Variant report

Variant	rs11127045
Chromosome Location	chr2:86759498-86759499
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr2:86754212..86756941-chr2:86758517..86760046,2	K562	blood:
2	chr2:86755933..86757641-chr2:86759393..86762137,2	K562	blood:
3	chr2:86758704..86760548-chr2:86763114..86765137,2	K562	blood:
4	chr2:86752024..86755712-chr2:86758517..86761265,3	K562	blood:
5	chr2:86757651..86761789-chr2:86788885..86791715,3	MCF-7	breast:

Variant related genes	Relation type
ENSG00000228363	Chromatin interaction
ENSG00000115561	Chromatin interaction

Extended variants
information (count: 81 )
Associated
traits (count: 7 )

rSNPs within LD-proxies of this variant (count:79)

rs_ID	r²[population]
rs1015117	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];0.95[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.88[AFR][1000 genomes];0.91[AMR][1000 genomes];0.93[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs10169746	0.93[ASN][1000 genomes]
rs10180036	0.93[CEU][hapmap];0.85[YRI][hapmap]
rs10184879	1.00[CEU][hapmap];1.00[CHB][hapmap];0.94[JPT][hapmap];1.00[YRI][hapmap];0.84[AFR][1000 genomes];0.83[AMR][1000 genomes];0.88[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs10187880	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10188515	0.93[ASN][1000 genomes]
rs1020306	0.89[AMR][1000 genomes];0.92[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs10432704	0.94[ASN][1000 genomes]
rs1080551	0.93[ASN][1000 genomes]
rs11127046	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1137684	0.88[AFR][1000 genomes];0.91[AMR][1000 genomes];0.94[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs11676576	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11684230	0.88[AFR][1000 genomes];0.91[AMR][1000 genomes];0.93[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs11689330	0.92[AFR][1000 genomes];0.87[AMR][1000 genomes];0.86[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs11689593	0.92[ASN][1000 genomes]
rs12328637	0.84[AFR][1000 genomes];0.85[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs12613282	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.90[AFR][1000 genomes];0.84[AMR][1000 genomes];0.89[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs12614447	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];0.91[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.88[AFR][1000 genomes];0.91[AMR][1000 genomes];0.93[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs12615285	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];0.95[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12623509	0.96[CEU][hapmap];1.00[CHB][hapmap];0.87[GIH][hapmap];0.88[MEX][hapmap]
rs12714186	0.96[CEU][hapmap];0.80[GIH][hapmap];0.88[LWK][hapmap];0.93[TSI][hapmap]
rs12714188	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12714190	1.00[CHB][hapmap];0.97[CHD][hapmap];0.89[GIH][hapmap];1.00[JPT][hapmap];0.84[MEX][hapmap];0.91[ASN][1000 genomes]
rs12714198	0.86[ASW][hapmap];0.96[CEU][hapmap];0.87[CHD][hapmap];0.85[GIH][hapmap];0.94[JPT][hapmap];0.95[LWK][hapmap];1.00[MKK][hapmap];0.87[TSI][hapmap];1.00[YRI][hapmap]
rs12714199	1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[ASN][1000 genomes]
rs12987172	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];0.95[LWK][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.92[AFR][1000 genomes];0.89[AMR][1000 genomes];0.90[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs12991654	0.90[AFR][1000 genomes];0.86[AMR][1000 genomes];0.89[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs13015620	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.96[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];0.95[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.92[AFR][1000 genomes];0.87[AMR][1000 genomes];0.90[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs13034615	0.86[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13390713	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13408041	0.88[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs13429696	0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1465813	0.88[AFR][1000 genomes];0.91[AMR][1000 genomes];0.89[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs1518807	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.86[AFR][1000 genomes];0.91[AMR][1000 genomes];0.93[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs1629293	1.00[CHB][hapmap];0.90[CHD][hapmap];0.93[GIH][hapmap];1.00[JPT][hapmap];0.90[MKK][hapmap];0.82[TSI][hapmap];0.88[ASN][1000 genomes]
rs218059	0.85[ASN][1000 genomes]
rs2241803	1.00[ASW][hapmap];0.96[CEU][hapmap];1.00[CHB][hapmap];0.96[CHD][hapmap];0.98[GIH][hapmap];0.94[JPT][hapmap];0.95[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.88[AFR][1000 genomes];0.91[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs2292887	1.00[ASW][hapmap];0.96[CEU][hapmap];0.95[LWK][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap]
rs2367574	0.87[AMR][1000 genomes];0.89[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs308902	0.89[GIH][hapmap]
rs308903	0.86[GIH][hapmap]
rs308910	0.91[GIH][hapmap];0.82[TSI][hapmap]
rs308914	0.93[GIH][hapmap];0.87[MKK][hapmap];0.80[TSI][hapmap]
rs308915	0.84[GIH][hapmap]
rs3201448	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];0.95[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.84[AFR][1000 genomes];0.91[AMR][1000 genomes];0.93[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs34666164	0.93[ASN][1000 genomes]
rs3731812	0.88[AFR][1000 genomes];0.91[AMR][1000 genomes];0.94[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs3755002	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.96[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];0.95[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.88[AFR][1000 genomes];0.90[AMR][1000 genomes];0.88[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs3770058	0.88[AFR][1000 genomes];0.90[AMR][1000 genomes];0.89[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs422240	0.90[CHD][hapmap];0.91[GIH][hapmap];0.83[JPT][hapmap];0.88[MKK][hapmap];0.82[TSI][hapmap]
rs4832040	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4832041	0.89[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs4832042	0.84[AFR][1000 genomes];0.85[AMR][1000 genomes];0.87[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs4832045	0.90[ASN][1000 genomes]
rs4832296	1.00[ASN][1000 genomes]
rs4832297	1.00[CEU][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4832299	0.85[AFR][1000 genomes];0.88[AMR][1000 genomes];0.91[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs4832300	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];0.95[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.92[AFR][1000 genomes];0.89[AMR][1000 genomes];0.90[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4832302	0.93[ASN][1000 genomes]
rs4832304	1.00[ASW][hapmap];1.00[CEU][hapmap];0.93[CHD][hapmap];0.89[GIH][hapmap];0.83[JPT][hapmap];0.95[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.84[AFR][1000 genomes];0.83[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs62147239	0.81[AFR][1000 genomes];0.81[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs6725080	0.88[AFR][1000 genomes];0.89[AMR][1000 genomes];0.88[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs6728211	0.88[AFR][1000 genomes];0.87[AMR][1000 genomes];0.85[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs6731025	0.90[ASN][1000 genomes]
rs6738663	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.93[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];0.95[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.92[AFR][1000 genomes];0.89[AMR][1000 genomes];0.90[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs6750226	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];0.95[LWK][hapmap];1.00[MEX][hapmap];0.93[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.92[AFR][1000 genomes];0.89[AMR][1000 genomes];0.90[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6752371	1.00[CHB][hapmap];0.96[CHD][hapmap];0.89[GIH][hapmap];1.00[JPT][hapmap];0.84[MEX][hapmap];0.94[ASN][1000 genomes]
rs7369138	0.88[AFR][1000 genomes];0.91[AMR][1000 genomes];0.93[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs7557796	0.88[CHB][hapmap];0.83[ASN][1000 genomes]
rs7568840	0.88[CHB][hapmap]
rs7570640	0.93[ASN][1000 genomes]
rs7584882	1.00[CHB][hapmap];0.97[CHD][hapmap];0.89[GIH][hapmap];1.00[JPT][hapmap];0.94[ASN][1000 genomes]
rs7593151	1.00[ASN][1000 genomes]
rs7596717	1.00[CHB][hapmap];0.97[CHD][hapmap];0.89[GIH][hapmap];1.00[JPT][hapmap];0.83[MEX][hapmap];1.00[ASN][1000 genomes]
rs7601115	0.84[AFR][1000 genomes];0.85[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs8179729	1.00[ASN][1000 genomes]
rs9284788	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];0.95[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs958561	0.86[ASW][hapmap];0.96[CEU][hapmap];0.87[LWK][hapmap];0.98[MKK][hapmap];0.93[TSI][hapmap];0.85[YRI][hapmap]
rs9789777	0.81[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:2 , 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

mRNA abundance (count:7)

SNP	Gene	Cis/trans	Tissue	Source
rs11127045	POLR1A	cis	cerebellum	SCAN
rs11127045	VPS24	cis	lymphoblastoid	seeQTL
rs11127045	PTCD3	cis	cerebellum	SCAN
rs11127045	C2orf68	cis	cerebellum	SCAN
rs11127045	RNF103	cis	cerebellum	SCAN
rs11127045	VPS24	Cis_1M	lymphoblastoid	RTeQTL
rs11127045	POLR1A	cis	parietal	SCAN

Chromatin state (count:72 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:86734000-86784800	Weak transcription	Osteobl	bone
2	chr2:86736400-86770600	Weak transcription	Brain Angular Gyrus	brain
3	chr2:86737000-86761200	Weak transcription	Rectal Smooth Muscle	rectum
4	chr2:86737000-86772800	Weak transcription	Pancreas	Pancrea
5	chr2:86737400-86788400	Weak transcription	Brain Hippocampus Middle	brain
6	chr2:86737600-86768400	Weak transcription	Ovary	ovary
7	chr2:86737800-86779600	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
8	chr2:86738200-86772400	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
9	chr2:86738200-86772600	Weak transcription	Right Ventricle	heart
10	chr2:86741400-86768400	Weak transcription	Psoas Muscle	Psoas
11	chr2:86746000-86768000	Weak transcription	Fetal Heart	heart
12	chr2:86748000-86760600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
13	chr2:86748000-86770600	Weak transcription	Gastric	stomach
14	chr2:86749400-86772600	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
15	chr2:86749400-86775000	Weak transcription	NH-A	brain
16	chr2:86750000-86772400	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
17	chr2:86750400-86773600	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
18	chr2:86753600-86761600	Weak transcription	Muscle Satellite Cultured Cells	--
19	chr2:86753800-86788400	Weak transcription	HSMM	muscle
20	chr2:86754000-86774000	Weak transcription	Hela-S3	cervix
21	chr2:86755600-86760600	Weak transcription	Fetal Intestine Small	intestine
22	chr2:86755600-86761600	Weak transcription	HUVEC	blood vessel
23	chr2:86755800-86759600	Weak transcription	Breast Myoepithelial Primary Cells	Breast
24	chr2:86756000-86788400	Weak transcription	Brain Anterior Caudate	brain
25	chr2:86756200-86759800	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
26	chr2:86756400-86760200	Weak transcription	HUES64 Cell Line	embryonic stem cell
27	chr2:86756400-86760600	Weak transcription	Primary T cells fromperipheralblood	blood
28	chr2:86756400-86760600	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
29	chr2:86756400-86760600	Weak transcription	NHEK	skin
30	chr2:86756400-86761000	Weak transcription	Primary B cells from peripheral blood	blood
31	chr2:86756400-86772600	Weak transcription	Lung	lung
32	chr2:86756400-86773800	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
33	chr2:86756600-86759600	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
34	chr2:86756600-86759600	Weak transcription	Primary monocytes fromperipheralblood	blood
35	chr2:86756600-86759600	Weak transcription	Primary neutrophils fromperipheralblood	blood
36	chr2:86756600-86759600	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
37	chr2:86756600-86759800	Weak transcription	Fetal Intestine Large	intestine
38	chr2:86756600-86760000	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
39	chr2:86756600-86760600	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
40	chr2:86756600-86760600	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
41	chr2:86756600-86760600	Weak transcription	Adipose Nuclei	Adipose
42	chr2:86756600-86760600	Weak transcription	Duodenum Mucosa	Duodenum
43	chr2:86756600-86760800	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
44	chr2:86756600-86760800	Weak transcription	Primary B cells from cord blood	blood
45	chr2:86756600-86760800	Weak transcription	HSMMtube	muscle
46	chr2:86756600-86761000	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
47	chr2:86756600-86766400	Weak transcription	Fetal Brain Male	brain
48	chr2:86756600-86770400	Weak transcription	Liver	Liver
49	chr2:86756600-86770400	Weak transcription	HepG2	liver
50	chr2:86756600-86771800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived

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