosome Location	chr15:43661459-43661460
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	POLR2A	chr15:43661129-43661750	GM12878	blood:	n/a	n/a
2	POLR2A	chr15:43661375-43661693	MCF10A-Er-Src	breast:	n/a	n/a
3	HCFC1	chr15:43661352-43665311	Hela-S3	cervix:	n/a	n/a
4	POLR2A	chr15:43661060-43663929	Hela-S3	cervix:	n/a	n/a
5	POLR2A	chr15:43660982-43661711	K562	blood:	n/a	n/a
6	POLR2A	chr15:43661415-43661715	MCF10A-Er-Src	breast:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr15:43660016..43662796-chr15:43702586..43705983,3	K562	blood:
2	chr15:43618581..43624264-chr15:43661265..43664929,7	MCF-7	breast:
3	chr15:43620486..43624109-chr15:43661175..43665421,4	K562	blood:

Variant related genes	Relation type
TUBGCP4	TF binding region
ENSG00000168803	Chromatin interaction
ENSG00000067369	Chromatin interaction
ENSG00000168806	Chromatin interaction

Extended variants
information (count: 168 )
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];0.89[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs11070399	1.00[ASN][1000 genomes]
rs1123947	0.91[AMR][1000 genomes];0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1133395	1.00[ASN][1000 genomes]
rs11858152	0.96[AFR][1000 genomes];0.92[AMR][1000 genomes];0.90[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs11858640	0.84[AMR][1000 genomes]
rs12101673	0.91[AMR][1000 genomes];0.89[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12102205	1.00[ASN][1000 genomes]
rs12148735	0.87[ASN][1000 genomes]
rs12323999	0.85[AFR][1000 genomes];0.94[AMR][1000 genomes];0.85[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs12324572	0.96[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12324584	0.92[AMR][1000 genomes];0.85[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs12905772	1.00[ASN][1000 genomes]
rs1549523	0.93[AFR][1000 genomes];0.92[AMR][1000 genomes];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1549525	0.95[AFR][1000 genomes];0.92[AMR][1000 genomes];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs16957627	0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs16957630	0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs16957632	0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1814538	0.83[AMR][1000 genomes]
rs1837959	0.80[AFR][1000 genomes];0.87[ASN][1000 genomes]
rs1837960	0.85[AFR][1000 genomes];0.87[ASN][1000 genomes]
rs2012467	0.90[ASN][1000 genomes]
rs2242068	0.84[ASN][1000 genomes]
rs2242069	0.81[AMR][1000 genomes]
rs2243434	0.94[AMR][1000 genomes];0.85[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2244746	0.86[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	0.81[AFR][1000 genomes];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	0.81[AFR][1000 genomes];0.84[AMR][1000 genomes]
rs2264876	0.84[AMR][1000 genomes]
rs2278856	1.00[ASN][1000 genomes]
rs2278857	1.00[ASN][1000 genomes]
rs2278859	0.91[AMR][1000 genomes];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2278860	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2412778	0.80[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2412779	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2412780	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2412781	0.97[ASN][1000 genomes]
rs2412782	0.89[AMR][1000 genomes];0.84[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2439831	0.82[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	0.87[AFR][1000 genomes];0.89[ASN][1000 genomes]
rs2444247	0.87[AMR][1000 genomes]
rs2444249	0.84[AMR][1000 genomes]
rs2444250	0.83[AMR][1000 genomes]
rs2467733	0.86[AFR][1000 genomes];0.89[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	0.83[ASN][1000 genomes]
rs2584701	0.92[ASN][1000 genomes]
rs2584702	0.88[AFR][1000 genomes];0.94[AMR][1000 genomes];0.85[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2584703	0.87[ASN][1000 genomes]
rs2584706	0.83[AMR][1000 genomes]
rs2584726	0.87[AMR][1000 genomes]
rs28415933	0.96[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28653441	0.83[AMR][1000 genomes];0.81[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs28666488	0.84[AMR][1000 genomes]
rs28702649	1.00[ASN][1000 genomes]
rs28729853	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs28758627	0.89[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs2899082	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3213990	0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs3213991	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs3742969	0.93[AFR][1000 genomes];0.92[AMR][1000 genomes];0.89[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs3742971	0.93[AFR][1000 genomes];0.92[AMR][1000 genomes];0.89[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs3809481	0.92[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs3809482	1.00[ASN][1000 genomes]
rs4075674	0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4296223	0.99[ASN][1000 genomes]
rs4401024	0.99[ASN][1000 genomes]
rs4547312	1.00[ASN][1000 genomes]
rs45585139	0.83[AMR][1000 genomes]
rs4583210	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs471229	0.87[AMR][1000 genomes]
rs478028	0.97[ASN][1000 genomes]
rs478104	0.89[AMR][1000 genomes];0.87[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs483724	0.86[AMR][1000 genomes]
rs484029	0.89[AMR][1000 genomes];0.89[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs484846	0.88[AMR][1000 genomes];0.89[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs485148	0.82[ASN][1000 genomes]
rs488756	0.82[AMR][1000 genomes];0.97[ASN][1000 genomes]
rs491800	0.84[ASN][1000 genomes]
rs498837	0.88[AMR][1000 genomes];0.89[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs499035	0.92[ASN][1000 genomes]
rs507178	0.97[ASN][1000 genomes]
rs510108	0.92[ASN][1000 genomes]
rs511673	0.88[AMR][1000 genomes];0.89[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs512628	0.99[ASN][1000 genomes]
rs526083	0.81[AMR][1000 genomes]
rs528517	0.86[AMR][1000 genomes];0.89[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs537115	0.86[AMR][1000 genomes]
rs540031	0.88[AMR][1000 genomes];0.89[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs550239	0.87[AMR][1000 genomes]
rs552701	0.97[ASN][1000 genomes]
rs558656	0.89[AMR][1000 genomes]
rs561863	0.83[AMR][1000 genomes]
rs565007	0.87[AMR][1000 genomes]
rs573615	0.97[ASN][1000 genomes]
rs576557	0.88[ASN][1000 genomes]
rs6493081	0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6493082	0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6493083	1.00[ASN][1000 genomes]
rs6493084	1.00[ASN][1000 genomes]
rs6493085	0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6493086	1.00[ASN][1000 genomes]
rs6493087	0.97[AMR][1000 genomes];0.94[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs6493088	0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[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	0.81[AFR][1000 genomes];0.84[AMR][1000 genomes]
rs690466	0.81[AMR][1000 genomes]
rs7163245	0.95[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7165471	0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7166812	1.00[ASN][1000 genomes]
rs7167882	0.92[ASN][1000 genomes]
rs7168940	0.91[AMR][1000 genomes];0.89[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7169790	0.90[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs7170152	0.93[ASN][1000 genomes]
rs7170489	0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7172374	0.93[ASN][1000 genomes]
rs7175434	0.95[AFR][1000 genomes];0.92[AMR][1000 genomes];0.89[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7176849	0.92[ASN][1000 genomes]
rs8033714	0.95[AMR][1000 genomes];0.90[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs8039638	0.96[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs8041132	0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs8042688	1.00[ASN][1000 genomes]
rs825739	0.89[AMR][1000 genomes];0.87[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs825740	0.88[AMR][1000 genomes];0.87[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs884704	0.90[AFR][1000 genomes];0.90[ASN][1000 genomes]
rs933941	0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs935901	0.89[EUR][1000 genomes]
rs956391	0.84[AMR][1000 genomes];0.88[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs9920879	1.00[ASN][1000 genomes]
rs999026	0.90[ASN][1000 genomes]
rs999047	0.91[AFR][1000 genomes];0.90[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:3 , 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	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
3	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
rs28461955	ADAL	cis	Artery Aorta	GTEx
rs28461955	CKMT1A	cis	Esophagus Mucosa	GTEx
rs28461955	ADAL	cis	Skin Sun Exposed Lower leg	GTEx
rs28461955	ADAL	cis	Artery Tibial	GTEx
rs28461955	ADAL	cis	Thyroid	GTEx
rs28461955	ADAL	cis	Stomach	GTEx
rs28461955	ADAL	cis	lung	GTEx
rs28461955	ADAL	cis	Esophagus Muscularis	GTEx
rs28461955	ADAL	cis	Nerve Tibial	GTEx
rs28461955	ELL3	Cis_1M	lymphoblastoid	RTeQTL
rs28461955	ADAL	cis	Adipose Subcutaneous	GTEx
rs28461955	ADAL	cis	multi-tissue	Pritchard

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:43650200-43661600	ZNF genes & repeats	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
2	chr15:43654400-43662000	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
3	chr15:43654600-43661800	Strong transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
4	chr15:43654800-43661800	Strong transcription	HSMM	muscle
5	chr15:43656000-43661600	Strong transcription	iPS-20b Cell Line	embryonic stem cell
6	chr15:43656200-43661600	Strong transcription	HUES6 Cell Line	embryonic stem cell
7	chr15:43656400-43661800	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
8	chr15:43656600-43661800	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
9	chr15:43656800-43661800	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
10	chr15:43656800-43661800	Weak transcription	Pancreatic Islets	Pancreatic Islet
11	chr15:43657800-43661800	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
12	chr15:43658800-43661800	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
13	chr15:43659000-43661600	Weak transcription	Brain Substantia Nigra	brain
14	chr15:43659200-43662200	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
15	chr15:43659800-43661600	Weak transcription	Rectal Smooth Muscle	rectum
16	chr15:43659800-43661800	Weak transcription	iPS-15b Cell Line	embryonic stem cell
17	chr15:43659800-43661800	Weak transcription	Primary monocytes fromperipheralblood	blood
18	chr15:43659800-43661800	Enhancers	Fetal Heart	heart
19	chr15:43659800-43662000	Weak transcription	Aorta	Aorta
20	chr15:43659800-43662000	Weak transcription	Esophagus	oesophagus
21	chr15:43660000-43661600	Weak transcription	H9 Cell Line	embryonic stem cell
22	chr15:43660000-43661600	Genic enhancers	Monocytes-CD14+_RO01746	blood
23	chr15:43660000-43661800	Weak transcription	NHLF	lung
24	chr15:43660000-43662000	Weak transcription	ES-I3 Cell Line	embryonic stem cell
25	chr15:43660000-43662000	Weak transcription	Primary neutrophils fromperipheralblood	blood
26	chr15:43660000-43662000	Weak transcription	NH-A	brain
27	chr15:43660000-43662000	Weak transcription	Osteobl	bone
28	chr15:43660000-43662200	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
29	chr15:43660200-43661800	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
30	chr15:43660200-43661800	Weak transcription	Colonic Mucosa	Colon
31	chr15:43660200-43662000	Weak transcription	Fetal Kidney	kidney
32	chr15:43660400-43661600	Weak transcription	Placenta Amnion	Placenta Amnion
33	chr15:43660400-43661800	Weak transcription	Primary T cells from cord blood	blood
34	chr15:43660600-43661800	Weak transcription	iPS-18 Cell Line	embryonic stem cell
35	chr15:43660600-43661800	Weak transcription	HMEC	breast
36	chr15:43660800-43661600	Transcr. at gene 5' and 3'	Brain Germinal Matrix	brain
37	chr15:43660800-43661600	Enhancers	Fetal Brain Male	brain
38	chr15:43661000-43661600	ZNF genes & repeats	Primary T killer memory cells from peripheral blood	blood
39	chr15:43661000-43661600	Transcr. at gene 5' and 3'	Ganglion Eminence derived primary cultured neurospheres	brain
40	chr15:43661000-43661600	Genic enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
41	chr15:43661000-43661600	Genic enhancers	Brain Hippocampus Middle	brain
42	chr15:43661000-43661600	Enhancers	Brain Dorsolateral Prefrontal Cortex	brain
43	chr15:43661000-43661600	Transcr. at gene 5' and 3'	Fetal Brain Female	brain
44	chr15:43661000-43661600	Enhancers	Rectal Mucosa Donor 29	rectum
45	chr15:43661000-43661800	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
46	chr15:43661000-43661800	ZNF genes & repeats	Primary hematopoietic stem cells short term culture	blood
47	chr15:43661000-43661800	Enhancers	Muscle Satellite Cultured Cells	--
48	chr15:43661000-43661800	Enhancers	Adipose Nuclei	Adipose
49	chr15:43661000-43661800	Enhancers	Brain Inferior Temporal Lobe	brain
50	chr15:43661000-43661800	Enhancers	Psoas Muscle	Psoas

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