Variant report

Variant	rs560097
Chromosome Location	chr11:65042530-65042531
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:0)
CpG islands
(count:0)
Chromatin interactive
region (count:29)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

(count:29 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr11:65041572..65044091-chr11:65265077..65268379,3	K562	blood:
2	chr11:65041689..65044108-chr11:65046608..65048416,2	K562	blood:
3	chr11:65040522..65042675-chr11:65046632..65049065,2	MCF-7	breast:
4	chr11:65036376..65038161-chr11:65042505..65044159,2	K562	blood:
5	chr11:65041377..65044455-chr11:65188184..65190315,3	K562	blood:
6	chr11:65042439..65045431-chr11:65275213..65278438,3	K562	blood:
7	chr11:65028356..65033825-chr11:65042510..65045720,5	K562	blood:
8	chr11:65041089..65045233-chr11:65046251..65051065,9	K562	blood:
9	chr11:65042207..65042764-chr11:65149476..65150366,2	K562	blood:
10	chr11:65042082..65043119-chr11:65082469..65083465,6	MCF-7	breast:
11	chr11:65040759..65043607-chr11:65273276..65276715,4	K562	blood:
12	chr11:65039896..65042561-chr11:65057779..65060143,2	K562	blood:
13	chr11:65040873..65044246-chr11:65095281..65099603,5	K562	blood:
14	chr11:65040759..65043462-chr11:65272919..65274800,4	K562	blood:
15	chr11:65041213..65044091-chr11:65264341..65268021,3	K562	blood:
16	chr11:65042279..65043014-chr11:65083936..65084499,2	MCF-7	breast:
17	chr11:65040374..65045284-chr11:65188184..65192530,7	K562	blood:
18	chr11:65041049..65042672-chr11:65082211..65085008,2	K562	blood:
19	chr11:65042217..65043163-chr11:65097074..65097976,7	K562	blood:
20	chr11:65038616..65040270-chr11:65041217..65044135,3	MCF-7	breast:
21	chr11:65041045..65043287-chr11:65194863..65197595,2	K562	blood:
22	chr11:65041054..65044148-chr11:65081241..65085369,4	MCF-7	breast:
23	chr11:65039583..65044108-chr11:65096986..65102768,8	MCF-7	breast:
24	chr11:65027816..65030800-chr11:65040130..65042677,3	MCF-7	breast:
25	chr11:65042183..65043475-chr11:65081996..65083744,16	K562	blood:
26	chr11:65042188..65043155-chr11:65096938..65098152,6	MCF-7	breast:
27	chr11:65041123..65044004-chr11:65191868..65194729,3	K562	blood:
28	chr11:65042197..65043185-chr11:65082109..65083720,21	MCF-7	breast:
29	chr11:65041172..65042887-chr11:65082211..65084564,3	K562	blood:

No data

Variant related genes	Relation type
ENSG00000245532	Chromatin interaction
ENSG00000014138	Chromatin interaction
ENSG00000162241	Chromatin interaction
ENSG00000251562	Chromatin interaction
ENSG00000133884	Chromatin interaction
ENSG00000149798	Chromatin interaction
ENSG00000270117	Chromatin interaction

Extended variants
information (count: 58 )
Associated
traits (count: 3 )

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

rs_ID	r²[population]
rs1152611	0.90[AMR][1000 genomes];0.87[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs1195733	1.00[CEU][hapmap];1.00[JPT][hapmap];0.87[EUR][1000 genomes]
rs12269727	0.96[AMR][1000 genomes];0.86[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs1633466	1.00[CEU][hapmap];1.00[JPT][hapmap];0.88[YRI][hapmap];0.83[AFR][1000 genomes];0.88[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs1783486	1.00[ASW][hapmap];1.00[CEU][hapmap];0.89[CHD][hapmap];0.94[GIH][hapmap];1.00[JPT][hapmap];0.94[LWK][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];0.81[YRI][hapmap];0.82[EUR][1000 genomes]
rs1858783	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];1.00[TSI][hapmap];0.83[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs239261	0.80[CEU][hapmap];0.94[CHD][hapmap];1.00[JPT][hapmap];0.94[LWK][hapmap];0.96[MKK][hapmap]
rs2904966	1.00[CHB][hapmap];0.84[GIH][hapmap];0.83[ASN][1000 genomes]
rs2904967	1.00[ASW][hapmap];0.90[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];0.88[LWK][hapmap];1.00[MKK][hapmap];0.95[TSI][hapmap]
rs2904979	0.80[CEU][hapmap];0.89[CHD][hapmap];0.82[GIH][hapmap];1.00[JPT][hapmap];0.94[LWK][hapmap];0.96[MKK][hapmap]
rs2904980	1.00[CEU][hapmap];0.89[CHD][hapmap];0.94[GIH][hapmap];1.00[JPT][hapmap]
rs2904981	0.86[CEU][hapmap];0.80[EUR][1000 genomes]
rs2904982	1.00[CHB][hapmap]
rs2904984	1.00[CEU][hapmap];1.00[JPT][hapmap]
rs2904986	0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs3015997	0.80[CEU][hapmap];0.89[CHD][hapmap];1.00[JPT][hapmap];0.94[LWK][hapmap];0.96[MKK][hapmap]
rs3015999	0.82[ASN][1000 genomes]
rs3016000	1.00[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3016001	0.81[EUR][1000 genomes]
rs3741386	1.00[CHB][hapmap]
rs4149813	0.86[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs482842	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];0.94[LWK][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];0.81[YRI][hapmap];0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs487568	0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs487989	1.00[ASW][hapmap];0.90[CEU][hapmap];1.00[CHB][hapmap];0.93[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MKK][hapmap];0.89[TSI][hapmap];0.81[YRI][hapmap];0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs488289	0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs499027	0.97[AFR][1000 genomes];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs503277	0.81[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.83[AMR][1000 genomes];0.85[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs506280	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]
rs507005	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]
rs509303	0.90[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.97[GIH][hapmap];0.95[TSI][hapmap];0.83[AMR][1000 genomes];0.87[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs526502	0.91[CEU][hapmap];1.00[CHB][hapmap];0.94[CHD][hapmap];0.94[GIH][hapmap];0.95[TSI][hapmap];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs542142	0.83[ASN][1000 genomes]
rs551523	1.00[CHB][hapmap]
rs554122	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];1.00[TSI][hapmap]
rs571128	0.83[EUR][1000 genomes]
rs592050	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs603286	0.82[AMR][1000 genomes];0.86[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs611910	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];0.88[YRI][hapmap];0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs612392	0.83[CHD][hapmap]
rs620427	1.00[CHB][hapmap];1.00[CHD][hapmap];0.85[GIH][hapmap]
rs625427	0.82[EUR][1000 genomes]
rs626555	0.90[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.83[AMR][1000 genomes];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs626802	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];1.00[TSI][hapmap];0.88[AMR][1000 genomes];0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs630055	0.90[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];0.95[TSI][hapmap];0.81[AMR][1000 genomes];0.85[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs636928	0.80[AFR][1000 genomes];0.98[AMR][1000 genomes];0.87[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs655433	0.90[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[YRI][hapmap];0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.90[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs667341	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.94[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];0.88[YRI][hapmap];0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs668735	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];1.00[TSI][hapmap];0.83[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs673147	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.94[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];0.88[YRI][hapmap];0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs676114	1.00[CHB][hapmap];1.00[CHD][hapmap];0.85[GIH][hapmap];0.83[ASN][1000 genomes]
rs676573	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[YRI][hapmap];0.97[AFR][1000 genomes];0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[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];0.83[AMR][1000 genomes];0.89[EUR][1000 genomes];0.95[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:3)

SNP	Gene	Cis/trans	Tissue	Source
rs560097	POLA2	Cis_1M	lymphoblastoid	RTeQTL
rs560097	POLA2	cis	multi-tissue	Pritchard
rs560097	POLA2	cis	lymphoblastoid	seeQTL

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	chr11:65030600-65042600	Weak transcription	Brain Inferior Temporal Lobe	brain
5	chr11:65030600-65042600	Weak transcription	Colonic Mucosa	Colon
6	chr11:65030600-65042600	Weak transcription	Rectal Smooth Muscle	rectum
7	chr11:65030600-65042600	Weak transcription	NHEK	skin
8	chr11:65030600-65042800	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
9	chr11:65030600-65042800	Weak transcription	Brain Substantia Nigra	brain
10	chr11:65030600-65042800	Weak transcription	Pancreatic Islets	Pancreatic Islet
11	chr11:65030600-65043000	Weak transcription	Brain Angular Gyrus	brain
12	chr11:65030600-65044400	Weak transcription	Pancreas	Pancrea
13	chr11:65030600-65045400	Weak transcription	Duodenum Smooth Muscle	Duodenum
14	chr11:65030600-65046200	Weak transcription	Gastric	stomach
15	chr11:65030600-65047800	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
16	chr11:65030600-65048200	Weak transcription	Aorta	Aorta
17	chr11:65030600-65049400	Weak transcription	Right Ventricle	heart
18	chr11:65030600-65056800	Weak transcription	Right Atrium	heart
19	chr11:65030600-65058000	Weak transcription	Fetal Brain Male	brain
20	chr11:65030600-65058800	Weak transcription	Psoas Muscle	Psoas
21	chr11:65030800-65045200	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
22	chr11:65031000-65046200	Weak transcription	Small Intestine	intestine
23	chr11:65031000-65046400	Weak transcription	Lung	lung
24	chr11:65031000-65049800	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
25	chr11:65031200-65064800	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
26	chr11:65031400-65042800	Weak transcription	Fetal Heart	heart
27	chr11:65031800-65058000	Strong transcription	Primary hematopoietic stem cells short term culture	blood
28	chr11:65035200-65043000	Weak transcription	NHLF	lung
29	chr11:65036800-65042800	Weak transcription	Fetal Lung	lung
30	chr11:65036800-65045200	Weak transcription	ES-I3 Cell Line	embryonic stem cell
31	chr11:65037200-65042600	Weak transcription	Fetal Kidney	kidney
32	chr11:65037400-65042600	Weak transcription	Colon Smooth Muscle	Colon
33	chr11:65038200-65047000	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
34	chr11:65038400-65042600	Weak transcription	Skeletal Muscle Female	skeletal muscle
35	chr11:65038400-65042800	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
36	chr11:65038400-65044400	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
37	chr11:65038400-65046200	Weak transcription	Sigmoid Colon	Sigmoid Colon
38	chr11:65038400-65046400	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
39	chr11:65038600-65042600	Weak transcription	Rectal Mucosa Donor 31	rectum
40	chr11:65038600-65042800	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
41	chr11:65038600-65042800	Weak transcription	Brain Hippocampus Middle	brain
42	chr11:65038600-65045000	Weak transcription	Placenta Amnion	Placenta Amnion
43	chr11:65038600-65046200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
44	chr11:65038600-65046200	Weak transcription	Brain Germinal Matrix	brain
45	chr11:65038600-65046200	Weak transcription	Esophagus	oesophagus
46	chr11:65038600-65048400	Weak transcription	Left Ventricle	heart
47	chr11:65038800-65042600	Weak transcription	K562	blood
48	chr11:65038800-65044400	Weak transcription	Fetal Brain Female	brain
49	chr11:65038800-65045000	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
50	chr11:65038800-65046200	Weak transcription	Primary T helper naive cells from peripheral blood	blood

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