Variant report

Variant	rs11228706
Chromosome Location	chr11:56427652-56427653
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	chr11:56427334-56427828	H1-hESC	embryonic stem cell:	n/a	n/a
2	SP1	chr11:56427096-56427691	H1-hESC	embryonic stem cell:	n/a	n/a
3	NANOG	chr11:56427176-56427683	H1-hESC	embryonic stem cell:	n/a	chr11:56427430-56427444
4	TEAD4	chr11:56427130-56427733	H1-hESC	embryonic stem cell:	n/a	n/a
5	MAX	chr11:56427171-56427773	H1-hESC	embryonic stem cell:	n/a	n/a
6	CREB1	chr11:56427178-56427725	H1-hESC	embryonic stem cell:	n/a	n/a
7	POLR2A	chr11:56427348-56427660	H1-hESC	embryonic stem cell:	n/a	n/a
8	EP300	chr11:56427090-56427691	H1-hESC	embryonic stem cell:	n/a	n/a
9	POLR2A	chr11:56427233-56427841	H1-hESC	embryonic stem cell:	n/a	n/a
10	TEAD4	chr11:56427184-56427678	H1-hESC	embryonic stem cell:	n/a	n/a
11	TAF1	chr11:56427306-56427780	H1-hESC	embryonic stem cell:	n/a	n/a
12	POLR2A	chr11:56427420-56427742	H1-hESC	embryonic stem cell:	n/a	n/a
13	GTF2F1	chr11:56427341-56427654	H1-hESC	embryonic stem cell:	n/a	n/a
14	POU5F1	chr11:56427154-56427745	H1-hESC	embryonic stem cell:	n/a	n/a
15	HDAC2	chr11:56427184-56427766	H1-hESC	embryonic stem cell:	n/a	chr11:56427361-56427375
16	POLR2A	chr11:56427215-56427889	H1-hESC	embryonic stem cell:	n/a	n/a
17	RAD21	chr11:56427418-56427838	H1-hESC	embryonic stem cell:	n/a	n/a

Variant related genes	Relation type
OR5AR1	TF binding region

Extended variants
information (count: 74 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:69)

rs_ID	r²[population]
rs10501354	1.00[CEU][hapmap];1.00[CHB][hapmap];0.94[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[TSI][hapmap]
rs10736676	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs10736677	1.00[CHB][hapmap];0.94[CHD][hapmap];1.00[JPT][hapmap];0.85[ASN][1000 genomes]
rs10736678	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs10792038	1.00[CHB][hapmap];0.94[CHD][hapmap];1.00[JPT][hapmap]
rs10792039	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs10792040	1.00[CHB][hapmap];1.00[JPT][hapmap];0.85[ASN][1000 genomes]
rs10792043	1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[ASN][1000 genomes]
rs10896501	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs11228641	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.82[MEX][hapmap];1.00[TSI][hapmap]
rs11228673	0.90[CEU][hapmap];1.00[CHB][hapmap];0.90[JPT][hapmap]
rs11228676	1.00[CHB][hapmap];0.94[CHD][hapmap];1.00[JPT][hapmap]
rs11228684	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs11228686	0.88[AMR][1000 genomes];0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs11228687	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[YRI][hapmap];0.89[AFR][1000 genomes];0.97[AMR][1000 genomes];0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs11228693	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.95[LWK][hapmap];0.82[MEX][hapmap];0.87[MKK][hapmap];1.00[TSI][hapmap];0.90[YRI][hapmap];0.93[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11228694	0.93[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11228698	0.93[AFR][1000 genomes];0.94[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11228701	0.93[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11228708	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][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]
rs11228759	0.94[CHD][hapmap];0.83[GIH][hapmap];0.91[JPT][hapmap]
rs11228760	0.94[CHD][hapmap];0.83[GIH][hapmap];0.91[JPT][hapmap]
rs11228763	0.94[CHD][hapmap];0.83[GIH][hapmap];0.91[JPT][hapmap]
rs11228769	0.90[JPT][hapmap]
rs12222989	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12223492	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs12418150	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.83[YRI][hapmap];0.81[AFR][1000 genomes];0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs12418301	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1473592	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs1605924	0.88[AMR][1000 genomes];0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs17150739	0.85[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs1945196	0.86[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs1945206	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs1945261	0.85[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.89[LWK][hapmap];1.00[MEX][hapmap];0.81[MKK][hapmap];1.00[TSI][hapmap];0.91[YRI][hapmap]
rs1945263	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs1945282	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap]
rs2202932	0.94[ASN][1000 genomes]
rs2511143	0.82[ASN][1000 genomes]
rs2865516	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs33995115	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[TSI][hapmap]
rs4500505	0.85[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs4939061	1.00[CHB][hapmap];1.00[JPT][hapmap];0.85[ASN][1000 genomes]
rs4939065	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap]
rs4939066	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs583216	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs583589	0.82[ASN][1000 genomes]
rs584608	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs588805	0.82[ASN][1000 genomes]
rs592744	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs597680	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs600187	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs611397	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs614942	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs61710550	0.88[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs628524	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap]
rs637912	0.82[ASN][1000 genomes]
rs642630	0.82[ASN][1000 genomes]
rs643384	0.82[ASN][1000 genomes]
rs645351	1.00[CHB][hapmap];0.94[CHD][hapmap];1.00[JPT][hapmap]
rs646286	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs654634	0.82[ASN][1000 genomes]
rs655779	0.82[ASN][1000 genomes]
rs656565	0.82[ASN][1000 genomes]
rs6591381	1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[ASN][1000 genomes]
rs674431	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs676901	0.82[ASN][1000 genomes]
rs688832	1.00[CHB][hapmap];0.94[CHD][hapmap];1.00[JPT][hapmap]
rs7924528	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs7939886	0.86[EUR][1000 genomes];0.82[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	nsv1050024	chr11:55900482-56518943	Enhancers Weak transcription ZNF genes & repeats Flanking Active TSS Active TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA	52 gene(s)	inside rSNPs	diseases
2	nsv497854	chr11:55917298-56537994	Enhancers ZNF genes & repeats Active TSS Weak transcription Flanking Active TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA	50 gene(s)	inside rSNPs	diseases
3	nsv971952	chr11:56361311-56452186	Enhancers Weak transcription Active TSS Flanking Active TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
4	nsv949349	chr11:56371633-56593610	Enhancers Flanking Active TSS Active TSS Weak transcription Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA	18 gene(s)	inside rSNPs	diseases
5	nsv1051853	chr11:56393347-56523720	Enhancers Weak transcription Active TSS Flanking Active TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA	12 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:16 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr11:56426600-56428000	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
2	chr11:56427000-56427800	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
3	chr11:56427400-56427800	Active TSS	ES-I3 Cell Line	embryonic stem cell
4	chr11:56427400-56427800	Enhancers	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
5	chr11:56427400-56427800	Active TSS	H9 Cell Line	embryonic stem cell
6	chr11:56427400-56428000	Enhancers	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
7	chr11:56427400-56428000	Flanking Active TSS	iPS-15b Cell Line	embryonic stem cell
8	chr11:56427600-56427800	Flanking Active TSS	H1 Cell Line	embryonic stem cell
9	chr11:56427600-56427800	Flanking Active TSS	iPS-20b Cell Line	embryonic stem cell
10	chr11:56427600-56427800	Enhancers	iPS DF 6.9 Cell Line	embryonic stem cell
11	chr11:56427600-56428000	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
12	chr11:56427600-56428000	Flanking Active TSS	HUES6 Cell Line	embryonic stem cell
13	chr11:56427600-56428200	Flanking Active TSS	HUES64 Cell Line	embryonic stem cell
14	chr11:56427600-56428200	Flanking Active TSS	iPS-18 Cell Line	embryonic stem cell
15	chr11:56427600-56428400	Flanking Active TSS	HUES48 Cell Line	embryonic stem cell
16	chr11:56427600-56428800	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell

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