Variant report

Variant	rs10772997
Chromosome Location	chr12:123719880-123719881
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:4)
CpG islands
(count:0)
Chromatin interactive
region (count:11)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:4 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	POLR2A	chr12:123719666-123719942	HCT-116	colon:	n/a	n/a
2	POLR2A	chr12:123719467-123720110	SK-N-MC	brain:	n/a	n/a
3	POLR2A	chr12:123719874-123719890	MCF10A-Er-Src	breast:	n/a	n/a
4	POLR2A	chr12:123719543-123720549	HepG2	liver:	n/a	n/a

No data

(count:11 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr12:123344301..123346489-chr12:123716077..123720315,3	K562	blood:
2	chr12:123470053..123472975-chr12:123718822..123721771,2	K562	blood:
3	chr12:123714199..123721299-chr12:123733822..123739052,7	MCF-7	breast:
4	chr12:123452751..123454277-chr12:123718785..123720840,2	MCF-7	breast:
5	chr12:123463210..123468211-chr12:123716151..123721062,7	MCF-7	breast:
6	chr12:123715079..123721002-chr12:123721919..123730378,16	K562	blood:
7	chr12:123459054..123462367-chr12:123715409..123720380,5	K562	blood:
8	chr12:123558968..123563276-chr12:123716606..123719909,6	MCF-7	breast:
9	chr12:123458147..123462549-chr12:123715608..123720287,8	MCF-7	breast:
10	chr12:123717014..123719935-chr12:123753310..123757333,7	K562	blood:
11	chr12:123716353..123719935-chr12:123753594..123757800,6	K562	blood:

No data

Variant related genes	Relation type
MPHOSPH9	TF binding region
ENSG00000130787	Chromatin interaction
ENSG00000130921	Chromatin interaction
ENSG00000051825	Chromatin interaction
ENSG00000150967	Chromatin interaction
ENSG00000182196	Chromatin interaction
ENSG00000111328	Chromatin interaction
ENSG00000111325	Chromatin interaction
ENSG00000090975	Chromatin interaction
ENSG00000256028	Chromatin interaction

Extended variants
information (count: 110 )
Associated
traits (count: 6 )

rSNPs within LD-proxies of this variant (count:104)

rs_ID	r²[population]
rs10444439	0.83[JPT][hapmap]
rs10732573	0.95[CHB][hapmap];0.94[JPT][hapmap];0.88[AFR][1000 genomes];0.87[AMR][1000 genomes];0.88[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs10734901	0.88[AFR][1000 genomes];0.87[AMR][1000 genomes];0.88[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs10744150	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]
rs10744151	0.95[CHB][hapmap];1.00[JPT][hapmap];0.95[AFR][1000 genomes];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10744152	1.00[JPT][hapmap]
rs10772998	0.83[EUR][1000 genomes]
rs10772999	0.93[AFR][1000 genomes];0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs10773002	0.95[CHB][hapmap];0.94[JPT][hapmap];0.83[AFR][1000 genomes];0.85[AMR][1000 genomes];0.87[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs10773003	0.84[JPT][hapmap]
rs10773005	0.84[JPT][hapmap]
rs10846487	0.80[EUR][1000 genomes]
rs10846517	1.00[JPT][hapmap]
rs10846519	1.00[JPT][hapmap]
rs10846520	0.94[JPT][hapmap]
rs10846523	1.00[JPT][hapmap]
rs11057189	0.80[AFR][1000 genomes];0.91[AMR][1000 genomes];0.86[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs11057202	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11057204	0.82[EUR][1000 genomes]
rs11057205	0.90[AFR][1000 genomes];0.90[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs11057206	0.82[EUR][1000 genomes]
rs11057207	0.93[AFR][1000 genomes];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs11057209	0.83[AFR][1000 genomes];0.96[AMR][1000 genomes];0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs11057210	0.80[EUR][1000 genomes]
rs11057251	0.84[JPT][hapmap]
rs11057276	0.84[JPT][hapmap]
rs11057287	1.00[JPT][hapmap]
rs11532322	0.81[AFR][1000 genomes]
rs11554169	0.87[ASN][1000 genomes]
rs11608305	0.85[JPT][hapmap]
rs12317452	0.85[JPT][hapmap]
rs12366872	0.85[JPT][hapmap]
rs1568427	0.91[CHB][hapmap];0.94[JPT][hapmap];0.92[AFR][1000 genomes];0.87[AMR][1000 genomes];0.90[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs1609520	0.95[CHB][hapmap];0.94[JPT][hapmap];0.90[AMR][1000 genomes];0.94[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs1615350	0.86[AMR][1000 genomes]
rs1660	0.94[JPT][hapmap]
rs1716170	0.82[EUR][1000 genomes]
rs1716171	0.82[EUR][1000 genomes]
rs1727319	0.88[AFR][1000 genomes];0.96[AMR][1000 genomes];0.86[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs1727331	0.95[CHB][hapmap];0.94[JPT][hapmap];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1727332	0.95[AFR][1000 genomes];0.99[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1727334	0.82[EUR][1000 genomes]
rs1879379	0.81[ASN][1000 genomes]
rs1969355	0.92[AFR][1000 genomes];0.87[AMR][1000 genomes];0.90[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs1980251	0.86[AFR][1000 genomes];0.87[AMR][1000 genomes];0.88[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2090764	0.91[ASN][1000 genomes]
rs2102949	0.91[AMR][1000 genomes];0.84[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs2271976	0.80[JPT][hapmap]
rs2280424	0.95[CHB][hapmap];0.94[JPT][hapmap];0.93[ASN][1000 genomes]
rs28362667	0.93[ASN][1000 genomes]
rs28362669	0.92[ASN][1000 genomes]
rs28410096	0.84[JPT][hapmap]
rs28414347	1.00[JPT][hapmap]
rs28501453	1.00[JPT][hapmap]
rs2851443	0.88[AFR][1000 genomes];0.94[AMR][1000 genomes];0.87[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2851447	0.90[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs28532037	0.84[JPT][hapmap]
rs28533432	0.84[JPT][hapmap]
rs28587386	1.00[JPT][hapmap]
rs28595660	1.00[JPT][hapmap]
rs28613486	1.00[JPT][hapmap]
rs28660993	0.84[JPT][hapmap]
rs3088303	0.84[JPT][hapmap]
rs34841857	0.81[ASN][1000 genomes]
rs36121382	0.88[ASN][1000 genomes]
rs3759111	0.85[CHB][hapmap];0.84[JPT][hapmap];0.87[ASN][1000 genomes]
rs3759113	0.85[CHB][hapmap];0.84[JPT][hapmap];0.82[ASN][1000 genomes]
rs3759114	0.95[CHB][hapmap];0.94[JPT][hapmap];0.83[ASN][1000 genomes]
rs3803001	1.00[JPT][hapmap]
rs3825141	1.00[JPT][hapmap]
rs4460848	0.85[CHB][hapmap];0.84[JPT][hapmap];0.91[AMR][1000 genomes];0.85[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs4474478	0.95[ASN][1000 genomes]
rs4474479	0.95[ASN][1000 genomes]
rs4594040	0.95[ASN][1000 genomes]
rs4759367	0.86[CHB][hapmap];0.83[JPT][hapmap];0.81[ASN][1000 genomes]
rs4759372	0.87[ASN][1000 genomes]
rs4759377	0.84[JPT][hapmap]
rs4759406	0.85[ASN][1000 genomes]
rs4759407	0.85[CHB][hapmap];0.84[JPT][hapmap];0.87[ASN][1000 genomes]
rs4759408	0.94[ASN][1000 genomes]
rs4759409	0.82[EUR][1000 genomes]
rs4759411	0.90[CHB][hapmap];0.94[JPT][hapmap];0.87[ASN][1000 genomes]
rs4759413	0.86[CHB][hapmap];0.89[JPT][hapmap];0.86[ASN][1000 genomes]
rs4759414	0.91[CHB][hapmap];0.94[JPT][hapmap];0.86[ASN][1000 genomes]
rs4759418	0.89[ASN][1000 genomes]
rs57676984	0.94[ASN][1000 genomes]
rs60077920	0.94[ASN][1000 genomes]
rs60254089	0.84[ASN][1000 genomes]
rs60296110	0.85[ASN][1000 genomes]
rs61231969	0.89[ASN][1000 genomes]
rs61519741	0.97[ASN][1000 genomes]
rs7137286	0.93[AFR][1000 genomes];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7139321	0.80[JPT][hapmap];0.84[ASN][1000 genomes]
rs7297649	1.00[JPT][hapmap]
rs7304782	0.95[CHB][hapmap];0.94[JPT][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7313483	0.80[EUR][1000 genomes]
rs7315453	0.84[JPT][hapmap]
rs73231928	0.84[ASN][1000 genomes]
rs7959415	1.00[JPT][hapmap]
rs7972811	0.84[JPT][hapmap]
rs941305	0.82[EUR][1000 genomes]
rs941306	0.82[EUR][1000 genomes]
rs9795522	0.82[EUR][1000 genomes]
rs9795593	1.00[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
rs10772997	MPHOSPH9	Cis_1M	lymphoblastoid	RTeQTL
rs10772997	ARL6IP4	Cis_1M	lymphoblastoid	RTeQTL
rs10772997	CDK2AP1	Cis_1M	lymphoblastoid	RTeQTL
rs10772997	RP11-282O18.3	cis	Esophagus Mucosa	GTEx
rs10772997	SBNO1	Cis_1M	lymphoblastoid	RTeQTL
rs10772997	CDK2AP1	cis	Esophagus Mucosa	GTEx

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:123718400-123720000	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Female	--
2	chr12:123718800-123720000	Enhancers	Small Intestine	intestine
3	chr12:123718800-123720200	Enhancers	Pancreas	Pancrea
4	chr12:123718800-123721000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
5	chr12:123718800-123722200	Weak transcription	Stomach Mucosa	stomach
6	chr12:123718800-123728400	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
7	chr12:123718800-123728400	Weak transcription	H9 Cell Line	embryonic stem cell
8	chr12:123718800-123733000	Weak transcription	Esophagus	oesophagus
9	chr12:123718800-123733800	Weak transcription	Aorta	Aorta
10	chr12:123718800-123739600	Weak transcription	Fetal Kidney	kidney
11	chr12:123719000-123720000	Enhancers	Muscle Satellite Cultured Cells	--
12	chr12:123719000-123720000	Enhancers	Cortex derived primary cultured neurospheres	brain
13	chr12:123719000-123720000	Enhancers	Adipose Nuclei	Adipose
14	chr12:123719000-123720000	Enhancers	Brain Cingulate Gyrus	brain
15	chr12:123719000-123720000	Enhancers	Brain Inferior Temporal Lobe	brain
16	chr12:123719000-123720000	Enhancers	Colon Smooth Muscle	Colon
17	chr12:123719000-123720000	Enhancers	Duodenum Mucosa	Duodenum
18	chr12:123719000-123720000	Enhancers	Fetal Heart	heart
19	chr12:123719000-123720000	Enhancers	HUVEC	blood vessel
20	chr12:123719000-123720200	Enhancers	Primary T helper 17 cells PMA-I stimulated	--
21	chr12:123719000-123720600	Enhancers	Skeletal Muscle Female	skeletal muscle
22	chr12:123719000-123720800	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
23	chr12:123719000-123721200	Enhancers	Liver	Liver
24	chr12:123719000-123722200	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
25	chr12:123719000-123722200	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
26	chr12:123719000-123722200	Enhancers	Primary B cells from cord blood	blood
27	chr12:123719000-123722200	Enhancers	Primary T killer memory cells from peripheral blood	blood
28	chr12:123719000-123722200	Weak transcription	HSMMtube	muscle
29	chr12:123719000-123722600	Weak transcription	Placenta	Placenta
30	chr12:123719000-123724400	Weak transcription	HSMM	muscle
31	chr12:123719000-123725000	Weak transcription	HUES48 Cell Line	embryonic stem cell
32	chr12:123719000-123725400	Weak transcription	H1 Cell Line	embryonic stem cell
33	chr12:123719000-123725400	Weak transcription	HUES64 Cell Line	embryonic stem cell
34	chr12:123719000-123726200	Weak transcription	Right Ventricle	heart
35	chr12:123719000-123726200	Weak transcription	Monocytes-CD14+_RO01746	blood
36	chr12:123719000-123726800	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
37	chr12:123719000-123728400	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
38	chr12:123719000-123731600	Weak transcription	ES-I3 Cell Line	embryonic stem cell
39	chr12:123719000-123732600	Weak transcription	iPS-18 Cell Line	embryonic stem cell
40	chr12:123719000-123735000	Weak transcription	iPS-15b Cell Line	embryonic stem cell
41	chr12:123719200-123720000	Flanking Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
42	chr12:123719200-123720000	Enhancers	Foreskin Fibroblast Primary Cells skin02	Skin
43	chr12:123719200-123720000	Enhancers	Primary mononuclear cells fromperipheralblood	Blood
44	chr12:123719200-123720000	Enhancers	Brain Hippocampus Middle	brain
45	chr12:123719200-123720400	Enhancers	Brain Germinal Matrix	brain
46	chr12:123719200-123720600	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
47	chr12:123719200-123720800	Enhancers	Primary T cells fromperipheralblood	blood
48	chr12:123719200-123721200	Genic enhancers	Primary B cells from peripheral blood	blood
49	chr12:123719200-123723200	Weak transcription	Fetal Muscle Trunk	muscle
50	chr12:123719200-123725800	Weak transcription	Primary monocytes fromperipheralblood	blood

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