Variant report

Variant	rs1568427
Chromosome Location	chr12:123738678-123738679
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr12:123714199..123721299-chr12:123733822..123739052,7	MCF-7	breast:
2	chr12:123737328..123740075-chr12:123754040..123756567,3	MCF-7	breast:
3	chr12:123737049..123739965-chr12:123755070..123757447,2	K562	blood:
4	chr12:123736848..123739836-chr12:123749677..123753155,4	K562	blood:

Variant related genes	Relation type
ENSG00000111328	Chromatin interaction
ENSG00000051825	Chromatin interaction
ENSG00000130921	Chromatin interaction

Extended variants
information (count: 123 )
Associated
traits (count: 9 )

rSNPs within LD-proxies of this variant (count:119)

rs_ID	r²[population]
rs10444439	0.81[JPT][hapmap]
rs1051431	0.84[ASW][hapmap]
rs1060105	0.85[GIH][hapmap]
rs10732573	0.90[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs10734901	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs10744150	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]
rs10744151	0.95[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.87[AFR][1000 genomes];0.87[AMR][1000 genomes];0.91[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs10744152	0.94[JPT][hapmap]
rs10772997	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]
rs10772998	0.81[CEU][hapmap]
rs10772999	0.98[AFR][1000 genomes];0.84[AMR][1000 genomes];0.92[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs10773000	0.85[CHD][hapmap];0.84[JPT][hapmap]
rs10773001	0.83[EUR][1000 genomes]
rs10773002	1.00[ASW][hapmap];0.85[CEU][hapmap];0.95[CHB][hapmap];1.00[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];0.95[MEX][hapmap];0.95[MKK][hapmap];0.95[TSI][hapmap];0.92[AFR][1000 genomes];0.99[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs10773921	0.83[ASW][hapmap]
rs10846489	0.83[ASW][hapmap];0.83[CHB][hapmap];0.89[CHD][hapmap];0.84[JPT][hapmap]
rs10846517	0.94[JPT][hapmap]
rs10846519	0.94[JPT][hapmap]
rs10846520	0.88[JPT][hapmap]
rs10846523	0.94[JPT][hapmap]
rs10848428	0.83[ASW][hapmap]
rs11057189	0.83[ASN][1000 genomes]
rs11057202	0.92[AFR][1000 genomes];0.87[AMR][1000 genomes];0.90[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs11057205	0.95[AFR][1000 genomes];0.82[AMR][1000 genomes];0.92[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs11057207	0.98[AFR][1000 genomes];0.89[AMR][1000 genomes];0.92[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs11057209	0.88[AFR][1000 genomes];0.88[AMR][1000 genomes];0.93[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs11057223	0.83[CHB][hapmap];0.89[CHD][hapmap];0.84[JPT][hapmap]
rs11057276	0.83[ASW][hapmap]
rs11057287	0.94[JPT][hapmap]
rs1109559	0.83[ASW][hapmap];0.83[CHB][hapmap];0.89[CHD][hapmap];0.84[JPT][hapmap]
rs1109560	0.83[CHB][hapmap];0.83[JPT][hapmap]
rs11532322	0.86[AFR][1000 genomes]
rs11554169	0.94[ASN][1000 genomes]
rs12298826	0.85[GIH][hapmap]
rs12316131	0.85[GIH][hapmap]
rs12322888	0.85[GIH][hapmap]
rs1402275	0.84[GIH][hapmap]
rs1533703	0.83[EUR][1000 genomes]
rs1568428	0.83[ASW][hapmap];0.83[CHB][hapmap];0.94[CHD][hapmap];0.84[JPT][hapmap];0.81[TSI][hapmap];0.84[ASN][1000 genomes]
rs1609520	0.90[CEU][hapmap];0.95[CHB][hapmap];0.91[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.83[MKK][hapmap];0.97[TSI][hapmap];0.82[AMR][1000 genomes];0.94[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1615350	0.83[ASW][hapmap];0.81[CEU][hapmap];0.82[MEX][hapmap];0.86[TSI][hapmap];1.00[YRI][hapmap]
rs1660	0.88[JPT][hapmap]
rs1716165	0.84[ASW][hapmap]
rs1716167	0.84[ASW][hapmap]
rs1716168	0.84[ASW][hapmap]
rs1716170	0.88[GIH][hapmap]
rs1716171	0.88[GIH][hapmap]
rs1727293	0.83[ASW][hapmap]
rs1727302	0.81[CEU][hapmap];0.81[MEX][hapmap];0.86[TSI][hapmap]
rs1727315	0.84[ASW][hapmap]
rs1727319	0.80[AFR][1000 genomes];0.83[AMR][1000 genomes];0.81[ASN][1000 genomes]
rs1727331	0.90[CEU][hapmap];0.95[CHB][hapmap];0.85[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.82[MEX][hapmap];0.95[TSI][hapmap];0.86[AMR][1000 genomes];0.89[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs1727332	0.87[AFR][1000 genomes];0.86[AMR][1000 genomes];0.88[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs1790106	0.83[ASW][hapmap]
rs1790116	0.92[ASW][hapmap]
rs1879379	0.83[ASW][hapmap];0.83[CHB][hapmap];0.88[CHD][hapmap];0.84[JPT][hapmap];0.81[ASN][1000 genomes]
rs1879380	0.88[GIH][hapmap];0.81[EUR][1000 genomes]
rs1969354	0.84[ASW][hapmap];0.88[GIH][hapmap];0.81[TSI][hapmap];0.83[EUR][1000 genomes]
rs1969355	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs1980251	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs1980252	0.82[EUR][1000 genomes]
rs2090764	0.93[ASN][1000 genomes]
rs2102949	0.81[ASN][1000 genomes]
rs2271976	0.83[CHB][hapmap];0.84[JPT][hapmap]
rs2280424	0.95[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.99[ASN][1000 genomes]
rs2337630	0.82[ASN][1000 genomes]
rs2337631	0.82[ASN][1000 genomes]
rs2337934	0.84[ASW][hapmap];0.85[GIH][hapmap];0.82[EUR][1000 genomes]
rs28362667	0.86[ASN][1000 genomes]
rs28362669	0.84[ASN][1000 genomes]
rs28406193	0.85[GIH][hapmap]
rs28414347	0.94[JPT][hapmap]
rs28458312	0.85[GIH][hapmap]
rs28472704	0.85[GIH][hapmap]
rs28501453	0.94[JPT][hapmap]
rs2851443	0.80[AFR][1000 genomes];0.81[AMR][1000 genomes];0.82[ASN][1000 genomes]
rs28587386	0.94[JPT][hapmap]
rs28595660	0.94[JPT][hapmap]
rs28613486	0.94[JPT][hapmap]
rs28636834	0.85[GIH][hapmap]
rs34841857	0.81[ASN][1000 genomes]
rs36121382	0.84[ASN][1000 genomes]
rs3759111	0.86[CHB][hapmap];0.80[CHD][hapmap];0.89[JPT][hapmap];0.83[ASN][1000 genomes]
rs3759113	0.86[CHB][hapmap];0.80[CHD][hapmap];0.89[JPT][hapmap]
rs3759114	0.95[CHB][hapmap];0.94[CHD][hapmap];1.00[JPT][hapmap];0.89[ASN][1000 genomes]
rs3803001	0.94[JPT][hapmap]
rs3825141	0.94[JPT][hapmap]
rs4460848	0.92[ASW][hapmap];0.81[CEU][hapmap];0.86[CHB][hapmap];0.80[CHD][hapmap];0.84[GIH][hapmap];0.89[JPT][hapmap];0.82[LWK][hapmap];0.86[MEX][hapmap];0.89[TSI][hapmap];1.00[YRI][hapmap];0.81[ASN][1000 genomes]
rs4474478	0.97[ASN][1000 genomes]
rs4474479	0.97[ASN][1000 genomes]
rs4594040	0.97[ASN][1000 genomes]
rs4759367	0.86[CHB][hapmap];0.88[JPT][hapmap]
rs4759371	0.84[ASW][hapmap];0.88[GIH][hapmap];0.83[EUR][1000 genomes]
rs4759372	0.93[ASN][1000 genomes]
rs4759406	0.81[ASN][1000 genomes]
rs4759407	0.86[CHB][hapmap];0.80[CHD][hapmap];0.89[JPT][hapmap];0.83[ASN][1000 genomes]
rs4759408	0.87[ASN][1000 genomes]
rs4759411	0.90[CHB][hapmap];1.00[JPT][hapmap];0.94[ASN][1000 genomes]
rs4759413	0.85[CHB][hapmap];0.94[JPT][hapmap];0.92[ASN][1000 genomes]
rs4759414	0.91[CHB][hapmap];1.00[JPT][hapmap];0.92[ASN][1000 genomes]
rs4759415	0.84[ASW][hapmap];0.88[GIH][hapmap];0.82[EUR][1000 genomes]
rs4759416	0.80[EUR][1000 genomes]
rs4759417	0.81[EUR][1000 genomes]
rs4759418	0.95[ASN][1000 genomes]
rs57676984	0.87[ASN][1000 genomes]
rs60077920	0.87[ASN][1000 genomes]
rs60254089	0.92[ASN][1000 genomes]
rs60296110	0.81[ASN][1000 genomes]
rs61231969	0.95[ASN][1000 genomes]
rs61519741	0.96[ASN][1000 genomes]
rs7137286	0.98[AFR][1000 genomes];0.88[AMR][1000 genomes];0.92[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7139321	0.83[CHB][hapmap];0.84[JPT][hapmap]
rs7297649	0.94[JPT][hapmap]
rs7304782	1.00[ASW][hapmap];0.90[CEU][hapmap];0.95[CHB][hapmap];0.94[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.95[LWK][hapmap];0.91[MEX][hapmap];0.95[MKK][hapmap];0.95[TSI][hapmap];1.00[YRI][hapmap];0.92[AFR][1000 genomes];0.87[AMR][1000 genomes];0.88[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs7313483	0.81[CEU][hapmap]
rs7953929	0.85[GIH][hapmap]
rs7959415	0.94[JPT][hapmap]
rs949143	0.83[ASW][hapmap]
rs9795593	0.94[JPT][hapmap]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	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
2	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
3	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
4	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:9)

SNP	Gene	Cis/trans	Tissue	Source
rs1568427	TMEM120B	cis	parietal	SCAN
rs1568427	PITPNM2	cis	cerebellum	SCAN
rs1568427	ANAPC5	cis	parietal	SCAN
rs1568427	CDK2AP1	cis	Esophagus Mucosa	GTEx
rs1568427	SBNO1	Cis_1M	lymphoblastoid	RTeQTL
rs1568427	RP11-282O18.3	cis	Esophagus Mucosa	GTEx
rs1568427	MPHOSPH9	Cis_1M	lymphoblastoid	RTeQTL
rs1568427	CDK2AP1	Cis_1M	lymphoblastoid	RTeQTL
rs1568427	ARL6IP4	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:126 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:123718800-123739600	Weak transcription	Fetal Kidney	kidney
2	chr12:123725800-123746400	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
3	chr12:123727600-123739200	Weak transcription	Duodenum Smooth Muscle	Duodenum
4	chr12:123733400-123745000	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
5	chr12:123734600-123753200	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
6	chr12:123735000-123740400	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
7	chr12:123735200-123738800	Enhancers	Brain Cingulate Gyrus	brain
8	chr12:123735200-123739600	Enhancers	Fetal Brain Male	brain
9	chr12:123735200-123751800	Strong transcription	Fetal Stomach	stomach
10	chr12:123735400-123739200	Enhancers	Brain Dorsolateral Prefrontal Cortex	brain
11	chr12:123735400-123745400	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
12	chr12:123735600-123738800	Weak transcription	Primary T killer memory cells from peripheral blood	blood
13	chr12:123735600-123743400	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
14	chr12:123735600-123752400	Strong transcription	Thymus	Thymus
15	chr12:123736000-123738800	Weak transcription	HSMMtube	muscle
16	chr12:123736000-123739400	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
17	chr12:123736000-123739600	Weak transcription	ES-I3 Cell Line	embryonic stem cell
18	chr12:123736000-123740600	Weak transcription	iPS-15b Cell Line	embryonic stem cell
19	chr12:123736000-123745400	Strong transcription	HUES64 Cell Line	embryonic stem cell
20	chr12:123736000-123747800	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
21	chr12:123736000-123748000	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
22	chr12:123736000-123752200	Strong transcription	Dnd41	blood
23	chr12:123736200-123742400	Strong transcription	Fetal Thymus	thymus
24	chr12:123736200-123744200	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
25	chr12:123736200-123751400	Strong transcription	Primary hematopoietic stem cells short term culture	blood
26	chr12:123736400-123750600	Strong transcription	Fetal Lung	lung
27	chr12:123736400-123752200	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
28	chr12:123736400-123752600	Strong transcription	NHLF	lung
29	chr12:123736600-123740400	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
30	chr12:123737000-123744000	Strong transcription	Primary T helper naive cells fromperipheralblood	blood
31	chr12:123737000-123753000	Strong transcription	Fetal Intestine Small	intestine
32	chr12:123737200-123752000	Strong transcription	A549	lung
33	chr12:123737400-123749000	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
34	chr12:123737600-123740000	Strong transcription	Hela-S3	cervix
35	chr12:123737800-123739800	Genic enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
36	chr12:123737800-123741400	Strong transcription	Colonic Mucosa	Colon
37	chr12:123737800-123742000	Strong transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
38	chr12:123737800-123743800	Strong transcription	GM12878-XiMat	blood
39	chr12:123737800-123745000	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
40	chr12:123737800-123745600	Strong transcription	HUES48 Cell Line	embryonic stem cell
41	chr12:123737800-123746800	Strong transcription	Primary neutrophils fromperipheralblood	blood
42	chr12:123738000-123738800	Flanking Active TSS	Fetal Brain Female	brain
43	chr12:123738000-123738800	Genic enhancers	Right Ventricle	heart
44	chr12:123738000-123738800	Strong transcription	Small Intestine	intestine
45	chr12:123738000-123739000	Genic enhancers	Muscle Satellite Cultured Cells	--
46	chr12:123738000-123739200	Strong transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
47	chr12:123738000-123739200	Genic enhancers	Stomach Mucosa	stomach
48	chr12:123738000-123739800	Strong transcription	Primary T killer naive cells fromperipheralblood	blood
49	chr12:123738000-123739800	Genic enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
50	chr12:123738000-123739800	Genic enhancers	Colon Smooth Muscle	Colon

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