Variant report

Variant	rs12275736
Chromosome Location	chr11:58958732-58958733
allele	C/T
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	SPI1	chr11:58958476-58958837	GM12891	blood:	n/a	n/a
2	NFIC	chr11:58958413-58958864	GM12878	blood:	n/a	n/a
3	HNF4A	chr11:58958600-58958996	HepG2	liver:	n/a	chr11:58958791-58958803 chr11:58958790-58958803 chr11:58958791-58958804 chr11:58958790-58958805 chr11:58958790-58958803 chr11:58958790-58958805 chr11:58958790-58958805 chr11:58958790-58958805 chr11:58958789-58958804 chr11:58958792-58958804
4	EP300	chr11:58958688-58958859	HepG2	liver:	n/a	chr11:58958699-58958708
5	HNF4G	chr11:58958574-58958956	HepG2	liver:	n/a	chr11:58958791-58958803 chr11:58958790-58958803 chr11:58958791-58958804 chr11:58958788-58958803 chr11:58958790-58958805 chr11:58958790-58958803 chr11:58958790-58958805 chr11:58958790-58958805 chr11:58958790-58958805 chr11:58958792-58958804
6	POLR2A	chr11:58958298-58959184	GM12878	blood:	n/a	n/a
7	PML	chr11:58958284-58958761	GM12878	blood:	n/a	n/a
8	POLR2A	chr11:58957541-58959226	GM12892	blood:	n/a	n/a
9	HNF4A	chr11:58958597-58958979	HepG2	liver:	n/a	chr11:58958791-58958803 chr11:58958790-58958803 chr11:58958791-58958804 chr11:58958790-58958805 chr11:58958790-58958803 chr11:58958790-58958805 chr11:58958790-58958805 chr11:58958790-58958805 chr11:58958789-58958804 chr11:58958792-58958804
10	SPI1	chr11:58958495-58958808	GM12878	blood:	n/a	n/a
11	RUNX3	chr11:58958350-58958868	GM12878	blood:	n/a	n/a
12	RUNX3	chr11:58958469-58958893	GM12878	blood:	n/a	n/a
13	SP1	chr11:58958609-58958965	HepG2	liver:	n/a	chr11:58958834-58958848
14	SPI1	chr11:58958431-58958740	GM12891	blood:	n/a	n/a
15	RCOR1	chr11:58958685-58958758	HepG2	liver:	n/a	n/a

Variant related genes	Relation type
DTX4	TF binding region

Extended variants
information (count: 36 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:31)

rs_ID	r²[population]
rs10896948	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10896951	0.87[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10896954	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[YRI][hapmap];0.82[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs11229825	1.00[CEU][hapmap]
rs11229835	1.00[CEU][hapmap]
rs11229836	1.00[CEU][hapmap]
rs11229841	1.00[CEU][hapmap]
rs11229845	1.00[CEU][hapmap]
rs11229847	1.00[CEU][hapmap]
rs11229853	1.00[CEU][hapmap]
rs11229871	1.00[ASW][hapmap];1.00[CEU][hapmap];0.85[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11229876	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11229878	1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs11229888	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs11229890	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs11229891	1.00[CEU][hapmap];1.00[JPT][hapmap];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs11229892	1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs11229893	1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs11229894	1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs11229905	1.00[CEU][hapmap];0.86[CHB][hapmap];1.00[JPT][hapmap];1.00[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs12221768	1.00[CEU][hapmap]
rs12222675	1.00[CEU][hapmap]
rs12223085	1.00[CEU][hapmap]
rs12223473	1.00[CEU][hapmap]
rs12225328	1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs12225532	1.00[CEU][hapmap]
rs12225972	1.00[CEU][hapmap]
rs12226710	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12275799	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12284698	0.87[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7951382	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.87[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:5 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1050013	chr11:58394598-59221090	Active TSS Weak transcription Flanking Active TSS Enhancers Bivalent Enhancer ZNF genes & repeats Genic enhancers Strong transcription Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	67 gene(s)	inside rSNPs	diseases
2	nsv948365	chr11:58515163-59156405	Weak transcription Flanking Bivalent TSS/Enh Active TSS Flanking Active TSS Strong transcription Genic enhancers Enhancers Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	59 gene(s)	inside rSNPs	diseases
3	esv2758272	chr11:58700092-59008673	Bivalent/Poised TSS Active TSS Weak transcription Enhancers Strong transcription Flanking Active TSS ZNF genes & repeats Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	44 gene(s)	inside rSNPs	diseases
4	esv2759830	chr11:58700092-59008673	Active TSS Weak transcription Enhancers Flanking Active TSS Bivalent/Poised TSS ZNF genes & repeats Strong transcription Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	44 gene(s)	inside rSNPs	diseases
5	esv1821250	chr11:58925860-59059179	Enhancers Flanking Active TSS Weak transcription Genic enhancers Strong transcription Flanking Bivalent TSS/Enh Active TSS Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	18 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:91 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr11:58941600-58964000	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
2	chr11:58943600-58975400	Weak transcription	NHEK	skin
3	chr11:58949400-58973400	Weak transcription	Right Ventricle	heart
4	chr11:58950000-58978400	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
5	chr11:58950400-58972200	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
6	chr11:58952400-58960200	Genic enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
7	chr11:58952800-58959400	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
8	chr11:58953600-58960800	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
9	chr11:58953800-58959400	Genic enhancers	Fetal Intestine Large	intestine
10	chr11:58953800-58959800	Genic enhancers	Fetal Intestine Small	intestine
11	chr11:58954200-58960000	Weak transcription	ES-I3 Cell Line	embryonic stem cell
12	chr11:58954200-58962400	Strong transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
13	chr11:58954200-58962600	Strong transcription	Cortex derived primary cultured neurospheres	brain
14	chr11:58954200-58962800	Strong transcription	Primary B cells from peripheral blood	blood
15	chr11:58954200-58963400	Strong transcription	iPS-20b Cell Line	embryonic stem cell
16	chr11:58954200-58964000	Strong transcription	HUES6 Cell Line	embryonic stem cell
17	chr11:58954400-58960600	Strong transcription	Brain Germinal Matrix	brain
18	chr11:58954400-58965200	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
19	chr11:58954600-58963000	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
20	chr11:58954600-58966200	Strong transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
21	chr11:58954800-58959800	Weak transcription	Colon Smooth Muscle	Colon
22	chr11:58954800-58959800	Genic enhancers	Rectal Mucosa Donor 29	rectum
23	chr11:58954800-58963800	Strong transcription	H1 Cell Line	embryonic stem cell
24	chr11:58955000-58963000	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
25	chr11:58955000-58967200	Strong transcription	Breast Myoepithelial Primary Cells	Breast
26	chr11:58955200-58963000	Weak transcription	Primary hematopoietic stem cells	blood
27	chr11:58955200-58965400	Strong transcription	Fetal Brain Female	brain
28	chr11:58955400-58963600	Strong transcription	Primary B cells from cord blood	blood
29	chr11:58955400-58966000	Strong transcription	HUES64 Cell Line	embryonic stem cell
30	chr11:58955400-58966000	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
31	chr11:58955400-58970800	Strong transcription	iPS-18 Cell Line	embryonic stem cell
32	chr11:58955600-58959600	Genic enhancers	Rectal Mucosa Donor 31	rectum
33	chr11:58955600-58964800	Strong transcription	HUES48 Cell Line	embryonic stem cell
34	chr11:58955600-58965400	Strong transcription	Fetal Muscle Trunk	muscle
35	chr11:58955600-58965800	Strong transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
36	chr11:58955800-58959200	Genic enhancers	Duodenum Mucosa	Duodenum
37	chr11:58955800-58964000	Weak transcription	Primary monocytes fromperipheralblood	blood
38	chr11:58956000-58961400	Strong transcription	Brain Hippocampus Middle	brain
39	chr11:58956000-58962200	Strong transcription	Brain Cingulate Gyrus	brain
40	chr11:58956000-58965200	Weak transcription	Skeletal Muscle Female	skeletal muscle
41	chr11:58956200-58961200	Strong transcription	Brain Inferior Temporal Lobe	brain
42	chr11:58956200-58962200	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
43	chr11:58956200-58963600	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
44	chr11:58956200-58963800	Strong transcription	Monocytes-CD14+_RO01746	blood
45	chr11:58956200-58965000	Strong transcription	Primary neutrophils fromperipheralblood	blood
46	chr11:58956200-58965000	Strong transcription	Ovary	ovary
47	chr11:58956400-58959600	Weak transcription	Muscle Satellite Cultured Cells	--
48	chr11:58956400-58964800	Strong transcription	Fetal Brain Male	brain
49	chr11:58956400-58965400	Weak transcription	Psoas Muscle	Psoas
50	chr11:58956400-58977400	Weak transcription	Hela-S3	cervix

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