Variant report

Variant	rs10744149
Chromosome Location	chr12:123708490-123708491
allele	A/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 102 )
Associated
traits (count: 6 )

rSNPs within LD-proxies of this variant (count:96)

rs_ID	r²[population]
rs1047158	0.84[AMR][1000 genomes]
rs1051431	0.84[AMR][1000 genomes]
rs10744148	0.80[AMR][1000 genomes]
rs10772995	0.88[AMR][1000 genomes]
rs10772996	0.83[AMR][1000 genomes]
rs10772998	0.94[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs10773001	0.83[AMR][1000 genomes]
rs10846478	0.89[AMR][1000 genomes]
rs10846486	0.92[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs10846487	0.85[AMR][1000 genomes]
rs10846491	0.84[AMR][1000 genomes]
rs11057192	0.93[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs11057204	0.91[AMR][1000 genomes]
rs11057206	0.94[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs11057210	0.94[AMR][1000 genomes]
rs1402274	0.89[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs1402275	0.85[AMR][1000 genomes]
rs1533703	0.85[AMR][1000 genomes]
rs1615694	0.89[AMR][1000 genomes]
rs1621194	0.84[AMR][1000 genomes]
rs1626899	0.96[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs1627724	0.80[AMR][1000 genomes]
rs1630693	0.95[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs1630905	0.96[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs1716156	0.85[AMR][1000 genomes]
rs1716157	0.89[AMR][1000 genomes]
rs1716158	0.81[AMR][1000 genomes]
rs1716159	0.88[AMR][1000 genomes]
rs1716160	0.96[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs1716164	0.88[AMR][1000 genomes]
rs1716165	0.84[AMR][1000 genomes]
rs1716167	0.84[AMR][1000 genomes]
rs1716168	0.84[AMR][1000 genomes]
rs1716170	0.96[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs1716171	0.96[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs1716172	0.96[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs1716173	0.88[AMR][1000 genomes]
rs1716175	0.88[AMR][1000 genomes]
rs1716176	0.89[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs1716177	0.89[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs1716182	0.89[AMR][1000 genomes]
rs1727290	0.89[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs1727296	0.84[AMR][1000 genomes]
rs1727300	0.88[AMR][1000 genomes]
rs1727306	0.90[AMR][1000 genomes]
rs1727314	0.84[AMR][1000 genomes]
rs1727315	0.82[AMR][1000 genomes]
rs1727320	0.96[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs1727323	0.93[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs1727324	0.80[EUR][1000 genomes]
rs1727325	0.92[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs1727334	0.96[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs1790086	0.89[AMR][1000 genomes]
rs1790087	0.89[AMR][1000 genomes]
rs1790089	0.89[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs1790095	0.89[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs1790098	0.89[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs1790100	0.89[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs1790101	0.96[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs1790102	0.94[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs1790108	0.82[AMR][1000 genomes]
rs1790109	0.82[AMR][1000 genomes]
rs1790124	0.88[AMR][1000 genomes]
rs1790125	0.85[AMR][1000 genomes]
rs1790130	0.96[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs1790131	0.96[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs1969354	0.85[AMR][1000 genomes]
rs1980252	0.84[AMR][1000 genomes]
rs2049114	0.88[AMR][1000 genomes]
rs2337934	0.85[AMR][1000 genomes]
rs2682429	0.84[AMR][1000 genomes]
rs2682430	0.96[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs2682431	0.96[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs2682433	0.81[EUR][1000 genomes]
rs2682434	0.93[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs2695476	0.81[EUR][1000 genomes]
rs2695481	0.84[AMR][1000 genomes]
rs2851435	0.82[EUR][1000 genomes]
rs2851436	0.88[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs2851438	0.84[AMR][1000 genomes]
rs2851450	0.93[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs2851451	0.92[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs2947099	0.84[AMR][1000 genomes]
rs2950537	0.89[AMR][1000 genomes]
rs3018098	0.89[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs4268544	0.89[AMR][1000 genomes]
rs4372492	0.93[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs4759371	0.85[AMR][1000 genomes]
rs4759409	0.94[AMR][1000 genomes]
rs4759415	0.85[AMR][1000 genomes]
rs4759416	0.84[AMR][1000 genomes]
rs4759417	0.85[AMR][1000 genomes]
rs7313483	0.89[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs941305	0.96[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs941306	0.96[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs9795522	0.94[AMR][1000 genomes];0.80[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:6 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv427924	chr12:123412172-123722059	Enhancers Active TSS Weak transcription Strong transcription Flanking Active TSS Transcr. at gene 5' and 3' Genic enhancers Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	78 gene(s)	inside rSNPs	diseases
2	esv1825473	chr12:123582855-123822503	Weak transcription Strong transcription Flanking Active TSS Genic enhancers Enhancers Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	73 gene(s)	inside rSNPs	diseases
3	nsv870326	chr12:123585990-123719323	Enhancers Weak transcription Strong transcription Flanking Active TSS Active TSS Bivalent Enhancer Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	56 gene(s)	inside rSNPs	diseases
4	esv2761773	chr12:123616003-123723460	Flanking Active TSS Strong transcription Weak transcription Enhancers Active TSS Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	53 gene(s)	inside rSNPs	diseases
5	esv1803368	chr12:123640853-123822503	Weak transcription Strong transcription Flanking Active TSS Genic enhancers Enhancers 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 target site	70 gene(s)	inside rSNPs	diseases
6	esv1830566	chr12:123640853-123822503	Flanking Active TSS Strong transcription Enhancers Weak transcription Genic enhancers Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	70 gene(s)	inside rSNPs	diseases

mRNA abundance (count:6)

SNP	Gene	Cis/trans	Tissue	Source
rs10744149	SBNO1	Cis_1M	lymphoblastoid	RTeQTL
rs10744149	ARL6IP4	Cis_1M	lymphoblastoid	RTeQTL
rs10744149	RP11-282O18.3	cis	Esophagus Mucosa	GTEx
rs10744149	CDK2AP1	cis	Esophagus Mucosa	GTEx
rs10744149	CDK2AP1	Cis_1M	lymphoblastoid	RTeQTL
rs10744149	MPHOSPH9	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:125 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:123636600-123716600	Weak transcription	Esophagus	oesophagus
2	chr12:123637000-123713000	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
3	chr12:123637200-123716400	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
4	chr12:123650600-123716400	Weak transcription	Placenta Amnion	Placenta Amnion
5	chr12:123654200-123712000	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
6	chr12:123654200-123715400	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
7	chr12:123655000-123712000	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
8	chr12:123674600-123713400	Weak transcription	Pancreatic Islets	Pancreatic Islet
9	chr12:123680600-123716600	Weak transcription	Colonic Mucosa	Colon
10	chr12:123684000-123709800	Strong transcription	Liver	Liver
11	chr12:123685400-123711600	Strong transcription	Fetal Stomach	stomach
12	chr12:123687200-123711600	Strong transcription	Fetal Intestine Small	intestine
13	chr12:123687800-123716600	Weak transcription	Gastric	stomach
14	chr12:123687800-123716600	Weak transcription	Pancreas	Pancrea
15	chr12:123687800-123717000	Weak transcription	Aorta	Aorta
16	chr12:123688000-123715200	Weak transcription	Fetal Heart	heart
17	chr12:123689600-123712200	Strong transcription	HUES6 Cell Line	embryonic stem cell
18	chr12:123690600-123710800	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
19	chr12:123690800-123716000	Weak transcription	Psoas Muscle	Psoas
20	chr12:123694600-123716800	Weak transcription	Ovary	ovary
21	chr12:123696200-123709600	Strong transcription	Fetal Muscle Leg	muscle
22	chr12:123696200-123715000	Strong transcription	iPS-20b Cell Line	embryonic stem cell
23	chr12:123696400-123710400	Strong transcription	Monocytes-CD14+_RO01746	blood
24	chr12:123696400-123710600	Strong transcription	HUES48 Cell Line	embryonic stem cell
25	chr12:123696400-123711600	Strong transcription	Fetal Muscle Trunk	muscle
26	chr12:123698400-123716600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
27	chr12:123698800-123713400	Weak transcription	Fetal Brain Male	brain
28	chr12:123699200-123709200	Weak transcription	NH-A	brain
29	chr12:123699200-123716400	Weak transcription	iPS-15b Cell Line	embryonic stem cell
30	chr12:123699200-123716400	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
31	chr12:123699400-123716400	Weak transcription	HSMM	muscle
32	chr12:123699600-123716400	Weak transcription	Rectal Smooth Muscle	rectum
33	chr12:123699600-123716600	Weak transcription	Spleen	Spleen
34	chr12:123699600-123716600	Weak transcription	HSMMtube	muscle
35	chr12:123700400-123709400	Strong transcription	Brain Anterior Caudate	brain
36	chr12:123701200-123715200	Weak transcription	NHDF-Ad	bronchial
37	chr12:123701800-123709600	Strong transcription	Placenta	Placenta
38	chr12:123702400-123710000	Strong transcription	Ganglion Eminence derived primary cultured neurospheres	brain
39	chr12:123702400-123710600	Strong transcription	Cortex derived primary cultured neurospheres	brain
40	chr12:123702600-123711600	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
41	chr12:123702600-123715000	Strong transcription	HUES64 Cell Line	embryonic stem cell
42	chr12:123703000-123713200	Weak transcription	Brain Cingulate Gyrus	brain
43	chr12:123703400-123715200	Weak transcription	Brain Angular Gyrus	brain
44	chr12:123703600-123712400	Weak transcription	Brain Germinal Matrix	brain
45	chr12:123703800-123709600	Strong transcription	K562	blood
46	chr12:123704600-123715600	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
47	chr12:123704800-123709400	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
48	chr12:123705000-123716600	Weak transcription	Lung	lung
49	chr12:123705200-123716200	Weak transcription	NHEK	skin
50	chr12:123705600-123708600	Strong transcription	Fetal Lung	lung

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