Variant report

Variant	rs11057202
Chromosome Location	chr12:123720775-123720776
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:1)
CpG islands
(count:0)
Chromatin interactive
region (count:6)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

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

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	POLR2A	chr12:123720719-123721039	HepG2	liver:	n/a	n/a

No data

(count:6 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr12:123470053..123472975-chr12:123718822..123721771,2	K562	blood:
2	chr12:123714199..123721299-chr12:123733822..123739052,7	MCF-7	breast:
3	chr12:123715385..123717743-chr12:123720225..123722840,2	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:

No data

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

Extended variants
information (count: 81 )
Associated
traits (count: 6 )

rSNPs within LD-proxies of this variant (count:75)

rs_ID	r²[population]
rs10732573	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	0.98[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs10744151	0.95[AFR][1000 genomes];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10772997	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
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	0.83[AFR][1000 genomes];0.85[AMR][1000 genomes];0.88[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs10846487	0.81[EUR][1000 genomes]
rs11057189	0.80[AFR][1000 genomes];0.91[AMR][1000 genomes];0.86[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs11057204	0.83[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];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs11057210	0.81[EUR][1000 genomes]
rs11532322	0.81[AFR][1000 genomes]
rs11554169	0.87[ASN][1000 genomes]
rs12817892	0.81[EUR][1000 genomes]
rs12818067	0.81[EUR][1000 genomes]
rs12829456	0.81[EUR][1000 genomes]
rs1568427	0.92[AFR][1000 genomes];0.87[AMR][1000 genomes];0.90[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs1609520	0.90[AMR][1000 genomes];0.95[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs1615350	0.86[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs1716170	0.82[EUR][1000 genomes]
rs1716171	0.82[EUR][1000 genomes]
rs1727319	0.88[AFR][1000 genomes];0.96[AMR][1000 genomes];0.87[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs1727331	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];0.85[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs2280424	0.93[ASN][1000 genomes]
rs28362667	0.93[ASN][1000 genomes]
rs28362669	0.92[ASN][1000 genomes]
rs2851443	0.88[AFR][1000 genomes];0.94[AMR][1000 genomes];0.88[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2851447	0.90[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs34341465	0.81[EUR][1000 genomes]
rs34841857	0.81[ASN][1000 genomes]
rs36121382	0.88[ASN][1000 genomes]
rs3759111	0.87[ASN][1000 genomes]
rs3759113	0.82[ASN][1000 genomes]
rs3759114	0.83[ASN][1000 genomes]
rs4460848	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	0.81[ASN][1000 genomes]
rs4759372	0.87[ASN][1000 genomes]
rs4759406	0.85[ASN][1000 genomes]
rs4759407	0.87[ASN][1000 genomes]
rs4759408	0.94[ASN][1000 genomes]
rs4759409	0.82[EUR][1000 genomes]
rs4759411	0.87[ASN][1000 genomes]
rs4759413	0.86[ASN][1000 genomes]
rs4759414	0.86[ASN][1000 genomes]
rs4759418	0.89[ASN][1000 genomes]
rs57676984	0.94[ASN][1000 genomes]
rs58809476	0.81[EUR][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];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7139321	0.84[ASN][1000 genomes]
rs7304782	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7313483	0.81[EUR][1000 genomes]
rs73231928	0.84[ASN][1000 genomes]
rs941305	0.82[EUR][1000 genomes]
rs941306	0.82[EUR][1000 genomes]
rs9795522	0.82[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	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
rs11057202	CDK2AP1	Cis_1M	lymphoblastoid	RTeQTL
rs11057202	RP11-282O18.3	cis	Esophagus Mucosa	GTEx
rs11057202	ARL6IP4	Cis_1M	lymphoblastoid	RTeQTL
rs11057202	SBNO1	Cis_1M	lymphoblastoid	RTeQTL
rs11057202	MPHOSPH9	Cis_1M	lymphoblastoid	RTeQTL
rs11057202	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	chr12:123718800-123721000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
2	chr12:123718800-123722200	Weak transcription	Stomach Mucosa	stomach
3	chr12:123718800-123728400	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
4	chr12:123718800-123728400	Weak transcription	H9 Cell Line	embryonic stem cell
5	chr12:123718800-123733000	Weak transcription	Esophagus	oesophagus
6	chr12:123718800-123733800	Weak transcription	Aorta	Aorta
7	chr12:123718800-123739600	Weak transcription	Fetal Kidney	kidney
8	chr12:123719000-123720800	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
9	chr12:123719000-123721200	Enhancers	Liver	Liver
10	chr12:123719000-123722200	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
11	chr12:123719000-123722200	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
12	chr12:123719000-123722200	Enhancers	Primary B cells from cord blood	blood
13	chr12:123719000-123722200	Enhancers	Primary T killer memory cells from peripheral blood	blood
14	chr12:123719000-123722200	Weak transcription	HSMMtube	muscle
15	chr12:123719000-123722600	Weak transcription	Placenta	Placenta
16	chr12:123719000-123724400	Weak transcription	HSMM	muscle
17	chr12:123719000-123725000	Weak transcription	HUES48 Cell Line	embryonic stem cell
18	chr12:123719000-123725400	Weak transcription	H1 Cell Line	embryonic stem cell
19	chr12:123719000-123725400	Weak transcription	HUES64 Cell Line	embryonic stem cell
20	chr12:123719000-123726200	Weak transcription	Right Ventricle	heart
21	chr12:123719000-123726200	Weak transcription	Monocytes-CD14+_RO01746	blood
22	chr12:123719000-123726800	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
23	chr12:123719000-123728400	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
24	chr12:123719000-123731600	Weak transcription	ES-I3 Cell Line	embryonic stem cell
25	chr12:123719000-123732600	Weak transcription	iPS-18 Cell Line	embryonic stem cell
26	chr12:123719000-123735000	Weak transcription	iPS-15b Cell Line	embryonic stem cell
27	chr12:123719200-123720800	Enhancers	Primary T cells fromperipheralblood	blood
28	chr12:123719200-123721200	Genic enhancers	Primary B cells from peripheral blood	blood
29	chr12:123719200-123723200	Weak transcription	Fetal Muscle Trunk	muscle
30	chr12:123719200-123725800	Weak transcription	Primary monocytes fromperipheralblood	blood
31	chr12:123719200-123726600	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
32	chr12:123719200-123733000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
33	chr12:123719200-123735200	Weak transcription	Ovary	ovary
34	chr12:123719400-123720800	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
35	chr12:123719400-123721200	Strong transcription	iPS-20b Cell Line	embryonic stem cell
36	chr12:123719400-123721600	Genic enhancers	Primary Natural Killer cells fromperipheralblood	blood
37	chr12:123719400-123721600	Transcr. at gene 5' and 3'	Thymus	Thymus
38	chr12:123719400-123723400	Transcr. at gene 5' and 3'	Fetal Thymus	thymus
39	chr12:123719400-123726600	Weak transcription	Rectal Mucosa Donor 31	rectum
40	chr12:123719600-123722400	Weak transcription	Osteobl	bone
41	chr12:123719600-123723200	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
42	chr12:123719600-123726400	Weak transcription	Rectal Smooth Muscle	rectum
43	chr12:123719600-123734200	Weak transcription	Colonic Mucosa	Colon
44	chr12:123719600-123738400	Weak transcription	NH-A	brain
45	chr12:123719800-123720800	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
46	chr12:123719800-123721000	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
47	chr12:123719800-123721200	Genic enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
48	chr12:123719800-123721400	Genic enhancers	Primary T helper naive cells from peripheral blood	blood
49	chr12:123719800-123722000	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
50	chr12:123719800-123722000	Weak transcription	Pancreatic Islets	Pancreatic Islet

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