Variant report

Variant	rs10744150
Chromosome Location	chr12:123721614-123721615
allele	A/C
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	FOXM1	chr12:123721127-123722025	GM12878	blood:	n/a	n/a
2	BHLHE40	chr12:123721200-123721652	GM12878	blood:	n/a	n/a
3	RUNX3	chr12:123721143-123721775	GM12878	blood:	n/a	n/a
4	ZNF384	chr12:123721461-123721633	GM12878	blood:	n/a	n/a
5	PAX5	chr12:123721309-123721655	GM12878	blood:	n/a	n/a
6	PAX5	chr12:123721219-123721838	GM12878	blood:	n/a	n/a
7	PAX5	chr12:123721262-123721670	GM12878	blood:	n/a	n/a
8	MAX	chr12:123721441-123721631	GM12878	blood:	n/a	n/a
9	PAX5	chr12:123721257-123721746	GM12892	blood:	n/a	n/a
10	MEF2A	chr12:123721005-123721683	GM12878	blood:	n/a	chr12:123721326-123721347 chr12:123721333-123721342 chr12:123721332-123721343 chr12:123721331-123721345 chr12:123721326-123721347 chr12:123721330-123721346
11	PAX5	chr12:123721276-123721859	GM12878	blood:	n/a	n/a
12	MTA3	chr12:123721211-123723033	GM12878	blood:	n/a	n/a
13	MXI1	chr12:123721267-123721635	GM12878	blood:	n/a	n/a
14	POLR2A	chr12:123721337-123722769	HepG2	liver:	n/a	n/a
15	CEBPB	chr12:123721535-123723150	GM12878	blood:	n/a	n/a
16	POLR2A	chr12:123721316-123721775	GM12878	blood:	n/a	n/a
17	PAX5	chr12:123721198-123721860	GM12891	blood:	n/a	n/a
18	POLR2A	chr12:123721501-123721700	GM12878	blood:	n/a	n/a
19	PML	chr12:123721012-123721666	GM12878	blood:	n/a	n/a
20	POLR2A	chr12:123721282-123721856	K562	blood:	n/a	n/a
21	NFIC	chr12:123721159-123721943	GM12878	blood:	n/a	n/a
22	FOXM1	chr12:123721250-123721744	GM12878	blood:	n/a	n/a
23	TBL1XR1	chr12:123721192-123721853	GM12878	blood:	n/a	n/a
24	IKZF1	chr12:123721470-123722565	GM12878	blood:	n/a	n/a
25	MEF2A	chr12:123721052-123721663	GM12878	blood:	n/a	chr12:123721326-123721347 chr12:123721333-123721342 chr12:123721332-123721343 chr12:123721331-123721345 chr12:123721326-123721347 chr12:123721330-123721346
26	YY1	chr12:123721271-123721849	GM12878	blood:	n/a	n/a
27	MEF2C	chr12:123720996-123721665	GM12878	blood:	n/a	chr12:123721329-123721344 chr12:123721326-123721347 chr12:123721333-123721342 chr12:123721332-123721343 chr12:123721331-123721345 chr12:123721326-123721347 chr12:123721330-123721346
28	BCLAF1	chr12:123721174-123721652	GM12878	blood:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr12:123470053..123472975-chr12:123718822..123721771,2	K562	blood:
2	chr12:123717076..123718967-chr12:123720807..123722850,2	MCF-7	breast:
3	chr12:123715385..123717743-chr12:123720225..123722840,2	MCF-7	breast:
4	chr12:123344694..123345413-chr12:123721340..123722280,2	K562	blood:
5	chr12:123525430..123528340-chr12:123721388..123723225,2	MCF-7	breast:
6	chr12:123459434..123462270-chr12:123721239..123724536,4	MCF-7	breast:
7	chr12:123462884..123465858-chr12:123721353..123723553,2	MCF-7	breast:

Variant related genes	Relation type
MPHOSPH9	TF binding region
ENSG00000111325	Chromatin interaction
ENSG00000256028	Chromatin interaction
ENSG00000130787	Chromatin interaction
ENSG00000182196	Chromatin interaction
ENSG00000051825	Chromatin interaction
ENSG00000150967	Chromatin interaction
ENSG00000130921	Chromatin interaction

Extended variants
information (count: 95 )
Associated
traits (count: 6 )

rSNPs within LD-proxies of this variant (count:89)

rs_ID	r²[population]
rs10444439	0.83[JPT][hapmap]
rs10732573	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.87[AFR][1000 genomes];0.84[AMR][1000 genomes];0.88[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs10734901	0.87[AFR][1000 genomes];0.84[AMR][1000 genomes];0.88[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs10744151	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs10744152	0.94[JPT][hapmap]
rs10772997	0.95[CHB][hapmap];0.94[JPT][hapmap];0.98[AFR][1000 genomes];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs10772998	0.82[EUR][1000 genomes]
rs10772999	0.92[AFR][1000 genomes];0.90[AMR][1000 genomes];0.95[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs10773000	0.84[JPT][hapmap]
rs10773002	1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[AFR][1000 genomes];0.83[AMR][1000 genomes];0.87[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs10846489	0.82[CHB][hapmap];0.84[JPT][hapmap]
rs10846517	0.94[JPT][hapmap]
rs10846519	0.94[JPT][hapmap]
rs10846520	0.89[JPT][hapmap]
rs10846523	0.94[JPT][hapmap]
rs11057189	0.89[AMR][1000 genomes];0.85[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs11057202	0.98[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs11057204	0.81[EUR][1000 genomes]
rs11057205	0.88[AFR][1000 genomes];0.88[AMR][1000 genomes];0.97[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs11057206	0.80[EUR][1000 genomes]
rs11057207	0.92[AFR][1000 genomes];0.95[AMR][1000 genomes];0.95[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs11057209	0.81[AFR][1000 genomes];0.94[AMR][1000 genomes];0.94[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs11057223	0.86[CHB][hapmap];0.84[JPT][hapmap]
rs11057287	0.94[JPT][hapmap]
rs1109559	0.82[CHB][hapmap];0.84[JPT][hapmap]
rs1109560	0.82[CHB][hapmap];0.84[JPT][hapmap]
rs11554169	0.84[ASN][1000 genomes]
rs1568427	0.95[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.90[AFR][1000 genomes];0.84[AMR][1000 genomes];0.88[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs1568428	0.82[CHB][hapmap];0.84[JPT][hapmap]
rs1609520	1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[AMR][1000 genomes];0.93[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs1615350	1.00[YRI][hapmap];0.83[AMR][1000 genomes]
rs1660	0.89[JPT][hapmap]
rs1716170	0.80[EUR][1000 genomes]
rs1716171	0.80[EUR][1000 genomes]
rs1727319	0.87[AFR][1000 genomes];0.94[AMR][1000 genomes];0.85[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs1727331	1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs1727332	0.93[AFR][1000 genomes];0.96[AMR][1000 genomes];0.95[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs1727334	0.80[EUR][1000 genomes]
rs1879379	0.82[CHB][hapmap];0.84[JPT][hapmap]
rs1969355	0.90[AFR][1000 genomes];0.84[AMR][1000 genomes];0.88[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs1980251	0.85[AFR][1000 genomes];0.84[AMR][1000 genomes];0.88[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs2090764	0.87[ASN][1000 genomes]
rs2102949	0.89[AMR][1000 genomes];0.83[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs2271976	0.82[CHB][hapmap];0.85[JPT][hapmap]
rs2280424	1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[ASN][1000 genomes]
rs28362667	0.90[ASN][1000 genomes]
rs28362669	0.88[ASN][1000 genomes]
rs28414347	0.94[JPT][hapmap]
rs28501453	0.94[JPT][hapmap]
rs2851443	0.87[AFR][1000 genomes];0.91[AMR][1000 genomes];0.86[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs2851447	0.88[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs28587386	0.94[JPT][hapmap]
rs28595660	0.94[JPT][hapmap]
rs28613486	0.94[JPT][hapmap]
rs36121382	0.85[ASN][1000 genomes]
rs3759111	0.90[CHB][hapmap];0.89[JPT][hapmap];0.84[ASN][1000 genomes]
rs3759113	0.90[CHB][hapmap];0.89[JPT][hapmap]
rs3759114	1.00[CHB][hapmap];1.00[JPT][hapmap];0.80[ASN][1000 genomes]
rs3803001	0.94[JPT][hapmap]
rs3825141	0.94[JPT][hapmap]
rs4460848	0.90[CHB][hapmap];0.89[JPT][hapmap];1.00[YRI][hapmap];0.89[AMR][1000 genomes];0.83[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs4474478	0.92[ASN][1000 genomes]
rs4474479	0.92[ASN][1000 genomes]
rs4594040	0.92[ASN][1000 genomes]
rs4759367	0.90[CHB][hapmap];0.89[JPT][hapmap]
rs4759372	0.84[ASN][1000 genomes]
rs4759406	0.82[ASN][1000 genomes]
rs4759407	0.90[CHB][hapmap];0.89[JPT][hapmap];0.84[ASN][1000 genomes]
rs4759408	0.91[ASN][1000 genomes]
rs4759411	0.95[CHB][hapmap];1.00[JPT][hapmap];0.84[ASN][1000 genomes]
rs4759413	0.90[CHB][hapmap];0.94[JPT][hapmap];0.83[ASN][1000 genomes]
rs4759414	0.95[CHB][hapmap];1.00[JPT][hapmap];0.83[ASN][1000 genomes]
rs4759418	0.86[ASN][1000 genomes]
rs57676984	0.91[ASN][1000 genomes]
rs60077920	0.91[ASN][1000 genomes]
rs60254089	0.81[ASN][1000 genomes]
rs60296110	0.82[ASN][1000 genomes]
rs61231969	0.86[ASN][1000 genomes]
rs61519741	0.93[ASN][1000 genomes]
rs7137286	0.92[AFR][1000 genomes];0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7139321	0.82[CHB][hapmap];0.85[JPT][hapmap];0.81[ASN][1000 genomes]
rs7297649	0.94[JPT][hapmap]
rs7304782	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs73231928	0.81[ASN][1000 genomes]
rs7959415	0.94[JPT][hapmap]
rs941305	0.80[EUR][1000 genomes]
rs941306	0.80[EUR][1000 genomes]
rs9795522	0.80[EUR][1000 genomes]
rs9795593	0.94[JPT][hapmap]

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	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
4	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
5	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
6	esv1836043	chr12:123709409-123822503	Weak transcription Flanking Active TSS Strong transcription Enhancers 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
rs10744150	SBNO1	Cis_1M	lymphoblastoid	RTeQTL
rs10744150	RP11-282O18.3	cis	Esophagus Mucosa	GTEx
rs10744150	CDK2AP1	cis	Esophagus Mucosa	GTEx
rs10744150	MPHOSPH9	Cis_1M	lymphoblastoid	RTeQTL
rs10744150	ARL6IP4	Cis_1M	lymphoblastoid	RTeQTL
rs10744150	CDK2AP1	Cis_1M	lymphoblastoid	RTeQTL

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:123718800-123722200	Weak transcription	Stomach Mucosa	stomach
2	chr12:123718800-123728400	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
3	chr12:123718800-123728400	Weak transcription	H9 Cell Line	embryonic stem cell
4	chr12:123718800-123733000	Weak transcription	Esophagus	oesophagus
5	chr12:123718800-123733800	Weak transcription	Aorta	Aorta
6	chr12:123718800-123739600	Weak transcription	Fetal Kidney	kidney
7	chr12:123719000-123722200	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
8	chr12:123719000-123722200	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
9	chr12:123719000-123722200	Enhancers	Primary B cells from cord blood	blood
10	chr12:123719000-123722200	Enhancers	Primary T killer memory cells from peripheral blood	blood
11	chr12:123719000-123722200	Weak transcription	HSMMtube	muscle
12	chr12:123719000-123722600	Weak transcription	Placenta	Placenta
13	chr12:123719000-123724400	Weak transcription	HSMM	muscle
14	chr12:123719000-123725000	Weak transcription	HUES48 Cell Line	embryonic stem cell
15	chr12:123719000-123725400	Weak transcription	H1 Cell Line	embryonic stem cell
16	chr12:123719000-123725400	Weak transcription	HUES64 Cell Line	embryonic stem cell
17	chr12:123719000-123726200	Weak transcription	Right Ventricle	heart
18	chr12:123719000-123726200	Weak transcription	Monocytes-CD14+_RO01746	blood
19	chr12:123719000-123726800	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
20	chr12:123719000-123728400	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
21	chr12:123719000-123731600	Weak transcription	ES-I3 Cell Line	embryonic stem cell
22	chr12:123719000-123732600	Weak transcription	iPS-18 Cell Line	embryonic stem cell
23	chr12:123719000-123735000	Weak transcription	iPS-15b Cell Line	embryonic stem cell
24	chr12:123719200-123723200	Weak transcription	Fetal Muscle Trunk	muscle
25	chr12:123719200-123725800	Weak transcription	Primary monocytes fromperipheralblood	blood
26	chr12:123719200-123726600	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
27	chr12:123719200-123733000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
28	chr12:123719200-123735200	Weak transcription	Ovary	ovary
29	chr12:123719400-123723400	Transcr. at gene 5' and 3'	Fetal Thymus	thymus
30	chr12:123719400-123726600	Weak transcription	Rectal Mucosa Donor 31	rectum
31	chr12:123719600-123722400	Weak transcription	Osteobl	bone
32	chr12:123719600-123723200	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
33	chr12:123719600-123726400	Weak transcription	Rectal Smooth Muscle	rectum
34	chr12:123719600-123734200	Weak transcription	Colonic Mucosa	Colon
35	chr12:123719600-123738400	Weak transcription	NH-A	brain
36	chr12:123719800-123722000	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
37	chr12:123719800-123722000	Weak transcription	Pancreatic Islets	Pancreatic Islet
38	chr12:123719800-123722200	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
39	chr12:123719800-123722200	Genic enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
40	chr12:123719800-123722200	Weak transcription	Brain Substantia Nigra	brain
41	chr12:123719800-123722400	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
42	chr12:123719800-123723200	Enhancers	Primary T killer naive cells fromperipheralblood	blood
43	chr12:123719800-123723400	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
44	chr12:123719800-123726200	Weak transcription	Fetal Lung	lung
45	chr12:123719800-123726400	Weak transcription	Rectal Mucosa Donor 29	rectum
46	chr12:123719800-123726600	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
47	chr12:123719800-123726800	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
48	chr12:123719800-123726800	Weak transcription	NHDF-Ad	bronchial
49	chr12:123719800-123728800	Strong transcription	Fetal Stomach	stomach
50	chr12:123719800-123733600	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived

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