Variant report

Variant	rs11127047
Chromosome Location	chr2:86826508-86826509
allele	C/T
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	POLR2A	chr2:86826299-86826526	MCF-7	breast:	n/a	n/a
2	POLR2A	chr2:86825949-86826992	MCF10A-Er-Src	breast:	n/a	n/a
3	POLR2A	chr2:86826014-86826578	MCF10A-Er-Src	breast:	n/a	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr2:86825844..86830459-chr2:86849493..86852270,4	MCF-7	breast:
2	chr2:86825748..86827499-chr2:86830079..86832561,2	K562	blood:

Variant related genes	Relation type
ENSG00000228363	TF binding region
ENSG00000249884	Chromatin interaction
ENSG00000239305	Chromatin interaction
ENSG00000228363	Chromatin interaction

Extended variants
information (count: 57 )
Associated
traits (count: 5 )

rSNPs within LD-proxies of this variant (count:54)

rs_ID	r²[population]
rs1015117	0.81[CHD][hapmap];0.81[GIH][hapmap]
rs10169746	0.84[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs10184584	0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10184985	0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs10187753	0.99[ASN][1000 genomes]
rs1036940	0.83[GIH][hapmap]
rs10432704	0.82[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs1080551	0.86[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs11689593	0.83[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs12328637	0.83[ASN][1000 genomes]
rs12614447	0.81[CHD][hapmap];0.81[GIH][hapmap]
rs12615285	0.81[CHD][hapmap];0.81[GIH][hapmap]
rs12623509	1.00[CHD][hapmap];0.91[GIH][hapmap];0.84[MEX][hapmap];0.83[ASN][1000 genomes]
rs12714190	0.91[CEU][hapmap];0.81[CHD][hapmap];0.89[GIH][hapmap];0.88[MEX][hapmap];0.82[EUR][1000 genomes]
rs12714199	0.92[CEU][hapmap];0.85[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs12987172	0.81[CHD][hapmap];0.81[GIH][hapmap]
rs12995117	0.83[GIH][hapmap]
rs13015620	0.81[GIH][hapmap]
rs13034615	0.81[CHD][hapmap];0.81[GIH][hapmap]
rs2044230	0.83[GIH][hapmap]
rs218060	0.85[GIH][hapmap]
rs2241803	0.81[GIH][hapmap]
rs2367546	0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs308900	0.81[ASN][1000 genomes]
rs308901	0.85[GIH][hapmap]
rs308907	0.91[GIH][hapmap]
rs308911	0.91[GIH][hapmap]
rs3201448	0.81[CHD][hapmap];0.81[GIH][hapmap]
rs34666164	0.83[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs3755002	0.81[GIH][hapmap]
rs396354	0.85[GIH][hapmap]
rs422240	0.82[CHB][hapmap];0.81[ASN][1000 genomes]
rs4832043	0.82[ASN][1000 genomes]
rs4832290	0.83[GIH][hapmap]
rs4832294	0.83[GIH][hapmap]
rs4832300	0.81[CHD][hapmap];0.81[GIH][hapmap]
rs4832302	0.84[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs4832303	0.99[ASN][1000 genomes]
rs4832304	0.90[CHB][hapmap];0.83[ASN][1000 genomes]
rs6547700	0.80[GIH][hapmap]
rs6714826	0.83[GIH][hapmap]
rs6733569	0.99[ASN][1000 genomes]
rs6738663	0.83[CHD][hapmap];0.81[GIH][hapmap]
rs6750226	0.81[CHD][hapmap];0.81[GIH][hapmap]
rs6752371	0.92[CEU][hapmap];0.89[GIH][hapmap];0.88[MEX][hapmap];0.84[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs683139	0.82[GIH][hapmap]
rs7557796	0.96[CEU][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.83[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.83[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs7568840	0.96[CEU][hapmap];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs7570640	0.84[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs7584882	0.92[CEU][hapmap];0.81[CHD][hapmap];0.89[GIH][hapmap];0.88[MEX][hapmap];0.83[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs7587034	0.98[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7596717	0.92[CEU][hapmap];0.81[CHD][hapmap];0.89[GIH][hapmap];0.91[MEX][hapmap]
rs7601115	0.83[ASN][1000 genomes]
rs9284788	0.81[CHD][hapmap];0.81[GIH][hapmap]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv3412938	chr2:86370969-86867936	Strong transcription Enhancers Genic enhancers Weak transcription Flanking Bivalent TSS/Enh Active TSS Flanking Active TSS ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	77 gene(s)	inside rSNPs	diseases
2	nsv532724	chr2:86622295-87086407	Weak transcription Active TSS Genic enhancers Enhancers Flanking Active TSS Strong transcription Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	45 gene(s)	inside rSNPs	diseases
3	nsv1011590	chr2:86824181-86906114	Active TSS Strong transcription Genic enhancers Enhancers Weak transcription Transcr. at gene 5' and 3' Flanking Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	22 gene(s)	inside rSNPs	diseases

mRNA abundance (count:5)

SNP	Gene	Cis/trans	Tissue	Source
rs11127047	VPS24	Cis_1M	lymphoblastoid	RTeQTL
rs11127047	PTCD3	cis	cerebellum	SCAN
rs11127047	POLR1A	cis	cerebellum	SCAN
rs11127047	VPS24	cis	lymphoblastoid	seeQTL
rs11127047	IMMT	cis	lymphoblastoid	seeQTL

Chromatin state (count:31 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:86819800-86831000	Weak transcription	Fetal Brain Female	brain
2	chr2:86820000-86830600	Weak transcription	Brain Anterior Caudate	brain
3	chr2:86820000-86830800	Weak transcription	Duodenum Smooth Muscle	Duodenum
4	chr2:86820200-86831000	Weak transcription	Fetal Brain Male	brain
5	chr2:86820200-86831000	Weak transcription	Stomach Smooth Muscle	stomach
6	chr2:86820400-86828400	Weak transcription	Fetal Stomach	stomach
7	chr2:86820600-86831000	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
8	chr2:86823000-86830600	Weak transcription	Fetal Muscle Leg	muscle
9	chr2:86823200-86842800	Weak transcription	Psoas Muscle	Psoas
10	chr2:86823600-86831200	Weak transcription	HSMMtube	muscle
11	chr2:86824000-86830800	Weak transcription	Skeletal Muscle Female	skeletal muscle
12	chr2:86824000-86831000	Weak transcription	Skeletal Muscle Male	skeletal muscle
13	chr2:86824600-86840600	Weak transcription	Fetal Heart	heart
14	chr2:86824800-86831000	Weak transcription	Left Ventricle	heart
15	chr2:86825400-86849000	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
16	chr2:86825600-86830600	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
17	chr2:86825800-86826600	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
18	chr2:86825800-86826800	Enhancers	NHEK	skin
19	chr2:86825800-86831000	Weak transcription	Liver	Liver
20	chr2:86826000-86826600	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
21	chr2:86826000-86826600	Enhancers	HMEC	breast
22	chr2:86826000-86826800	Enhancers	Breast Myoepithelial Primary Cells	Breast
23	chr2:86826000-86831000	Weak transcription	HUVEC	blood vessel
24	chr2:86826200-86826600	Enhancers	Colon Smooth Muscle	Colon
25	chr2:86826200-86826800	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
26	chr2:86826200-86826800	Enhancers	Rectal Smooth Muscle	rectum
27	chr2:86826400-86826600	Enhancers	Aorta	Aorta
28	chr2:86826400-86826600	Enhancers	Gastric	stomach
29	chr2:86826400-86826800	Enhancers	Right Ventricle	heart
30	chr2:86826400-86830400	Weak transcription	Stomach Mucosa	stomach
31	chr2:86826400-86831000	Weak transcription	Hela-S3	cervix

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