Variant report

Variant	rs542380
Chromosome Location	chr11:64977937-64977938
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:1)
CpG islands
(count:0)
Chromatin interactive
region (count:8)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

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

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	POLR2A	chr11:64977622-64977989	K562	blood:	n/a	n/a

No data

(count:8 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr11:64900055..64903404-chr11:64975247..64978493,3	K562	blood:
2	chr11:64977630..64979829-chr11:65195403..65196904,2	K562	blood:
3	chr11:64977931..64980208-chr11:64990996..64992937,3	K562	blood:
4	chr11:64977079..64978948-chr11:65020056..65023023,2	MCF-7	breast:
5	chr11:64878401..64881338-chr11:64977302..64979744,2	MCF-7	breast:
6	chr11:64947686..64949760-chr11:64975928..64978193,2	MCF-7	breast:
7	chr11:64645585..64647902-chr11:64976722..64978280,2	K562	blood:
8	chr11:64936901..64940048-chr11:64977014..64981623,6	K562	blood:

No data

Variant related genes	Relation type
SLC22A20	TF binding region
ENSG00000110047	Chromatin interaction
ENSG00000254501	Chromatin interaction
ENSG00000162298	Chromatin interaction
ENSG00000204710	Chromatin interaction
ENSG00000254614	Chromatin interaction
ENSG00000149809	Chromatin interaction
ENSG00000014216	Chromatin interaction

Extended variants
information (count: 24 )
Associated
traits (count: 7 )

rSNPs within LD-proxies of this variant (count:22)

rs_ID	r²[population]
rs11227147	0.93[CEU][hapmap];0.95[CHB][hapmap];0.95[CHD][hapmap];0.89[GIH][hapmap];0.94[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.92[AMR][1000 genomes];0.94[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs11227153	0.81[CHB][hapmap];0.86[JPT][hapmap]
rs11227154	0.81[CHB][hapmap];0.88[JPT][hapmap]
rs1195963	0.83[ASN][1000 genomes]
rs1195964	0.82[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs12224555	0.82[CHB][hapmap];0.81[JPT][hapmap]
rs12279142	0.92[CEU][hapmap];0.95[CHB][hapmap];0.88[JPT][hapmap];0.92[AMR][1000 genomes];0.94[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs12789598	0.82[CHB][hapmap];0.82[JPT][hapmap]
rs171193	0.89[EUR][1000 genomes]
rs17884154	0.91[AMR][1000 genomes];0.94[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2089921	0.87[AMR][1000 genomes];0.83[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2271446	0.82[CHB][hapmap];0.88[JPT][hapmap]
rs2271449	0.82[CHB][hapmap];0.88[JPT][hapmap]
rs2904978	0.83[MEX][hapmap]
rs4492832	0.92[CEU][hapmap];0.95[CHB][hapmap];0.94[JPT][hapmap];0.88[AMR][1000 genomes];0.94[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs552403	0.93[CEU][hapmap];0.95[CHB][hapmap];0.88[JPT][hapmap];0.89[AMR][1000 genomes];0.94[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs580734	0.89[AMR][1000 genomes];0.93[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs600135	0.86[CEU][hapmap];0.95[CHB][hapmap];0.84[CHD][hapmap];0.92[GIH][hapmap];0.88[JPT][hapmap];0.92[MEX][hapmap];1.00[TSI][hapmap];0.89[AMR][1000 genomes];0.94[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs678296	0.85[CEU][hapmap];0.95[CHB][hapmap];0.88[JPT][hapmap];0.84[AMR][1000 genomes];0.91[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs678343	0.86[CEU][hapmap];0.95[CHB][hapmap];0.88[JPT][hapmap];0.81[AMR][1000 genomes];0.92[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs7102307	0.88[AMR][1000 genomes];0.87[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs7116156	0.93[CEU][hapmap];0.95[CHB][hapmap];0.95[CHD][hapmap];0.92[GIH][hapmap];0.94[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.92[AMR][1000 genomes];0.94[EUR][1000 genomes];0.96[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:2 , 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

mRNA abundance (count:7)

SNP	Gene	Cis/trans	Tissue	Source
rs542380	POLA2	cis	parietal	SCAN
rs542380	TM7SF2	cis	cerebellum	SCAN
rs542380	POLA2	cis	cerebellum	SCAN
rs542380	BBS1	cis	cerebellum	SCAN
rs542380	GAL3ST3	cis	cerebellum	SCAN
rs542380	DPP3	cis	cerebellum	SCAN
rs542380	RPS6KB2	cis	cerebellum	SCAN

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr11:64950600-64992400	Weak transcription	Right Atrium	heart
2	chr11:64951400-64979200	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
3	chr11:64951600-64979600	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
4	chr11:64952400-64980200	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
5	chr11:64952400-64992800	Weak transcription	Fetal Heart	heart
6	chr11:64952800-64978000	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
7	chr11:64953600-64978600	Strong transcription	Breast Myoepithelial Primary Cells	Breast
8	chr11:64964200-64980000	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
9	chr11:64964400-64979800	Strong transcription	Fetal Stomach	stomach
10	chr11:64964400-64981000	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
11	chr11:64969400-64980000	Strong transcription	HMEC	breast
12	chr11:64969800-64979400	Strong transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
13	chr11:64969800-64980000	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
14	chr11:64970000-64979200	Strong transcription	Adipose Nuclei	Adipose
15	chr11:64970000-64979600	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
16	chr11:64970000-64979600	Strong transcription	Thymus	Thymus
17	chr11:64970000-64979800	Strong transcription	Duodenum Smooth Muscle	Duodenum
18	chr11:64970000-64980200	Strong transcription	Primary B cells from peripheral blood	blood
19	chr11:64970200-64979600	Strong transcription	Fetal Brain Female	brain
20	chr11:64970200-64979600	Strong transcription	NHEK	skin
21	chr11:64970200-64979800	Strong transcription	Ovary	ovary
22	chr11:64970400-64979800	Strong transcription	Skeletal Muscle Male	skeletal muscle
23	chr11:64971000-64980000	Strong transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
24	chr11:64971000-64980200	Strong transcription	Gastric	stomach
25	chr11:64971200-64978600	Strong transcription	Primary T cells from cord blood	blood
26	chr11:64971400-64979800	Strong transcription	Primary T helper cells fromperipheralblood	blood
27	chr11:64971400-64979800	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
28	chr11:64971400-64980000	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
29	chr11:64971400-64980000	Strong transcription	Pancreas	Pancrea
30	chr11:64971400-64980200	Strong transcription	Cortex derived primary cultured neurospheres	brain
31	chr11:64971400-64980200	Strong transcription	NHLF	lung
32	chr11:64971600-64979400	Strong transcription	Ganglion Eminence derived primary cultured neurospheres	brain
33	chr11:64971600-64979600	Strong transcription	Stomach Smooth Muscle	stomach
34	chr11:64971600-64980000	Strong transcription	Right Ventricle	heart
35	chr11:64971600-64980400	Strong transcription	Esophagus	oesophagus
36	chr11:64971800-64978600	Strong transcription	Fetal Muscle Leg	muscle
37	chr11:64971800-64979200	Strong transcription	Rectal Smooth Muscle	rectum
38	chr11:64971800-64979800	Strong transcription	Primary T helper 17 cells PMA-I stimulated	--
39	chr11:64971800-64980400	Strong transcription	Skeletal Muscle Female	skeletal muscle
40	chr11:64972000-64979000	Strong transcription	Dnd41	blood
41	chr11:64972000-64979200	Strong transcription	Muscle Satellite Cultured Cells	--
42	chr11:64972000-64979200	Strong transcription	Aorta	Aorta
43	chr11:64972000-64979600	Strong transcription	Placenta Amnion	Placenta Amnion
44	chr11:64972000-64979800	Strong transcription	Brain Dorsolateral Prefrontal Cortex	brain
45	chr11:64972200-64979000	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
46	chr11:64972200-64979800	Strong transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
47	chr11:64972400-64979200	Strong transcription	Colon Smooth Muscle	Colon
48	chr11:64972400-64979800	Strong transcription	Brain Germinal Matrix	brain
49	chr11:64972600-64979200	Strong transcription	Primary T helper cells PMA-I stimulated	--
50	chr11:64972600-64979200	Strong transcription	Brain Anterior Caudate	brain

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