Variant report

Variant	rs681309
Chromosome Location	chr11:65151449-65151450
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	CEBPB	chr11:65151257-65151495	HepG2	liver:	n/a	chr11:65151401-65151412
2	FOXA2	chr11:65151263-65151615	HepG2	liver:	n/a	n/a
3	CEBPB	chr11:65151242-65151570	IMR90	lung:	n/a	chr11:65151401-65151412
4	CEBPB	chr11:65151222-65151596	HepG2	liver:	n/a	chr11:65151401-65151412
5	TCF7L2	chr11:65151273-65152128	HepG2	liver:	n/a	n/a
6	CEBPB	chr11:65151248-65151577	K562	blood:	n/a	chr11:65151401-65151412
7	MYBL2	chr11:65151122-65151599	HepG2	liver:	n/a	n/a
8	CEBPB	chr11:65151282-65151566	A549	lung:	n/a	chr11:65151401-65151412
9	ZBTB7A	chr11:65151264-65151520	HepG2	liver:	n/a	n/a
10	TCF7L2	chr11:65151312-65151706	Hela-S3	cervix:	n/a	n/a
11	EP300	chr11:65151389-65151600	HepG2	liver:	n/a	n/a
12	CEBPB	chr11:65151162-65151623	HepG2	liver:	n/a	chr11:65151401-65151412
13	HDAC2	chr11:65151188-65151594	HepG2	liver:	n/a	n/a
14	CEBPD	chr11:65151260-65151562	HepG2	liver:	n/a	n/a
15	CEBPD	chr11:65151290-65151570	HepG2	liver:	n/a	n/a
16	CEBPB	chr11:65151213-65151597	HepG2	liver:	n/a	chr11:65151401-65151412
17	EP300	chr11:65151243-65151680	HepG2	liver:	n/a	n/a
18	CEBPB	chr11:65151229-65151578	Hela-S3	cervix:	n/a	chr11:65151401-65151412

No.	Distal block	Cell Line	Cell type
1	chr11:65116402..65157784-chr11:65261420..65278410,154	K562	blood:
2	chr11:65098911..65102850-chr11:65147012..65151675,4	MCF-7	breast:
3	chr11:65120584..65123151-chr11:65148447..65152021,3	K562	blood:

Variant related genes	Relation type
FRMD8	TF binding region
SLC25A45	TF binding region
ENSG00000270117	Chromatin interaction
ENSG00000251562	Chromatin interaction
ENSG00000133884	Chromatin interaction
ENSG00000173825	Chromatin interaction

Extended variants
information (count: 24 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:10)

rs_ID	r²[population]
rs2073799	0.86[EUR][1000 genomes]
rs2073800	1.00[ASW][hapmap];0.96[CEU][hapmap];0.94[CHB][hapmap];1.00[CHD][hapmap];0.91[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];0.94[MEX][hapmap];0.85[MKK][hapmap];0.95[TSI][hapmap];1.00[YRI][hapmap];0.91[AFR][1000 genomes];0.97[AMR][1000 genomes];0.94[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs3782093	0.85[MKK][hapmap];1.00[YRI][hapmap]
rs4930154	0.87[AMR][1000 genomes];0.94[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs547221	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.94[MEX][hapmap];0.98[TSI][hapmap];0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs578270	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];0.94[MEX][hapmap];1.00[TSI][hapmap];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs585210	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs651283	0.90[AMR][1000 genomes];0.88[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs652501	0.96[CEU][hapmap];0.89[CHB][hapmap];0.97[CHD][hapmap];0.89[GIH][hapmap];1.00[JPT][hapmap];0.89[MEX][hapmap];0.95[TSI][hapmap];0.96[AMR][1000 genomes];0.94[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs666194	0.89[GIH][hapmap]

Variant overlapped rSNPs/rCNVs (count:14 , 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	esv2422285	chr11:65013294-65254540	Genic enhancers Enhancers Weak transcription Active TSS Bivalent Enhancer Flanking Active TSS Strong transcription Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	474 gene(s)	inside rSNPs	diseases
3	nsv897715	chr11:65083491-65427346	Enhancers Genic enhancers Active TSS Weak transcription Strong transcription Flanking Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	984 gene(s)	inside rSNPs	diseases
4	nsv897716	chr11:65083491-65481166	Weak transcription Enhancers Genic enhancers Flanking Active TSS Strong transcription Transcr. at gene 5' and 3' Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	999 gene(s)	inside rSNPs	diseases
5	nsv541065	chr11:65117387-65271894	Active TSS Flanking Active TSS Flanking Bivalent TSS/Enh Weak transcription Transcr. at gene 5' and 3' Enhancers Strong transcription Genic enhancers ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	835 gene(s)	inside rSNPs	diseases
6	esv1829999	chr11:65136686-65343124	Weak transcription Flanking Active TSS Enhancers Active TSS Strong transcription Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	963 gene(s)	inside rSNPs	diseases
7	nsv897717	chr11:65140209-65278461	Strong transcription Enhancers Weak transcription Flanking Active TSS Transcr. at gene 5' and 3' Active TSS Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	942 gene(s)	inside rSNPs	diseases
8	nsv897718	chr11:65140209-65577516	Enhancers Active TSS Flanking Active TSS Weak transcription Strong transcription Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	1003 gene(s)	inside rSNPs	diseases
9	nsv541066	chr11:65142779-65271894	Active TSS Weak transcription Strong transcription Flanking Active TSS Transcr. at gene 5' and 3' Genic enhancers Enhancers Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	833 gene(s)	inside rSNPs	diseases
10	nsv541067	chr11:65142779-65313799	Flanking Active TSS Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' Enhancers Active TSS Weak transcription Strong transcription Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	950 gene(s)	inside rSNPs	diseases
11	nsv541068	chr11:65142779-65331136	Flanking Active TSS Weak transcription Enhancers Active TSS Strong transcription Transcr. at gene 5' and 3' Genic enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	953 gene(s)	inside rSNPs	diseases
12	nsv541069	chr11:65142779-65368787	Transcr. at gene 5' and 3' Flanking Active TSS Genic enhancers Enhancers Strong transcription Flanking Bivalent TSS/Enh Weak transcription Active TSS Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	965 gene(s)	inside rSNPs	diseases
13	nsv541070	chr11:65142779-65397058	Flanking Active TSS Active TSS Enhancers Genic enhancers Bivalent Enhancer Weak transcription Strong transcription Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	972 gene(s)	inside rSNPs	diseases
14	nsv541071	chr11:65142779-65429352	Flanking Active TSS Enhancers Active TSS Weak transcription Bivalent Enhancer Strong transcription Transcr. at gene 5' and 3' Genic enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	984 gene(s)	inside rSNPs	diseases

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs681309	TPCN2	cis	parietal	SCAN
rs681309	HRASLS2	cis	parietal	SCAN
rs681309	SLC22A24	cis	parietal	SCAN
rs681309	CDK2AP2	cis	cerebellum	SCAN

Chromatin state (count:122 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr11:65148200-65153800	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
2	chr11:65149400-65151600	Enhancers	iPS DF 19.11 Cell Line	embryonic stem cell
3	chr11:65149800-65153600	Weak transcription	Pancreatic Islets	Pancreatic Islet
4	chr11:65149800-65153800	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
5	chr11:65149800-65153800	Enhancers	Placenta Amnion	Placenta Amnion
6	chr11:65150000-65151600	Flanking Active TSS	Hela-S3	cervix
7	chr11:65150000-65153800	Enhancers	Spleen	Spleen
8	chr11:65150200-65153400	Weak transcription	Brain Germinal Matrix	brain
9	chr11:65150200-65154000	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
10	chr11:65150400-65153600	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
11	chr11:65150400-65153600	Weak transcription	Aorta	Aorta
12	chr11:65150400-65153600	Enhancers	Fetal Adrenal Gland	Adrenal Gland
13	chr11:65150400-65153600	Enhancers	Fetal Stomach	stomach
14	chr11:65150400-65153800	Weak transcription	iPS-18 Cell Line	embryonic stem cell
15	chr11:65150400-65153800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
16	chr11:65150400-65153800	Enhancers	Sigmoid Colon	Sigmoid Colon
17	chr11:65150600-65151800	Enhancers	Primary T killer memory cells from peripheral blood	blood
18	chr11:65150600-65152000	Enhancers	Brain Hippocampus Middle	brain
19	chr11:65150600-65152600	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
20	chr11:65150600-65153400	Enhancers	K562	blood
21	chr11:65150600-65153600	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
22	chr11:65150600-65153600	Weak transcription	HUES64 Cell Line	embryonic stem cell
23	chr11:65150600-65153600	Weak transcription	iPS-15b Cell Line	embryonic stem cell
24	chr11:65150600-65153600	Enhancers	Primary T helper naive cells from peripheral blood	blood
25	chr11:65150600-65153600	Enhancers	Primary T helper naive cells fromperipheralblood	blood
26	chr11:65150600-65153600	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
27	chr11:65150600-65153600	Enhancers	Primary T killer naive cells fromperipheralblood	blood
28	chr11:65150600-65153600	Weak transcription	Fetal Brain Male	brain
29	chr11:65150600-65153600	Weak transcription	Fetal Brain Female	brain
30	chr11:65150600-65153600	Enhancers	Fetal Intestine Small	intestine
31	chr11:65150600-65153600	Weak transcription	Fetal Kidney	kidney
32	chr11:65150600-65153600	Enhancers	Placenta	Placenta
33	chr11:65150600-65153600	Enhancers	Fetal Thymus	thymus
34	chr11:65150600-65153800	Weak transcription	H9 Cell Line	embryonic stem cell
35	chr11:65150600-65153800	Weak transcription	HUES48 Cell Line	embryonic stem cell
36	chr11:65150600-65153800	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
37	chr11:65150600-65153800	Enhancers	Lung	lung
38	chr11:65150600-65153800	Enhancers	HUVEC	blood vessel
39	chr11:65150800-65151600	Enhancers	Primary monocytes fromperipheralblood	blood
40	chr11:65150800-65151600	Enhancers	HSMMtube	muscle
41	chr11:65150800-65152000	Enhancers	Esophagus	oesophagus
42	chr11:65150800-65152000	Enhancers	Psoas Muscle	Psoas
43	chr11:65150800-65152600	Enhancers	Right Atrium	heart
44	chr11:65150800-65153000	Enhancers	Primary T helper cells fromperipheralblood	blood
45	chr11:65150800-65153000	Enhancers	Colon Smooth Muscle	Colon
46	chr11:65150800-65153600	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
47	chr11:65150800-65153600	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
48	chr11:65150800-65153600	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
49	chr11:65150800-65153600	Enhancers	Primary T cells from cord blood	blood
50	chr11:65150800-65153600	Enhancers	Primary T cells fromperipheralblood	blood

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