Variant report

Variant	rs239253
Chromosome Location	chr11:64984743-64984744
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr11:64971880..64974071-chr11:64983696..64985630,2	K562	blood:
2	chr11:64983969..64987666-chr11:65274563..65276878,3	K562	blood:
3	chr11:64981290..64983424-chr11:64983464..64986635,3	K562	blood:
4	chr11:64983043..64986391-chr11:64991756..64994999,4	K562	blood:
5	chr11:64971045..64975621-chr11:64984238..64988273,4	MCF-7	breast:

Variant related genes	Relation type
ENSG00000014216	Chromatin interaction
ENSG00000197847	Chromatin interaction

Extended variants
information (count: 16 )
Associated
traits (count: 8 )

rSNPs within LD-proxies of this variant (count:12)

rs_ID	r²[population]
rs11227147	0.82[GIH][hapmap]
rs184734	0.90[AMR][1000 genomes]
rs239254	0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs239255	0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs239256	0.88[ASW][hapmap];1.00[CEU][hapmap];0.86[CHB][hapmap];0.93[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.83[MKK][hapmap];1.00[TSI][hapmap];0.88[AMR][1000 genomes];0.87[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs239260	0.80[AMR][1000 genomes]
rs2513087	0.95[AMR][1000 genomes];0.96[ASN][1000 genomes]
rs2904978	0.87[ASW][hapmap];1.00[CEU][hapmap];0.82[CHB][hapmap];0.92[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.92[TSI][hapmap];0.94[AMR][1000 genomes];0.92[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs514076	1.00[CEU][hapmap];0.86[CHB][hapmap];1.00[JPT][hapmap];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs600135	0.84[GIH][hapmap]
rs676573	0.81[CEU][hapmap]
rs7116156	0.84[GIH][hapmap]

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	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
4	esv3380436	chr11:64982801-64985349	Weak transcription Enhancers Genic enhancers Flanking Active TSS Active TSS Bivalent Enhancer Strong transcription	TF binding region Chromatin interactive region	4 gene(s)	inside rSNPs	diseases

mRNA abundance (count:8)

SNP	Gene	Cis/trans	Tissue	Source
rs239253	POLA2	cis	cerebellum	SCAN
rs239253	BBS1	cis	cerebellum	SCAN
rs239253	POLA2	Cis_1M	lymphoblastoid	RTeQTL
rs239253	POLA2	cis	parietal	SCAN
rs239253	FERMT3	cis	parietal	SCAN
rs239253	RPS6KB2	cis	cerebellum	SCAN
rs239253	SLC22A20	cis	Esophagus Mucosa	GTEx
rs239253	GAL3ST3	cis	cerebellum	SCAN

Chromatin state (count:81 , 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	chr11:64979200-64986400	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
13	chr11:64979200-64987000	Weak transcription	Muscle Satellite Cultured Cells	--
14	chr11:64979200-64992400	Weak transcription	Rectal Mucosa Donor 29	rectum
15	chr11:64979200-64993000	Weak transcription	Aorta	Aorta
16	chr11:64979400-64987000	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
17	chr11:64979400-64992400	Weak transcription	A549	lung
18	chr11:64979600-64984800	Weak transcription	Fetal Brain Female	brain
19	chr11:64979600-64986400	Weak transcription	Stomach Smooth Muscle	stomach
20	chr11:64979600-64990600	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
21	chr11:64979600-64992200	Weak transcription	NHEK	skin
22	chr11:64979800-64984800	Weak transcription	Brain Germinal Matrix	brain
23	chr11:64979800-64984800	Weak transcription	Rectal Mucosa Donor 31	rectum
24	chr11:64979800-64989800	Weak transcription	Skeletal Muscle Male	skeletal muscle
25	chr11:64979800-64992400	Weak transcription	Duodenum Smooth Muscle	Duodenum
26	chr11:64979800-64993000	Weak transcription	Ovary	ovary
27	chr11:64980000-64986000	Weak transcription	Lung	lung
28	chr11:64980000-64989800	Weak transcription	Left Ventricle	heart
29	chr11:64980000-64992200	Weak transcription	HMEC	breast
30	chr11:64980200-64992200	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
31	chr11:64980200-64992600	Weak transcription	Colonic Mucosa	Colon
32	chr11:64980200-64993000	Weak transcription	Gastric	stomach
33	chr11:64980400-64985400	Weak transcription	Breast Myoepithelial Primary Cells	Breast
34	chr11:64980400-64990000	Weak transcription	Skeletal Muscle Female	skeletal muscle
35	chr11:64980400-64992600	Weak transcription	Esophagus	oesophagus
36	chr11:64980400-64992600	Weak transcription	Rectal Smooth Muscle	rectum
37	chr11:64980400-64993000	Weak transcription	Pancreas	Pancrea
38	chr11:64981000-64992600	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
39	chr11:64981200-64986400	Weak transcription	K562	blood
40	chr11:64981200-64986800	Weak transcription	Hela-S3	cervix
41	chr11:64981200-64987000	Weak transcription	NHLF	lung
42	chr11:64981200-64987200	Weak transcription	Adipose Nuclei	Adipose
43	chr11:64981200-64992200	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
44	chr11:64981400-64985400	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
45	chr11:64981400-64985600	Weak transcription	Fetal Stomach	stomach
46	chr11:64981400-64986400	Weak transcription	Placenta Amnion	Placenta Amnion
47	chr11:64981600-64992200	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
48	chr11:64981800-64986800	Weak transcription	Fetal Muscle Leg	muscle
49	chr11:64981800-64992000	Weak transcription	HUES48 Cell Line	embryonic stem cell
50	chr11:64981800-64993400	Weak transcription	Sigmoid Colon	Sigmoid Colon

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