Variant report

Variant	rs554122
Chromosome Location	chr11:65033874-65033875
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 65 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:61)

rs_ID	r²[population]
rs10750761	0.81[ASN][1000 genomes]
rs1152611	0.89[AMR][1000 genomes];0.86[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs1195733	1.00[CEU][hapmap];1.00[JPT][hapmap];0.84[AFR][1000 genomes];0.80[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs12269727	0.85[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs1633466	1.00[CEU][hapmap];1.00[JPT][hapmap];0.87[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs1783486	1.00[CEU][hapmap];0.89[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];0.90[MEX][hapmap];1.00[TSI][hapmap];0.81[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs1858783	0.83[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.89[LWK][hapmap];1.00[MEX][hapmap];0.96[MKK][hapmap];1.00[TSI][hapmap];1.00[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs239261	0.80[CEU][hapmap];0.94[CHD][hapmap];1.00[JPT][hapmap]
rs28781278	0.89[AMR][1000 genomes]
rs2904966	1.00[CHB][hapmap];0.88[GIH][hapmap]
rs2904967	0.90[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.95[TSI][hapmap]
rs2904978	0.82[MEX][hapmap]
rs2904979	0.80[CEU][hapmap];0.89[CHD][hapmap];0.85[GIH][hapmap];1.00[JPT][hapmap];0.83[ASN][1000 genomes]
rs2904980	0.83[ASW][hapmap];1.00[CEU][hapmap];0.89[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];0.91[MEX][hapmap];0.86[MKK][hapmap];0.83[ASN][1000 genomes]
rs2904981	0.86[CEU][hapmap];0.81[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs2904982	1.00[CHB][hapmap]
rs2904983	0.83[ASN][1000 genomes]
rs2904984	1.00[CEU][hapmap];1.00[JPT][hapmap]
rs2904986	0.98[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2957111	0.83[ASN][1000 genomes]
rs3015997	0.80[CEU][hapmap];0.89[CHD][hapmap];0.82[GIH][hapmap];1.00[JPT][hapmap];0.83[ASN][1000 genomes]
rs3015999	0.87[ASN][1000 genomes]
rs3016000	0.83[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs3016001	0.82[AMR][1000 genomes];0.82[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs3741386	1.00[CHB][hapmap]
rs4149813	0.88[AFR][1000 genomes];0.85[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs482842	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.90[MEX][hapmap];1.00[TSI][hapmap];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs487397	0.83[ASN][1000 genomes]
rs487568	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs487989	0.90[CEU][hapmap];1.00[CHB][hapmap];0.93[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.89[TSI][hapmap];0.88[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs488289	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs499027	0.83[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs503277	0.81[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[AFR][1000 genomes];0.96[AMR][1000 genomes];0.86[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs506280	0.90[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[AFR][1000 genomes];0.96[AMR][1000 genomes];0.90[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs507005	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.99[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs509303	0.90[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.90[MEX][hapmap];0.84[MKK][hapmap];0.95[TSI][hapmap];0.96[AMR][1000 genomes];0.86[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs526502	0.83[ASW][hapmap];0.91[CEU][hapmap];1.00[CHB][hapmap];0.94[CHD][hapmap];0.97[GIH][hapmap];0.87[LWK][hapmap];0.96[MKK][hapmap];0.95[TSI][hapmap];0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs541829	0.80[ASN][1000 genomes]
rs551523	1.00[CHB][hapmap]
rs560097	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];1.00[TSI][hapmap];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs571128	0.82[AFR][1000 genomes];0.82[AMR][1000 genomes];0.84[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs592050	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs603286	0.94[AMR][1000 genomes];0.87[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs611910	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.90[MEX][hapmap];1.00[TSI][hapmap];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs612392	0.83[CHD][hapmap]
rs620427	1.00[CHB][hapmap];1.00[CHD][hapmap];0.88[GIH][hapmap]
rs625427	0.81[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs626555	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];0.95[ASN][1000 genomes]
rs626802	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.90[MEX][hapmap];0.90[MKK][hapmap];1.00[TSI][hapmap];0.91[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs630055	0.83[ASW][hapmap];0.90[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.89[LWK][hapmap];0.90[MEX][hapmap];0.92[MKK][hapmap];0.95[TSI][hapmap];0.90[AFR][1000 genomes];0.94[AMR][1000 genomes];0.86[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs636928	0.86[EUR][1000 genomes]
rs650056	0.83[ASN][1000 genomes]
rs655433	0.90[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs667341	1.00[CEU][hapmap];1.00[CHB][hapmap];0.94[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.90[MEX][hapmap];1.00[TSI][hapmap];0.99[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs668735	0.83[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.89[LWK][hapmap];1.00[MEX][hapmap];0.96[MKK][hapmap];1.00[TSI][hapmap];1.00[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs673147	1.00[CEU][hapmap];1.00[CHB][hapmap];0.94[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.90[MEX][hapmap];1.00[TSI][hapmap];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs676114	1.00[CHB][hapmap];1.00[CHD][hapmap];0.88[GIH][hapmap]
rs676573	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs689288	0.83[CHD][hapmap]
rs7116674	0.94[CHD][hapmap]
rs8638	0.88[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]

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	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	nsv976461	chr11:65000821-65054446	Weak transcription Flanking Active TSS Strong transcription Enhancers Genic enhancers Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	30 gene(s)	inside rSNPs	diseases
4	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
rs554122	POLA2	Cis_1M	lymphoblastoid	RTeQTL
rs554122	POLA2	cis	multi-tissue	Pritchard

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr11:65030000-65044400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
2	chr11:65030200-65058800	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
3	chr11:65030400-65042800	Weak transcription	Stomach Mucosa	stomach
4	chr11:65030600-65034000	Weak transcription	H9 Cell Line	embryonic stem cell
5	chr11:65030600-65034000	Weak transcription	iPS-18 Cell Line	embryonic stem cell
6	chr11:65030600-65034000	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
7	chr11:65030600-65034000	Weak transcription	Rectal Mucosa Donor 29	rectum
8	chr11:65030600-65034600	Weak transcription	Primary T helper naive cells from peripheral blood	blood
9	chr11:65030600-65034600	Weak transcription	Skeletal Muscle Female	skeletal muscle
10	chr11:65030600-65034800	Weak transcription	ES-I3 Cell Line	embryonic stem cell
11	chr11:65030600-65034800	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
12	chr11:65030600-65034800	Weak transcription	Placenta	Placenta
13	chr11:65030600-65034800	Weak transcription	NHLF	lung
14	chr11:65030600-65035000	Weak transcription	Fetal Intestine Large	intestine
15	chr11:65030600-65036200	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
16	chr11:65030600-65036200	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
17	chr11:65030600-65036200	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
18	chr11:65030600-65036200	Weak transcription	Fetal Kidney	kidney
19	chr11:65030600-65036200	Weak transcription	Rectal Mucosa Donor 31	rectum
20	chr11:65030600-65036400	Weak transcription	Brain Anterior Caudate	brain
21	chr11:65030600-65036400	Weak transcription	Colon Smooth Muscle	Colon
22	chr11:65030600-65036400	Weak transcription	Left Ventricle	heart
23	chr11:65030600-65037000	Weak transcription	Placenta Amnion	Placenta Amnion
24	chr11:65030600-65037600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
25	chr11:65030600-65037600	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
26	chr11:65030600-65037600	Weak transcription	Fetal Brain Female	brain
27	chr11:65030600-65037600	Weak transcription	Ovary	ovary
28	chr11:65030600-65037600	Weak transcription	Sigmoid Colon	Sigmoid Colon
29	chr11:65030600-65037600	Weak transcription	Skeletal Muscle Male	skeletal muscle
30	chr11:65030600-65037600	Weak transcription	Stomach Smooth Muscle	stomach
31	chr11:65030600-65037600	Weak transcription	Spleen	Spleen
32	chr11:65030600-65037800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
33	chr11:65030600-65037800	Weak transcription	Brain Hippocampus Middle	brain
34	chr11:65030600-65038000	Weak transcription	Esophagus	oesophagus
35	chr11:65030600-65042200	Weak transcription	NH-A	brain
36	chr11:65030600-65042400	Weak transcription	Brain Cingulate Gyrus	brain
37	chr11:65030600-65042400	Weak transcription	HSMM	muscle
38	chr11:65030600-65042400	Weak transcription	HSMMtube	muscle
39	chr11:65030600-65042600	Weak transcription	Brain Inferior Temporal Lobe	brain
40	chr11:65030600-65042600	Weak transcription	Colonic Mucosa	Colon
41	chr11:65030600-65042600	Weak transcription	Rectal Smooth Muscle	rectum
42	chr11:65030600-65042600	Weak transcription	NHEK	skin
43	chr11:65030600-65042800	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
44	chr11:65030600-65042800	Weak transcription	Brain Substantia Nigra	brain
45	chr11:65030600-65042800	Weak transcription	Pancreatic Islets	Pancreatic Islet
46	chr11:65030600-65043000	Weak transcription	Brain Angular Gyrus	brain
47	chr11:65030600-65044400	Weak transcription	Pancreas	Pancrea
48	chr11:65030600-65045400	Weak transcription	Duodenum Smooth Muscle	Duodenum
49	chr11:65030600-65046200	Weak transcription	Gastric	stomach
50	chr11:65030600-65047800	Weak transcription	Primary T killer naive cells fromperipheralblood	blood

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