Variant report

Variant	rs239254
Chromosome Location	chr11:64986649-64986650
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr11:64936316..64940123-chr11:64985070..64987472,4	K562	blood:
2	chr11:64937568..64940123-chr11:64985972..64987505,2	K562	blood:
3	chr11:64983969..64987666-chr11:65274563..65276878,3	K562	blood:
4	chr11:64971045..64975621-chr11:64984238..64988273,4	MCF-7	breast:

Variant related genes	Relation type
ENSG00000204710	Chromatin interaction
ENSG00000014216	Chromatin interaction

Extended variants
information (count: 10 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:7)

rs_ID	r²[population]
rs184734	0.89[AMR][1000 genomes]
rs239253	0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs239255	1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs239256	0.99[AFR][1000 genomes];0.92[AMR][1000 genomes];0.88[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2513087	0.91[AFR][1000 genomes];0.96[AMR][1000 genomes];0.97[ASN][1000 genomes]
rs2904978	0.82[AFR][1000 genomes];0.93[AMR][1000 genomes];0.94[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs514076	1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[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	nsv897713	chr11:64915042-65000719	Flanking Active TSS Weak transcription Strong transcription Enhancers Genic enhancers Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	42 gene(s)	inside rSNPs	diseases
3	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

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs239254	POLA2	Cis_1M	lymphoblastoid	RTeQTL
rs239254	SLC22A20	cis	Esophagus Mucosa	GTEx

Chromatin state (count:76 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr11:64950600-64992400	Weak transcription	Right Atrium	heart
2	chr11:64952400-64992800	Weak transcription	Fetal Heart	heart
3	chr11:64973800-64992600	Weak transcription	Fetal Kidney	kidney
4	chr11:64976600-64992600	Weak transcription	Psoas Muscle	Psoas
5	chr11:64977400-64998400	Weak transcription	Small Intestine	intestine
6	chr11:64977600-64993200	Weak transcription	Pancreatic Islets	Pancreatic Islet
7	chr11:64978200-64986800	Weak transcription	HepG2	liver
8	chr11:64978400-64992200	Weak transcription	Stomach Mucosa	stomach
9	chr11:64978400-64992800	Weak transcription	HSMM	muscle
10	chr11:64978600-64992800	Weak transcription	HSMMtube	muscle
11	chr11:64978800-64987000	Weak transcription	NHDF-Ad	bronchial
12	chr11:64979200-64987000	Weak transcription	Muscle Satellite Cultured Cells	--
13	chr11:64979200-64992400	Weak transcription	Rectal Mucosa Donor 29	rectum
14	chr11:64979200-64993000	Weak transcription	Aorta	Aorta
15	chr11:64979400-64987000	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
16	chr11:64979400-64992400	Weak transcription	A549	lung
17	chr11:64979600-64990600	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
18	chr11:64979600-64992200	Weak transcription	NHEK	skin
19	chr11:64979800-64989800	Weak transcription	Skeletal Muscle Male	skeletal muscle
20	chr11:64979800-64992400	Weak transcription	Duodenum Smooth Muscle	Duodenum
21	chr11:64979800-64993000	Weak transcription	Ovary	ovary
22	chr11:64980000-64989800	Weak transcription	Left Ventricle	heart
23	chr11:64980000-64992200	Weak transcription	HMEC	breast
24	chr11:64980200-64992200	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
25	chr11:64980200-64992600	Weak transcription	Colonic Mucosa	Colon
26	chr11:64980200-64993000	Weak transcription	Gastric	stomach
27	chr11:64980400-64990000	Weak transcription	Skeletal Muscle Female	skeletal muscle
28	chr11:64980400-64992600	Weak transcription	Esophagus	oesophagus
29	chr11:64980400-64992600	Weak transcription	Rectal Smooth Muscle	rectum
30	chr11:64980400-64993000	Weak transcription	Pancreas	Pancrea
31	chr11:64981000-64992600	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
32	chr11:64981200-64986800	Weak transcription	Hela-S3	cervix
33	chr11:64981200-64987000	Weak transcription	NHLF	lung
34	chr11:64981200-64987200	Weak transcription	Adipose Nuclei	Adipose
35	chr11:64981200-64992200	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
36	chr11:64981600-64992200	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
37	chr11:64981800-64986800	Weak transcription	Fetal Muscle Leg	muscle
38	chr11:64981800-64992000	Weak transcription	HUES48 Cell Line	embryonic stem cell
39	chr11:64981800-64993400	Weak transcription	Sigmoid Colon	Sigmoid Colon
40	chr11:64982000-64987200	Weak transcription	Primary monocytes fromperipheralblood	blood
41	chr11:64982000-64987200	Weak transcription	Monocytes-CD14+_RO01746	blood
42	chr11:64982000-64992000	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
43	chr11:64982000-64992200	Weak transcription	HUES6 Cell Line	embryonic stem cell
44	chr11:64982200-64987000	Weak transcription	Fetal Thymus	thymus
45	chr11:64982200-64987200	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
46	chr11:64982200-64987200	Weak transcription	Thymus	Thymus
47	chr11:64982200-64987400	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
48	chr11:64982200-64992400	Weak transcription	ES-I3 Cell Line	embryonic stem cell
49	chr11:64983200-64987000	Weak transcription	Primary T helper cells PMA-I stimulated	--
50	chr11:64983200-64991800	Weak transcription	iPS-20b Cell Line	embryonic stem cell

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