Variant report

Variant	rs2412778
Chromosome Location	chr15:43660982-43660983
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	chr15:43660982-43661711	K562	blood:	n/a	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr15:43660016..43662796-chr15:43702586..43705983,3	K562	blood:
2	chr15:43632397..43634657-chr15:43658728..43661211,2	K562	blood:

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

Extended variants
information (count: 171 )
Associated
traits (count: 12 )

rSNPs within LD-proxies of this variant (count:166)

rs_ID	r²[population]
rs1095386	0.86[AMR][1000 genomes];0.89[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs11070399	1.00[ASN][1000 genomes]
rs1123947	0.87[AFR][1000 genomes];0.92[AMR][1000 genomes];0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1133395	1.00[ASN][1000 genomes]
rs11858152	0.91[AMR][1000 genomes];0.90[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs11858640	0.83[AMR][1000 genomes]
rs12101673	0.82[AFR][1000 genomes];0.92[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	0.92[AMR][1000 genomes];0.85[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs12324572	0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12324584	0.88[AFR][1000 genomes];0.94[AMR][1000 genomes];0.85[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs12905772	1.00[ASN][1000 genomes]
rs1549523	0.91[AMR][1000 genomes];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1549525	0.91[AMR][1000 genomes];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs16957627	0.96[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs16957630	0.97[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs16957632	0.97[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1814538	0.81[AMR][1000 genomes]
rs1837959	0.87[ASN][1000 genomes]
rs1837960	0.87[ASN][1000 genomes]
rs2012467	0.90[ASN][1000 genomes]
rs2242068	0.84[ASN][1000 genomes]
rs2243434	0.92[AMR][1000 genomes];0.85[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2244746	0.86[ASN][1000 genomes]
rs2245054	0.83[AMR][1000 genomes]
rs2245176	0.83[AMR][1000 genomes]
rs2245664	0.86[AMR][1000 genomes]
rs2245780	0.83[AMR][1000 genomes]
rs2245785	0.81[AMR][1000 genomes]
rs2245790	0.83[AMR][1000 genomes]
rs2245908	0.86[AMR][1000 genomes]
rs2251538	0.81[AMR][1000 genomes]
rs2253708	0.81[AMR][1000 genomes]
rs2254321	0.87[AMR][1000 genomes]
rs2254325	0.87[AMR][1000 genomes]
rs2255383	0.83[AMR][1000 genomes]
rs2256764	0.84[AMR][1000 genomes]
rs2264049	0.82[AFR][1000 genomes];0.84[AMR][1000 genomes]
rs2264239	0.83[AMR][1000 genomes]
rs2264876	0.83[AMR][1000 genomes]
rs2278856	1.00[ASN][1000 genomes]
rs2278857	1.00[ASN][1000 genomes]
rs2278859	0.96[AFR][1000 genomes];0.92[AMR][1000 genomes];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2278860	0.80[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2412779	0.80[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2412780	0.80[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2412781	0.97[ASN][1000 genomes]
rs2412782	0.86[AFR][1000 genomes];0.91[AMR][1000 genomes];0.84[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2439831	0.83[AMR][1000 genomes]
rs2439836	0.84[AMR][1000 genomes]
rs2439841	0.90[AMR][1000 genomes]
rs2439848	0.83[AMR][1000 genomes]
rs2439850	0.81[AMR][1000 genomes]
rs2444028	0.86[AMR][1000 genomes]
rs2444029	0.86[AMR][1000 genomes]
rs2444032	0.83[AMR][1000 genomes]
rs2444036	0.89[ASN][1000 genomes]
rs2444247	0.86[AMR][1000 genomes]
rs2444249	0.83[AMR][1000 genomes]
rs2444250	0.81[AMR][1000 genomes]
rs2467733	0.89[ASN][1000 genomes]
rs2467736	0.81[AMR][1000 genomes]
rs2467739	0.84[AMR][1000 genomes]
rs2467740	0.83[AMR][1000 genomes]
rs2467743	0.83[AMR][1000 genomes]
rs2467746	0.81[AMR][1000 genomes]
rs2584694	0.81[AMR][1000 genomes]
rs2584700	0.83[ASN][1000 genomes]
rs2584701	0.92[ASN][1000 genomes]
rs2584702	0.92[AMR][1000 genomes];0.85[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2584703	0.81[AFR][1000 genomes];0.87[ASN][1000 genomes]
rs2584706	0.81[AMR][1000 genomes]
rs2584726	0.86[AMR][1000 genomes]
rs2601014	0.81[AMR][1000 genomes]
rs28415933	0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28461955	0.80[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28578454	0.81[AMR][1000 genomes]
rs28653441	0.92[AFR][1000 genomes];0.84[AMR][1000 genomes];0.81[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs28666488	0.83[AMR][1000 genomes]
rs28702649	1.00[ASN][1000 genomes]
rs28729853	0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs28758627	0.90[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs2899082	0.80[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3213990	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs3213991	0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs3742969	0.91[AMR][1000 genomes];0.89[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs3742971	0.91[AMR][1000 genomes];0.89[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs3809481	0.94[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs3809482	1.00[ASN][1000 genomes]
rs4075674	0.97[AFR][1000 genomes];1.00[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	0.84[AMR][1000 genomes]
rs4583210	0.80[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs471229	0.89[AMR][1000 genomes]
rs478028	0.97[ASN][1000 genomes]
rs478104	0.88[AMR][1000 genomes];0.87[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs483724	0.84[AMR][1000 genomes]
rs484029	0.85[AFR][1000 genomes];0.91[AMR][1000 genomes];0.89[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs484846	0.87[AFR][1000 genomes];0.89[AMR][1000 genomes];0.89[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs485148	0.82[ASN][1000 genomes]
rs488756	0.89[AFR][1000 genomes];0.84[AMR][1000 genomes];0.97[ASN][1000 genomes]
rs491648	0.80[AMR][1000 genomes]
rs491800	0.84[ASN][1000 genomes]
rs498837	0.86[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	0.86[AMR][1000 genomes];0.89[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs512628	0.99[ASN][1000 genomes]
rs527921	0.81[AMR][1000 genomes]
rs528517	0.85[AMR][1000 genomes];0.89[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs537115	0.84[AMR][1000 genomes]
rs540031	0.86[AMR][1000 genomes];0.89[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs550239	0.86[AMR][1000 genomes]
rs552701	0.97[ASN][1000 genomes]
rs558656	0.87[AMR][1000 genomes]
rs561863	0.81[AMR][1000 genomes]
rs565007	0.86[AMR][1000 genomes]
rs573615	0.97[ASN][1000 genomes]
rs576557	0.88[ASN][1000 genomes]
rs6493081	0.91[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6493082	0.96[AFR][1000 genomes];0.97[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[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6493086	1.00[ASN][1000 genomes]
rs6493087	0.86[AFR][1000 genomes];0.98[AMR][1000 genomes];0.94[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs6493088	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs689596	0.81[AMR][1000 genomes]
rs689616	0.81[AMR][1000 genomes]
rs689754	0.82[AFR][1000 genomes]
rs689826	0.83[AMR][1000 genomes]
rs689835	0.84[AMR][1000 genomes]
rs690002	0.83[AMR][1000 genomes]
rs690038	0.87[AMR][1000 genomes]
rs690263	0.86[AMR][1000 genomes]
rs690316	0.86[AMR][1000 genomes]
rs690436	0.83[AMR][1000 genomes]
rs7163245	0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7165471	0.97[AFR][1000 genomes];0.97[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	0.96[AFR][1000 genomes];0.92[AMR][1000 genomes];0.89[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7169790	0.89[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs7170152	0.93[ASN][1000 genomes]
rs7170489	0.96[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7172374	0.93[ASN][1000 genomes]
rs7175434	0.91[AMR][1000 genomes];0.89[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7176849	0.84[AFR][1000 genomes];0.92[ASN][1000 genomes]
rs8033714	0.94[AMR][1000 genomes];0.90[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs8039638	0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs8039671	0.82[AFR][1000 genomes]
rs8041132	0.96[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs8042688	1.00[ASN][1000 genomes]
rs825739	0.88[AMR][1000 genomes];0.87[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs825740	0.85[AFR][1000 genomes];0.89[AMR][1000 genomes];0.87[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs884704	0.90[ASN][1000 genomes]
rs933941	0.96[AFR][1000 genomes];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs935901	0.89[EUR][1000 genomes]
rs956391	0.86[AMR][1000 genomes];0.88[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs9920879	1.00[ASN][1000 genomes]
rs999026	0.85[AFR][1000 genomes];0.90[ASN][1000 genomes]
rs999047	0.90[ASN][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	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
4	esv2618501	chr15:43659722-43661347	Weak transcription Enhancers Genic enhancers ZNF genes & repeats Strong transcription Transcr. at gene 5' and 3' Flanking Active TSS Active TSS	TF binding region Chromatin interactive region	4 gene(s)	inside rSNPs	n/a
5	esv8406	chr15:43660197-43661034	Enhancers Weak transcription Genic enhancers Strong transcription Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Active TSS	TF binding region Chromatin interactive region	2 gene(s)	inside rSNPs	n/a

mRNA abundance (count:12)

SNP	Gene	Cis/trans	Tissue	Source
rs2412778	ADAL	cis	multi-tissue	Pritchard
rs2412778	ADAL	cis	Nerve Tibial	GTEx
rs2412778	ADAL	cis	lung	GTEx
rs2412778	ADAL	cis	Artery Aorta	GTEx
rs2412778	ADAL	cis	Artery Tibial	GTEx
rs2412778	ADAL	cis	Stomach	GTEx
rs2412778	ADAL	cis	Skin Sun Exposed Lower leg	GTEx
rs2412778	ADAL	cis	Thyroid	GTEx
rs2412778	ADAL	cis	Adipose Subcutaneous	GTEx
rs2412778	CKMT1A	cis	Esophagus Mucosa	GTEx
rs2412778	ADAL	cis	Esophagus Muscularis	GTEx
rs2412778	ELL3	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:125 , 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	chr15:43650600-43661400	Strong transcription	Foreskin Fibroblast Primary Cells skin02	Skin
3	chr15:43654000-43661200	Strong transcription	Foreskin Fibroblast Primary Cells skin01	Skin
4	chr15:43654000-43661200	Strong transcription	Placenta	Placenta
5	chr15:43654400-43662000	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
6	chr15:43654600-43661800	Strong transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
7	chr15:43654800-43661000	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
8	chr15:43654800-43661000	Weak transcription	Stomach Mucosa	stomach
9	chr15:43654800-43661200	Strong transcription	H1 Cell Line	embryonic stem cell
10	chr15:43654800-43661400	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
11	chr15:43654800-43661800	Strong transcription	HSMM	muscle
12	chr15:43655200-43661000	Strong transcription	K562	blood
13	chr15:43655200-43661400	Strong transcription	NHDF-Ad	bronchial
14	chr15:43655800-43661000	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
15	chr15:43656000-43661400	Strong transcription	HUES48 Cell Line	embryonic stem cell
16	chr15:43656000-43661600	Strong transcription	iPS-20b Cell Line	embryonic stem cell
17	chr15:43656200-43661600	Strong transcription	HUES6 Cell Line	embryonic stem cell
18	chr15:43656400-43661800	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
19	chr15:43656600-43661000	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
20	chr15:43656600-43661200	Weak transcription	Primary T helper cells PMA-I stimulated	--
21	chr15:43656600-43661200	Strong transcription	Fetal Muscle Trunk	muscle
22	chr15:43656600-43661400	Strong transcription	HUES64 Cell Line	embryonic stem cell
23	chr15:43656600-43661800	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
24	chr15:43656800-43661000	Weak transcription	Primary B cells from peripheral blood	blood
25	chr15:43656800-43661800	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
26	chr15:43656800-43661800	Weak transcription	Pancreatic Islets	Pancreatic Islet
27	chr15:43657600-43661000	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
28	chr15:43657800-43661800	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
29	chr15:43658000-43661400	Strong transcription	Foreskin Melanocyte Primary Cells skin01	Skin
30	chr15:43658800-43661200	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
31	chr15:43658800-43661800	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
32	chr15:43659000-43661000	Weak transcription	Right Ventricle	heart
33	chr15:43659000-43661000	Weak transcription	Small Intestine	intestine
34	chr15:43659000-43661600	Weak transcription	Brain Substantia Nigra	brain
35	chr15:43659200-43661400	Weak transcription	HSMMtube	muscle
36	chr15:43659200-43662200	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
37	chr15:43659600-43661000	Weak transcription	Fetal Thymus	thymus
38	chr15:43659600-43661400	Weak transcription	Colon Smooth Muscle	Colon
39	chr15:43659800-43661000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
40	chr15:43659800-43661000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
41	chr15:43659800-43661000	Weak transcription	Muscle Satellite Cultured Cells	--
42	chr15:43659800-43661000	Strong transcription	Cortex derived primary cultured neurospheres	brain
43	chr15:43659800-43661000	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
44	chr15:43659800-43661000	Weak transcription	Fetal Intestine Small	intestine
45	chr15:43659800-43661000	Weak transcription	Fetal Stomach	stomach
46	chr15:43659800-43661000	Weak transcription	Gastric	stomach
47	chr15:43659800-43661000	Weak transcription	Lung	lung
48	chr15:43659800-43661000	Weak transcription	Psoas Muscle	Psoas
49	chr15:43659800-43661000	Weak transcription	Skeletal Muscle Male	skeletal muscle
50	chr15:43659800-43661000	Weak transcription	Spleen	Spleen

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