Variant report

Variant	rs506280
Chromosome Location	chr11:65069534-65069535
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr11:65066072..65068359-chr11:65068503..65070591,2	MCF-7	breast:
2	chr11:65067128..65069997-chr11:65080803..65083874,3	K562	blood:
3	chr11:65047637..65049685-chr11:65066933..65069852,2	MCF-7	breast:
4	chr11:65068343..65070835-chr11:65079174..65082064,2	MCF-7	breast:
5	chr11:65053971..65055888-chr11:65068050..65070262,2	MCF-7	breast:
6	chr11:65067115..65069965-chr11:65073669..65075619,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000149798	Chromatin interaction
ENSG00000014138	Chromatin interaction

Extended variants
information (count: 50 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:47)

rs_ID	r²[population]
rs1152611	0.92[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1195733	0.90[CEU][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap]
rs12269727	0.94[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs1633466	0.90[CEU][hapmap];1.00[JPT][hapmap]
rs1783486	0.90[CEU][hapmap];1.00[JPT][hapmap]
rs1858783	0.90[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];0.90[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs239261	1.00[JPT][hapmap]
rs28781278	0.92[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs2904966	1.00[CHB][hapmap];0.83[ASN][1000 genomes]
rs2904967	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs2904979	1.00[JPT][hapmap]
rs2904980	0.90[CEU][hapmap];1.00[JPT][hapmap];0.93[YRI][hapmap]
rs2904982	1.00[CHB][hapmap]
rs2904984	0.90[CEU][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap]
rs2904986	0.94[AFR][1000 genomes];0.92[AMR][1000 genomes];0.90[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs3015997	1.00[JPT][hapmap]
rs3016000	0.89[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs3741386	1.00[CHB][hapmap]
rs4149813	0.93[AFR][1000 genomes];0.89[AMR][1000 genomes];0.90[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs482842	0.90[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.83[AMR][1000 genomes];0.89[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs487568	0.95[AFR][1000 genomes];0.96[AMR][1000 genomes];0.90[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs487989	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.83[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs488289	0.94[AFR][1000 genomes];0.96[AMR][1000 genomes];0.89[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs499027	0.87[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs503277	0.90[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs507005	0.90[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[YRI][hapmap];0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];0.90[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs509303	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs526502	0.81[CEU][hapmap];1.00[CHB][hapmap];1.00[YRI][hapmap];0.93[AFR][1000 genomes];0.96[AMR][1000 genomes];0.88[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs542142	0.83[ASN][1000 genomes]
rs551523	1.00[CHB][hapmap]
rs554122	0.90[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs560097	0.90[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.83[AMR][1000 genomes];0.89[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs592050	0.90[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[AFR][1000 genomes];0.96[AMR][1000 genomes];0.90[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs603286	0.81[AFR][1000 genomes];0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs611910	0.90[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.83[AMR][1000 genomes];0.89[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs620427	1.00[CHB][hapmap]
rs626555	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[YRI][hapmap];0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs626802	0.90[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.87[AMR][1000 genomes];0.86[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs630055	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[YRI][hapmap];0.94[AFR][1000 genomes];0.98[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs636928	0.81[AMR][1000 genomes];0.95[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs655433	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.83[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs667341	0.90[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.83[AMR][1000 genomes];0.89[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs668735	0.90[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];0.90[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs673147	0.90[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.83[AMR][1000 genomes];0.88[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs676114	1.00[CHB][hapmap];0.83[ASN][1000 genomes]
rs676573	0.89[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.87[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs8638	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.97[YRI][hapmap];0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]

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	nsv526181	chr11:64638041-65257329	Flanking Active TSS Enhancers Strong transcription Active TSS Weak transcription Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	1539 gene(s)	inside rSNPs	diseases
2	nsv832190	chr11:64978144-65127613	Flanking Active TSS Weak transcription Enhancers Genic enhancers Bivalent Enhancer Strong transcription Bivalent/Poised TSS Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	48 gene(s)	inside rSNPs	diseases
3	esv2422285	chr11:65013294-65254540	Genic enhancers Enhancers Weak transcription Active TSS Bivalent Enhancer Flanking Active TSS Strong transcription Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	474 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs506280	POLA2	Cis_1M	lymphoblastoid	RTeQTL
rs506280	POLA2	cis	multi-tissue	Pritchard

Chromatin state (count:118 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr11:65042800-65072800	Strong transcription	Dnd41	blood
2	chr11:65047800-65075800	Weak transcription	Small Intestine	intestine
3	chr11:65060000-65069600	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
4	chr11:65062800-65069600	Weak transcription	Stomach Mucosa	stomach
5	chr11:65062800-65077200	Weak transcription	Fetal Brain Male	brain
6	chr11:65063800-65081200	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
7	chr11:65064000-65070000	Weak transcription	Primary T helper naive cells from peripheral blood	blood
8	chr11:65064000-65071200	Weak transcription	GM12878-XiMat	blood
9	chr11:65065000-65081800	Weak transcription	Primary T helper cells PMA-I stimulated	--
10	chr11:65065000-65081800	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
11	chr11:65066000-65073400	Strong transcription	Thymus	Thymus
12	chr11:65066000-65081800	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
13	chr11:65066200-65071000	Enhancers	Placenta	Placenta
14	chr11:65066200-65071200	Weak transcription	H9 Cell Line	embryonic stem cell
15	chr11:65066200-65076200	Weak transcription	Primary T cells from cord blood	blood
16	chr11:65066200-65078000	Weak transcription	HMEC	breast
17	chr11:65066400-65071200	Weak transcription	NHEK	skin
18	chr11:65066400-65080800	Weak transcription	Brain Germinal Matrix	brain
19	chr11:65066600-65071600	Weak transcription	Pancreas	Pancrea
20	chr11:65066600-65072800	Weak transcription	Duodenum Mucosa	Duodenum
21	chr11:65066600-65076000	Weak transcription	Osteobl	bone
22	chr11:65066600-65081600	Weak transcription	Primary T helper cells fromperipheralblood	blood
23	chr11:65066600-65081800	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
24	chr11:65066800-65071200	Weak transcription	Psoas Muscle	Psoas
25	chr11:65066800-65073000	Weak transcription	NH-A	brain
26	chr11:65067000-65069600	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
27	chr11:65067000-65075800	Weak transcription	Primary neutrophils fromperipheralblood	blood
28	chr11:65067000-65076400	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
29	chr11:65067000-65081800	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
30	chr11:65067200-65069600	Enhancers	HSMMtube	muscle
31	chr11:65067200-65071000	Weak transcription	Breast Myoepithelial Primary Cells	Breast
32	chr11:65067200-65071200	Enhancers	Fetal Muscle Leg	muscle
33	chr11:65067200-65071600	Weak transcription	Liver	Liver
34	chr11:65067200-65076000	Weak transcription	Fetal Brain Female	brain
35	chr11:65067400-65075200	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
36	chr11:65068000-65070600	Enhancers	HSMM	muscle
37	chr11:65068200-65070200	Enhancers	Brain Hippocampus Middle	brain
38	chr11:65068200-65070200	Enhancers	Colon Smooth Muscle	Colon
39	chr11:65068200-65079200	Genic enhancers	Fetal Intestine Small	intestine
40	chr11:65068400-65069600	Enhancers	Adipose Nuclei	Adipose
41	chr11:65068400-65070000	Enhancers	Brain Cingulate Gyrus	brain
42	chr11:65068400-65070000	Enhancers	Brain Inferior Temporal Lobe	brain
43	chr11:65068400-65070200	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
44	chr11:65068400-65070200	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
45	chr11:65068400-65070400	Enhancers	Fetal Lung	lung
46	chr11:65068400-65071200	Enhancers	Fetal Intestine Large	intestine
47	chr11:65068600-65070000	Enhancers	Duodenum Smooth Muscle	Duodenum
48	chr11:65068600-65070000	Enhancers	Rectal Mucosa Donor 29	rectum
49	chr11:65068600-65070000	Enhancers	Rectal Smooth Muscle	rectum
50	chr11:65068600-65070000	Enhancers	Spleen	Spleen

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