Variant report

Variant	rs488289
Chromosome Location	chr11:65039264-65039265
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr11:65032758..65036508-chr11:65038110..65042460,7	K562	blood:
2	chr11:65027012..65029894-chr11:65038362..65040940,3	K562	blood:
3	chr11:65038616..65040270-chr11:65041217..65044135,3	MCF-7	breast:
4	chr11:65033895..65035534-chr11:65037649..65040309,2	MCF-7	breast:
5	chr11:65038650..65040495-chr11:65081586..65083438,2	K562	blood:
6	chr11:65028264..65031673-chr11:65033494..65039309,8	MCF-7	breast:

Variant related genes	Relation type
ENSG00000149798	Chromatin interaction
ENSG00000014138	Chromatin interaction

Extended variants
information (count: 45 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:41)

rs_ID	r²[population]
rs1152611	0.89[AMR][1000 genomes];0.85[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs1195733	0.83[AFR][1000 genomes];0.80[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs12269727	0.84[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs1633466	0.86[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs1783486	0.80[EUR][1000 genomes]
rs1858783	0.99[AFR][1000 genomes];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28781278	0.89[AMR][1000 genomes]
rs2904966	0.83[ASN][1000 genomes]
rs2904981	0.80[EUR][1000 genomes]
rs2904986	0.98[AFR][1000 genomes];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs3015999	0.82[ASN][1000 genomes]
rs3016000	0.83[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3016001	0.82[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs4149813	0.87[AFR][1000 genomes];0.85[AMR][1000 genomes];0.86[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs482842	0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs487568	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs487989	0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs499027	0.83[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs503277	0.91[AFR][1000 genomes];0.96[AMR][1000 genomes];0.85[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs506280	0.94[AFR][1000 genomes];0.96[AMR][1000 genomes];0.89[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs507005	0.98[AFR][1000 genomes];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs509303	0.96[AMR][1000 genomes];0.85[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs526502	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs542142	0.83[ASN][1000 genomes]
rs560097	0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs571128	0.81[AFR][1000 genomes];0.82[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs592050	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs603286	0.94[AMR][1000 genomes];0.86[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs611910	0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs625427	0.80[EUR][1000 genomes]
rs626555	0.94[AFR][1000 genomes];0.96[AMR][1000 genomes];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs626802	0.91[AMR][1000 genomes];0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs630055	0.89[AFR][1000 genomes];0.94[AMR][1000 genomes];0.85[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs636928	0.85[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs655433	0.88[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs667341	0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs668735	0.99[AFR][1000 genomes];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs673147	0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs676114	0.83[ASN][1000 genomes]
rs676573	0.81[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs8638	0.94[AFR][1000 genomes];0.96[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:2)

SNP	Gene	Cis/trans	Tissue	Source
rs488289	POLA2	Cis_1M	lymphoblastoid	RTeQTL
rs488289	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	chr11:65030600-65042200	Weak transcription	NH-A	brain
5	chr11:65030600-65042400	Weak transcription	Brain Cingulate Gyrus	brain
6	chr11:65030600-65042400	Weak transcription	HSMM	muscle
7	chr11:65030600-65042400	Weak transcription	HSMMtube	muscle
8	chr11:65030600-65042600	Weak transcription	Brain Inferior Temporal Lobe	brain
9	chr11:65030600-65042600	Weak transcription	Colonic Mucosa	Colon
10	chr11:65030600-65042600	Weak transcription	Rectal Smooth Muscle	rectum
11	chr11:65030600-65042600	Weak transcription	NHEK	skin
12	chr11:65030600-65042800	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
13	chr11:65030600-65042800	Weak transcription	Brain Substantia Nigra	brain
14	chr11:65030600-65042800	Weak transcription	Pancreatic Islets	Pancreatic Islet
15	chr11:65030600-65043000	Weak transcription	Brain Angular Gyrus	brain
16	chr11:65030600-65044400	Weak transcription	Pancreas	Pancrea
17	chr11:65030600-65045400	Weak transcription	Duodenum Smooth Muscle	Duodenum
18	chr11:65030600-65046200	Weak transcription	Gastric	stomach
19	chr11:65030600-65047800	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
20	chr11:65030600-65048200	Weak transcription	Aorta	Aorta
21	chr11:65030600-65049400	Weak transcription	Right Ventricle	heart
22	chr11:65030600-65056800	Weak transcription	Right Atrium	heart
23	chr11:65030600-65058000	Weak transcription	Fetal Brain Male	brain
24	chr11:65030600-65058800	Weak transcription	Psoas Muscle	Psoas
25	chr11:65030800-65045200	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
26	chr11:65031000-65046200	Weak transcription	Small Intestine	intestine
27	chr11:65031000-65046400	Weak transcription	Lung	lung
28	chr11:65031000-65049800	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
29	chr11:65031200-65064800	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
30	chr11:65031400-65042800	Weak transcription	Fetal Heart	heart
31	chr11:65031800-65040000	Strong transcription	Fetal Stomach	stomach
32	chr11:65031800-65058000	Strong transcription	Primary hematopoietic stem cells short term culture	blood
33	chr11:65032200-65039400	Strong transcription	iPS-20b Cell Line	embryonic stem cell
34	chr11:65032200-65041200	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
35	chr11:65032600-65040000	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
36	chr11:65032800-65039800	Strong transcription	Fetal Intestine Small	intestine
37	chr11:65032800-65040000	Strong transcription	Primary T cells from cord blood	blood
38	chr11:65032800-65040000	Strong transcription	Fetal Muscle Leg	muscle
39	chr11:65032800-65040200	Strong transcription	Monocytes-CD14+_RO01746	blood
40	chr11:65033200-65039800	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
41	chr11:65033200-65040000	Strong transcription	Primary monocytes fromperipheralblood	blood
42	chr11:65033400-65039600	Strong transcription	H1 Cell Line	embryonic stem cell
43	chr11:65033400-65039800	Strong transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
44	chr11:65033400-65040000	Strong transcription	HUES64 Cell Line	embryonic stem cell
45	chr11:65033400-65040000	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
46	chr11:65033600-65040000	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
47	chr11:65033600-65040000	Strong transcription	Dnd41	blood
48	chr11:65033600-65040400	Strong transcription	HUES6 Cell Line	embryonic stem cell
49	chr11:65033800-65040000	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
50	chr11:65033800-65040200	Strong transcription	HUES48 Cell Line	embryonic stem cell

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