Variant report

Variant	rs4559682
Chromosome Location	chr11:8015651-8015652
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	POLR2A	chr11:8014911-8016449	K562	blood:	n/a	n/a
2	POLR2A	chr11:8015560-8017087	Hela-S3	cervix:	n/a	n/a
3	POLR2A	chr11:8015629-8015709	HepG2	liver:	n/a	n/a
4	POLR2A	chr11:8015540-8015872	K562	blood:	n/a	n/a
5	POLR2A	chr11:8015538-8015817	K562	blood:	n/a	n/a
6	POLR2A	chr11:8015619-8016535	HepG2	liver:	n/a	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr11:8011736..8013960-chr11:8014124..8015913,2	K562	blood:

Variant related genes	Relation type
EIF3F	TF binding region
ENSG00000175390	Chromatin interaction

Extended variants
information (count: 25 )
Associated
traits (count: 6 )

rSNPs within LD-proxies of this variant (count:24)

rs_ID	r²[population]
rs1044212	0.86[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs10839958	1.00[JPT][hapmap];0.83[ASN][1000 genomes]
rs10839960	1.00[JPT][hapmap];0.89[ASN][1000 genomes]
rs10839962	0.92[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.88[ASN][1000 genomes]
rs11041699	0.88[MEX][hapmap]
rs11041702	0.91[ASN][1000 genomes]
rs1105984	0.92[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.89[ASN][1000 genomes]
rs1132660	0.86[ASN][1000 genomes]
rs12275353	1.00[JPT][hapmap]
rs12278319	0.88[CHB][hapmap];1.00[JPT][hapmap];0.95[ASN][1000 genomes]
rs12294650	0.88[ASN][1000 genomes]
rs3892448	0.89[ASN][1000 genomes]
rs3903047	0.89[ASN][1000 genomes]
rs4076921	1.00[JPT][hapmap];0.89[ASN][1000 genomes]
rs4758038	0.89[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.95[ASN][1000 genomes]
rs6578918	1.00[JPT][hapmap];0.86[ASN][1000 genomes]
rs6578919	0.95[ASN][1000 genomes]
rs7125891	0.84[CEU][hapmap];1.00[CHB][hapmap];0.93[JPT][hapmap];0.84[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7126561	1.00[JPT][hapmap];0.89[ASN][1000 genomes]
rs7935597	1.00[JPT][hapmap];0.89[ASN][1000 genomes]
rs7941107	0.92[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.91[ASN][1000 genomes]
rs7941782	1.00[JPT][hapmap];1.00[MEX][hapmap];0.89[ASN][1000 genomes]
rs7950331	1.00[JPT][hapmap];0.88[ASN][1000 genomes]
rs922062	1.00[JPT][hapmap];0.86[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:1 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1052808	chr11:8011647-8129191	Bivalent Enhancer Strong transcription Active TSS Weak transcription Flanking Bivalent TSS/Enh Enhancers Bivalent/Poised TSS Genic enhancers Flanking Active TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	11 gene(s)	inside rSNPs	diseases

mRNA abundance (count:6)

SNP	Gene	Cis/trans	Tissue	Source
rs4559682	MTX2	trans	parietal	SCAN
rs4559682	EIF3F	cis	lymphoblastoid	seeQTL
rs4559682	EIF3F	cis	lymphoblastoid	GTEx
rs4559682	EIF3F	cis	Adipose Subcutaneous	GTEx
rs4559682	OR51V1	cis	cerebellum	SCAN
rs4559682	OR52E4	cis	parietal	SCAN

Chromatin state (count:127 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr11:8009800-8015800	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
2	chr11:8010400-8015800	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
3	chr11:8010600-8020400	Strong transcription	NH-A	brain
4	chr11:8010600-8020600	Strong transcription	iPS-20b Cell Line	embryonic stem cell
5	chr11:8010600-8020800	Strong transcription	HUES48 Cell Line	embryonic stem cell
6	chr11:8010600-8022000	Strong transcription	HUES6 Cell Line	embryonic stem cell
7	chr11:8010600-8022400	Strong transcription	Primary B cells from cord blood	blood
8	chr11:8010800-8019800	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
9	chr11:8010800-8021400	Strong transcription	HUES64 Cell Line	embryonic stem cell
10	chr11:8010800-8021400	Strong transcription	Primary T cells fromperipheralblood	blood
11	chr11:8010800-8021600	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
12	chr11:8010800-8022000	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
13	chr11:8010800-8022000	Strong transcription	Primary B cells from peripheral blood	blood
14	chr11:8010800-8022000	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
15	chr11:8010800-8033400	Weak transcription	Right Atrium	heart
16	chr11:8011000-8016000	Strong transcription	Primary T helper 17 cells PMA-I stimulated	--
17	chr11:8011000-8016800	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
18	chr11:8011000-8020200	Strong transcription	Hela-S3	cervix
19	chr11:8011000-8020200	Strong transcription	K562	blood
20	chr11:8011000-8021800	Strong transcription	Fetal Thymus	thymus
21	chr11:8011200-8016000	Strong transcription	Primary hematopoietic stem cells short term culture	blood
22	chr11:8011200-8016400	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
23	chr11:8011200-8020200	Strong transcription	HepG2	liver
24	chr11:8011200-8022800	Strong transcription	HSMM	muscle
25	chr11:8011400-8020600	Strong transcription	HSMMtube	muscle
26	chr11:8011400-8021200	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
27	chr11:8011400-8022000	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
28	chr11:8011400-8022000	Strong transcription	Ganglion Eminence derived primary cultured neurospheres	brain
29	chr11:8011400-8022200	Strong transcription	HMEC	breast
30	chr11:8011600-8022200	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
31	chr11:8011800-8016000	Strong transcription	HUVEC	blood vessel
32	chr11:8011800-8020000	Strong transcription	Primary T helper naive cells fromperipheralblood	blood
33	chr11:8011800-8020600	Strong transcription	Primary T helper cells PMA-I stimulated	--
34	chr11:8011800-8022000	Strong transcription	Primary T helper cells fromperipheralblood	blood
35	chr11:8011800-8022000	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
36	chr11:8011800-8022000	Strong transcription	Osteobl	bone
37	chr11:8012000-8022000	Strong transcription	Muscle Satellite Cultured Cells	--
38	chr11:8012000-8022200	Strong transcription	Rectal Mucosa Donor 29	rectum
39	chr11:8012200-8019800	Strong transcription	Brain Hippocampus Middle	brain
40	chr11:8012200-8022000	Strong transcription	Primary monocytes fromperipheralblood	blood
41	chr11:8012400-8020600	Strong transcription	Dnd41	blood
42	chr11:8012600-8017600	Strong transcription	Fetal Intestine Small	intestine
43	chr11:8012800-8017800	Strong transcription	Esophagus	oesophagus
44	chr11:8012800-8019400	Strong transcription	Brain Cingulate Gyrus	brain
45	chr11:8012800-8019600	Strong transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
46	chr11:8012800-8019800	Strong transcription	Cortex derived primary cultured neurospheres	brain
47	chr11:8012800-8020000	Strong transcription	Rectal Mucosa Donor 31	rectum
48	chr11:8012800-8020200	Strong transcription	ES-I3 Cell Line	embryonic stem cell
49	chr11:8012800-8020200	Strong transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
50	chr11:8012800-8020200	Strong transcription	Brain Germinal Matrix	brain

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