Variant report

Variant	rs4606447
Chromosome Location	chr11:46691737-46691738
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:24)
CpG islands
(count:0)
Chromatin interactive
region (count:2)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:24 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	CTCF	chr11:46691475-46691867	K562	blood:	n/a	n/a
2	RAD21	chr11:46691412-46691814	HepG2	liver:	n/a	n/a
3	CTCF	chr11:46691421-46691777	HepG2	liver:	n/a	n/a
4	RAD21	chr11:46691298-46691819	H1-hESC	embryonic stem cell:	n/a	n/a
5	CTCF	chr11:46691397-46691788	MCF-7	breast:	n/a	n/a
6	RAD21	chr11:46691445-46691747	Hela-S3	cervix:	n/a	n/a
7	RAD21	chr11:46691385-46691784	MCF-7	breast:	n/a	n/a
8	RAD21	chr11:46691482-46691827	ECC-1	luminal epithelium:	n/a	n/a
9	CTCF	chr11:46691396-46691744	A549	lung:	n/a	n/a
10	RAD21	chr11:46691353-46691783	H1-hESC	embryonic stem cell:	n/a	n/a
11	RAD21	chr11:46691377-46691816	HCT-116	colon:	n/a	n/a
12	RAD21	chr11:46691353-46691783	A549	lung:	n/a	n/a
13	CTCF	chr11:46691453-46691755	K562	blood:	n/a	n/a
14	CTCF	chr11:46691620-46691770	A549	lung:	n/a	n/a
15	RAD21	chr11:46691388-46691768	HepG2	liver:	n/a	n/a
16	CTCF	chr11:46691326-46691773	MCF-7	breast:	n/a	n/a
17	CTCF	chr11:46691007-46691851	A549	lung:	n/a	n/a
18	RAD21	chr11:46691337-46691745	A549	lung:	n/a	n/a
19	CTCF	chr11:46691273-46691841	HCT-116	colon:	n/a	n/a
20	CTCF	chr11:46691373-46691754	K562	blood:	n/a	n/a
21	RAD21	chr11:46691399-46691772	H1-hESC	embryonic stem cell:	n/a	n/a
22	RAD21	chr11:46691421-46691784	HCT-116	colon:	n/a	n/a
23	CTCF	chr11:46691240-46691752	H1-hESC	embryonic stem cell:	n/a	n/a
24	RAD21	chr11:46691422-46691789	HepG2	liver:	n/a	n/a

No data

(count:2 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr11:46690029..46694256-chr11:46694840..46696988,3	K562	blood:
2	chr11:46689739..46692664-chr11:46704932..46706618,2	K562	blood:

No data

Variant related genes	Relation type
ATG13	TF binding region

Extended variants
information (count: 21 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:19)

rs_ID	r²[population]
rs1007738	0.87[GIH][hapmap]
rs10734548	0.84[GIH][hapmap]
rs10769205	1.00[ASW][hapmap];0.94[CEU][hapmap];0.97[GIH][hapmap];0.95[LWK][hapmap];1.00[MKK][hapmap];0.88[TSI][hapmap];1.00[YRI][hapmap];0.81[AFR][1000 genomes];0.83[EUR][1000 genomes]
rs10769211	0.87[GIH][hapmap]
rs12274785	0.83[EUR][1000 genomes]
rs12361673	1.00[ASW][hapmap];0.94[CEU][hapmap];0.97[GIH][hapmap];0.95[LWK][hapmap];1.00[MKK][hapmap];0.88[TSI][hapmap];1.00[YRI][hapmap];0.81[AFR][1000 genomes];0.83[EUR][1000 genomes]
rs13448	0.94[CEU][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.86[MEX][hapmap];0.94[TSI][hapmap];0.83[AMR][1000 genomes];0.98[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs1551744	0.87[GIH][hapmap]
rs2070852	0.82[ASW][hapmap];0.94[CEU][hapmap];0.97[GIH][hapmap];0.87[MKK][hapmap];0.85[TSI][hapmap];1.00[YRI][hapmap];0.80[EUR][1000 genomes]
rs2282686	0.80[EUR][1000 genomes]
rs4752927	0.82[CHD][hapmap]
rs4752929	0.83[EUR][1000 genomes]
rs57804402	0.83[EUR][1000 genomes]
rs6485696	0.92[GIH][hapmap];0.84[LWK][hapmap]
rs7101374	0.87[GIH][hapmap]
rs7107778	0.84[GIH][hapmap]
rs7929294	0.84[GIH][hapmap]
rs7932354	0.94[CEU][hapmap];1.00[YRI][hapmap];0.81[AFR][1000 genomes];0.83[EUR][1000 genomes]
rs9704782	0.95[EUR][1000 genomes];0.92[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	nsv1044225	chr11:46472580-46771102	Enhancers Strong transcription Weak transcription Genic enhancers Flanking Active TSS Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	34 gene(s)	inside rSNPs	diseases
2	nsv541030	chr11:46472580-46771102	Weak transcription Strong transcription Genic enhancers Enhancers Active TSS Flanking Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	34 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs4606447	ACP2	cis	lymphoblastoid	seeQTL
rs4606447	DKFZp779M0652	cis	parietal	SCAN
rs4606447	C11orf49	cis	parietal	SCAN

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr11:46652200-46695600	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
2	chr11:46659600-46695200	Strong transcription	Rectal Mucosa Donor 29	rectum
3	chr11:46664200-46692600	Strong transcription	Duodenum Mucosa	Duodenum
4	chr11:46664200-46695400	Strong transcription	Primary B cells from peripheral blood	blood
5	chr11:46665800-46695200	Strong transcription	HUES6 Cell Line	embryonic stem cell
6	chr11:46666000-46695400	Strong transcription	Sigmoid Colon	Sigmoid Colon
7	chr11:46667200-46695400	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
8	chr11:46667200-46695600	Strong transcription	Breast Myoepithelial Primary Cells	Breast
9	chr11:46667200-46717000	Strong transcription	Brain Germinal Matrix	brain
10	chr11:46667400-46696000	Strong transcription	Fetal Brain Female	brain
11	chr11:46670600-46695600	Strong transcription	HUES64 Cell Line	embryonic stem cell
12	chr11:46671400-46696000	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
13	chr11:46671400-46696000	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
14	chr11:46677400-46695800	Strong transcription	Rectal Smooth Muscle	rectum
15	chr11:46678400-46694000	Weak transcription	Stomach Mucosa	stomach
16	chr11:46679400-46695200	Strong transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
17	chr11:46679400-46695800	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
18	chr11:46680000-46692200	Strong transcription	Placenta	Placenta
19	chr11:46680400-46695000	Strong transcription	Foreskin Fibroblast Primary Cells skin02	Skin
20	chr11:46681400-46695000	Strong transcription	Liver	Liver
21	chr11:46681800-46695000	Strong transcription	Fetal Intestine Small	intestine
22	chr11:46682000-46695200	Strong transcription	Fetal Intestine Large	intestine
23	chr11:46682800-46695600	Strong transcription	Hela-S3	cervix
24	chr11:46683400-46692200	Strong transcription	Foreskin Melanocyte Primary Cells skin01	Skin
25	chr11:46683400-46695200	Strong transcription	iPS-20b Cell Line	embryonic stem cell
26	chr11:46683400-46695400	Strong transcription	H1 Cell Line	embryonic stem cell
27	chr11:46683400-46695400	Strong transcription	HUES48 Cell Line	embryonic stem cell
28	chr11:46683400-46695400	Strong transcription	iPS-18 Cell Line	embryonic stem cell
29	chr11:46683600-46693200	Strong transcription	GM12878-XiMat	blood
30	chr11:46683600-46693400	Strong transcription	Rectal Mucosa Donor 31	rectum
31	chr11:46683600-46695600	Strong transcription	HepG2	liver
32	chr11:46683800-46692200	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
33	chr11:46685000-46693000	Strong transcription	Pancreas	Pancrea
34	chr11:46685000-46694000	Strong transcription	Gastric	stomach
35	chr11:46685200-46695400	Strong transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
36	chr11:46685200-46695600	Strong transcription	H9 Cell Line	embryonic stem cell
37	chr11:46685400-46695400	Strong transcription	NHEK	skin
38	chr11:46685400-46695800	Strong transcription	Foreskin Fibroblast Primary Cells skin01	Skin
39	chr11:46685400-46695800	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
40	chr11:46686200-46696000	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
41	chr11:46686400-46692400	Strong transcription	iPS DF 6.9 Cell Line	embryonic stem cell
42	chr11:46686400-46695000	Strong transcription	iPS-15b Cell Line	embryonic stem cell
43	chr11:46686600-46695200	Strong transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
44	chr11:46686800-46695400	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
45	chr11:46687000-46695200	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
46	chr11:46687200-46692800	Strong transcription	Spleen	Spleen
47	chr11:46687200-46695200	Strong transcription	Lung	lung
48	chr11:46688000-46691800	Strong transcription	NH-A	brain
49	chr11:46688800-46691800	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
50	chr11:46688800-46691800	Strong transcription	NHLF	lung

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