Variant report

Variant	rs7941782
Chromosome Location	chr11:8013450-8013451
allele	A/C
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	chr11:8012754-8013453	H1-hESC	embryonic stem cell:	n/a	n/a
2	POLR2A	chr11:8013324-8013540	HepG2	liver:	n/a	n/a
3	POLR2A	chr11:8012639-8013798	H1-hESC	embryonic stem cell:	n/a	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr11:8008425..8011151-chr11:8011381..8013712,2	MCF-7	breast:

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

Extended variants
information (count: 25 )
Associated
traits (count: 10 )

rSNPs within LD-proxies of this variant (count:23)

rs_ID	r²[population]
rs10839958	1.00[JPT][hapmap]
rs10839960	0.92[ASW][hapmap];0.86[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.89[LWK][hapmap];0.83[YRI][hapmap];0.85[AFR][1000 genomes];0.97[ASN][1000 genomes]
rs10839962	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.82[GIH][hapmap];1.00[JPT][hapmap];0.98[LWK][hapmap];1.00[MEX][hapmap];0.89[MKK][hapmap];0.90[TSI][hapmap];0.92[YRI][hapmap];0.92[AFR][1000 genomes];0.97[AMR][1000 genomes];0.89[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs11041699	0.87[CEU][hapmap];1.00[CHB][hapmap];0.88[MEX][hapmap]
rs11041702	0.96[AFR][1000 genomes];0.97[AMR][1000 genomes];0.89[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1105984	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.82[GIH][hapmap];1.00[JPT][hapmap];0.93[LWK][hapmap];1.00[MEX][hapmap];0.87[MKK][hapmap];0.93[TSI][hapmap];0.92[YRI][hapmap];0.91[AFR][1000 genomes];0.97[AMR][1000 genomes];0.89[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1132660	0.93[ASN][1000 genomes]
rs12275353	1.00[JPT][hapmap]
rs12278319	1.00[JPT][hapmap];0.87[ASN][1000 genomes]
rs12294650	0.90[AFR][1000 genomes];0.94[AMR][1000 genomes];0.89[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs3892448	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3903047	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4076921	0.88[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4559682	1.00[JPT][hapmap];1.00[MEX][hapmap];0.89[ASN][1000 genomes]
rs4758038	1.00[JPT][hapmap];0.85[ASN][1000 genomes]
rs6578918	0.86[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.93[ASN][1000 genomes]
rs6578919	0.85[ASN][1000 genomes]
rs7125891	0.93[JPT][hapmap];0.87[YRI][hapmap];0.85[AFR][1000 genomes];0.91[ASN][1000 genomes]
rs7126561	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[YRI][hapmap];0.96[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7935597	0.85[CHB][hapmap];1.00[JPT][hapmap];0.97[ASN][1000 genomes]
rs7941107	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.82[GIH][hapmap];1.00[JPT][hapmap];0.98[LWK][hapmap];1.00[MEX][hapmap];0.89[MKK][hapmap];0.92[YRI][hapmap];0.96[AFR][1000 genomes];0.97[AMR][1000 genomes];0.89[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7950331	1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[ASN][1000 genomes]
rs922062	0.86[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.93[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	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
2	nsv983088	chr11:8013451-8014557	Strong transcription Weak transcription	TF binding region Chromatin interactive region	1 gene(s)	inside rSNPs	diseases

mRNA abundance (count:10)

SNP	Gene	Cis/trans	Tissue	Source
rs7941782	SNORD116-29	trans	lymphoblastoid	seeQTL
rs7941782	EIF3F	cis	lung	GTEx
rs7941782	IPO7	cis	parietal	SCAN
rs7941782	EIF3F	Cis_1M	lymphoblastoid	RTeQTL
rs7941782	GALNTL4	cis	parietal	SCAN
rs7941782	C11orf42	cis	parietal	SCAN
rs7941782	SNORD50A	trans	lymphoblastoid	seeQTL
rs7941782	OR52K1	cis	parietal	SCAN
rs7941782	OR51A4	cis	parietal	SCAN
rs7941782	EIF3F	cis	lymphoblastoid	seeQTL

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr11:8009800-8014600	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
2	chr11:8009800-8015800	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
3	chr11:8010000-8014000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
4	chr11:8010400-8015800	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
5	chr11:8010600-8013800	Weak transcription	Placenta Amnion	Placenta Amnion
6	chr11:8010600-8014200	Weak transcription	Fetal Kidney	kidney
7	chr11:8010600-8020400	Strong transcription	NH-A	brain
8	chr11:8010600-8020600	Strong transcription	iPS-20b Cell Line	embryonic stem cell
9	chr11:8010600-8020800	Strong transcription	HUES48 Cell Line	embryonic stem cell
10	chr11:8010600-8022000	Strong transcription	HUES6 Cell Line	embryonic stem cell
11	chr11:8010600-8022400	Strong transcription	Primary B cells from cord blood	blood
12	chr11:8010800-8014000	Weak transcription	Stomach Mucosa	stomach
13	chr11:8010800-8014200	Weak transcription	Fetal Heart	heart
14	chr11:8010800-8014200	Weak transcription	Psoas Muscle	Psoas
15	chr11:8010800-8019800	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
16	chr11:8010800-8021400	Strong transcription	HUES64 Cell Line	embryonic stem cell
17	chr11:8010800-8021400	Strong transcription	Primary T cells fromperipheralblood	blood
18	chr11:8010800-8021600	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
19	chr11:8010800-8022000	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
20	chr11:8010800-8022000	Strong transcription	Primary B cells from peripheral blood	blood
21	chr11:8010800-8022000	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
22	chr11:8010800-8033400	Weak transcription	Right Atrium	heart
23	chr11:8011000-8014000	Weak transcription	Fetal Brain Male	brain
24	chr11:8011000-8016000	Strong transcription	Primary T helper 17 cells PMA-I stimulated	--
25	chr11:8011000-8016800	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
26	chr11:8011000-8020200	Strong transcription	Hela-S3	cervix
27	chr11:8011000-8020200	Strong transcription	K562	blood
28	chr11:8011000-8021800	Strong transcription	Fetal Thymus	thymus
29	chr11:8011200-8016000	Strong transcription	Primary hematopoietic stem cells short term culture	blood
30	chr11:8011200-8016400	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
31	chr11:8011200-8020200	Strong transcription	HepG2	liver
32	chr11:8011200-8022800	Strong transcription	HSMM	muscle
33	chr11:8011400-8020600	Strong transcription	HSMMtube	muscle
34	chr11:8011400-8021200	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
35	chr11:8011400-8022000	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
36	chr11:8011400-8022000	Strong transcription	Ganglion Eminence derived primary cultured neurospheres	brain
37	chr11:8011400-8022200	Strong transcription	HMEC	breast
38	chr11:8011600-8022200	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
39	chr11:8011800-8013600	Weak transcription	Pancreatic Islets	Pancreatic Islet
40	chr11:8011800-8013800	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
41	chr11:8011800-8014400	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
42	chr11:8011800-8016000	Strong transcription	HUVEC	blood vessel
43	chr11:8011800-8020000	Strong transcription	Primary T helper naive cells fromperipheralblood	blood
44	chr11:8011800-8020600	Strong transcription	Primary T helper cells PMA-I stimulated	--
45	chr11:8011800-8022000	Strong transcription	Primary T helper cells fromperipheralblood	blood
46	chr11:8011800-8022000	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
47	chr11:8011800-8022000	Strong transcription	Osteobl	bone
48	chr11:8012000-8014000	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
49	chr11:8012000-8022000	Strong transcription	Muscle Satellite Cultured Cells	--
50	chr11:8012000-8022200	Strong transcription	Rectal Mucosa Donor 29	rectum

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