Variant report

Variant	rs11229800
Chromosome Location	chr11:58864544-58864545
allele	A/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr11:58863409..58866220-chr11:58910202..58912249,2	K562	blood:

Variant related genes	Relation type
ENSG00000245571	Chromatin interaction
ENSG00000166801	Chromatin interaction

Extended variants
information (count: 109 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:88)

rs_ID	r²[population]
rs10128559	0.95[ASN][1000 genomes]
rs10128661	0.85[EUR][1000 genomes]
rs10437720	0.94[CEU][hapmap];0.96[TSI][hapmap];0.92[EUR][1000 genomes]
rs10792219	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.94[GIH][hapmap];1.00[JPT][hapmap];0.82[MEX][hapmap];0.86[MKK][hapmap];0.92[TSI][hapmap];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs10792221	0.85[CEU][hapmap];0.90[EUR][1000 genomes]
rs10896914	1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10896922	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs10896924	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.98[AMR][1000 genomes];0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs10896925	0.94[CEU][hapmap];0.96[TSI][hapmap];0.92[EUR][1000 genomes]
rs10896926	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[YRI][hapmap];0.82[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs10896928	0.94[CEU][hapmap];0.90[EUR][1000 genomes]
rs10896929	1.00[CHB][hapmap];0.80[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs10896930	0.90[EUR][1000 genomes]
rs10896931	1.00[CEU][hapmap];1.00[CHB][hapmap];0.93[EUR][1000 genomes]
rs10896932	0.89[CHB][hapmap];0.90[EUR][1000 genomes]
rs10896933	0.89[EUR][1000 genomes]
rs10896934	0.85[EUR][1000 genomes]
rs10896935	0.82[EUR][1000 genomes]
rs10896936	0.89[EUR][1000 genomes]
rs10896937	0.89[EUR][1000 genomes]
rs10896938	0.82[EUR][1000 genomes]
rs10896947	0.94[CEU][hapmap]
rs11229795	0.95[ASN][1000 genomes]
rs11229798	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11229799	0.88[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11229801	0.82[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11229837	1.00[CEU][hapmap];1.00[CHB][hapmap];0.82[MEX][hapmap];1.00[TSI][hapmap];0.80[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs11229840	0.94[CEU][hapmap];0.96[TSI][hapmap];0.88[EUR][1000 genomes]
rs11229848	0.96[TSI][hapmap];0.87[EUR][1000 genomes]
rs11229849	0.94[CEU][hapmap];0.90[EUR][1000 genomes]
rs11229850	1.00[CHB][hapmap]
rs11229851	0.90[EUR][1000 genomes]
rs11229852	0.90[EUR][1000 genomes]
rs11229854	0.90[EUR][1000 genomes]
rs11229856	0.89[EUR][1000 genomes]
rs11823977	0.98[AMR][1000 genomes];0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs11825017	0.98[AMR][1000 genomes];0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12271831	1.00[CEU][hapmap];1.00[CHB][hapmap];0.90[EUR][1000 genomes]
rs12272113	0.90[EUR][1000 genomes]
rs12274008	1.00[CHB][hapmap];0.82[MEX][hapmap];0.96[TSI][hapmap];0.90[EUR][1000 genomes]
rs12275487	1.00[CHB][hapmap];0.89[EUR][1000 genomes]
rs12278163	1.00[CHB][hapmap];0.90[EUR][1000 genomes]
rs12280068	1.00[CHB][hapmap];0.90[EUR][1000 genomes]
rs12283633	1.00[CHB][hapmap];0.80[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs12292185	0.87[EUR][1000 genomes]
rs12292779	1.00[ASW][hapmap]
rs12293649	1.00[CHB][hapmap];0.82[MEX][hapmap];0.96[TSI][hapmap];0.90[EUR][1000 genomes]
rs12293695	0.90[EUR][1000 genomes]
rs12362905	0.90[EUR][1000 genomes]
rs12802129	0.98[AMR][1000 genomes];0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs17153379	0.98[AMR][1000 genomes];0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs17153383	0.92[EUR][1000 genomes]
rs17153415	0.87[EUR][1000 genomes]
rs1938588	0.98[AMR][1000 genomes];0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1938589	0.92[EUR][1000 genomes]
rs1938781	0.94[CEU][hapmap];0.96[TSI][hapmap];0.90[EUR][1000 genomes]
rs1943146	0.92[ASN][1000 genomes]
rs1943147	0.92[ASN][1000 genomes]
rs2096544	0.90[EUR][1000 genomes]
rs2096586	0.85[EUR][1000 genomes]
rs2096587	0.88[EUR][1000 genomes]
rs2105506	1.00[CHB][hapmap];0.80[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs2105507	0.90[EUR][1000 genomes]
rs2154628	0.83[EUR][1000 genomes]
rs2186380	0.90[EUR][1000 genomes]
rs2282482	0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2282483	0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2839968	0.94[CEU][hapmap]
rs2844342	0.94[ASN][1000 genomes]
rs2849739	0.84[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34027305	0.82[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs34239454	0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34501069	0.90[EUR][1000 genomes]
rs35293773	1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3802961	0.96[AMR][1000 genomes];0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs474847	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs530386	0.87[ASN][1000 genomes]
rs55657403	0.84[EUR][1000 genomes]
rs55689653	0.90[EUR][1000 genomes]
rs55989038	0.82[EUR][1000 genomes]
rs56137001	0.80[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs56239606	0.83[EUR][1000 genomes]
rs58722008	0.87[EUR][1000 genomes]
rs61902181	0.90[EUR][1000 genomes]
rs61902223	0.90[EUR][1000 genomes]
rs7126078	0.98[AMR][1000 genomes];0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7933787	0.94[CEU][hapmap];1.00[TSI][hapmap];0.90[EUR][1000 genomes]
rs7950880	0.82[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:21 , 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	esv3393019	chr11:58679419-58880845	Flanking Active TSS Active TSS Enhancers ZNF genes & repeats Bivalent Enhancer Weak transcription Bivalent/Poised TSS Strong transcription Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	17 gene(s)	inside rSNPs	diseases
4	nsv428258	chr11:58700092-58878839	Bivalent Enhancer Flanking Bivalent TSS/Enh Flanking Active TSS Weak transcription Enhancers Active TSS Bivalent/Poised TSS Genic enhancers Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	17 gene(s)	inside rSNPs	diseases
5	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
6	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
7	nsv832171	chr11:58725930-58878839	Bivalent Enhancer Weak transcription Strong transcription Enhancers Bivalent/Poised TSS Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	15 gene(s)	inside rSNPs	diseases
8	nsv469559	chr11:58730785-58887639	Active TSS Flanking Bivalent TSS/Enh Flanking Active TSS Enhancers ZNF genes & repeats Weak transcription Bivalent/Poised TSS Genic enhancers Strong transcription Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	15 gene(s)	inside rSNPs	diseases
9	nsv482906	chr11:58730785-58887639	Enhancers Active TSS ZNF genes & repeats Flanking Active TSS Weak transcription Flanking Bivalent TSS/Enh Bivalent Enhancer Strong transcription Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	15 gene(s)	inside rSNPs	diseases
10	nsv471671	chr11:58730786-58887639	Active TSS Weak transcription Enhancers ZNF genes & repeats Flanking Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS Strong transcription Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	15 gene(s)	inside rSNPs	diseases
11	esv2757447	chr11:58746238-58906018	Weak transcription Flanking Bivalent TSS/Enh Bivalent Enhancer Enhancers Bivalent/Poised TSS ZNF genes & repeats Flanking Active TSS Active TSS Strong transcription Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	22 gene(s)	inside rSNPs	diseases
12	nsv975329	chr11:58767290-58907813	Weak transcription Flanking Active TSS Enhancers Active TSS Strong transcription Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	25 gene(s)	inside rSNPs	diseases
13	nsv430388	chr11:58769524-58925824	Enhancers Active TSS ZNF genes & repeats Flanking Active TSS Weak transcription Strong transcription Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	32 gene(s)	inside rSNPs	diseases
14	nsv468578	chr11:58790628-58901763	ZNF genes & repeats Active TSS Weak transcription Enhancers Flanking Active TSS Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Strong transcription Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	15 gene(s)	inside rSNPs	diseases
15	nsv555147	chr11:58790628-58901763	Active TSS Flanking Active TSS Strong transcription Enhancers Genic enhancers Bivalent/Poised TSS Weak transcription Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	15 gene(s)	inside rSNPs	diseases
16	nsv1050767	chr11:58790982-58864544	Enhancers Bivalent Enhancer Bivalent/Poised TSS Active TSS Weak transcription Flanking Active TSS Flanking Bivalent TSS/Enh Strong transcription Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
17	esv2760644	chr11:58798999-58869223	Active TSS Flanking Active TSS Enhancers Bivalent Enhancer Bivalent/Poised TSS Weak transcription Flanking Bivalent TSS/Enh Strong transcription Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
18	nsv1039379	chr11:58800374-58864544	Enhancers Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Weak transcription Flanking Active TSS Bivalent/Poised TSS Strong transcription Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
19	nsv1045695	chr11:58811241-58864544	Active TSS Enhancers Flanking Active TSS Bivalent Enhancer Bivalent/Poised TSS Weak transcription Genic enhancers Strong transcription Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
20	nsv1043956	chr11:58818144-58882570	Active TSS Flanking Active TSS Weak transcription Enhancers Bivalent/Poised TSS Bivalent Enhancer Strong transcription Flanking Bivalent TSS/Enh ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases
21	esv3381644	chr11:58822364-58866298	Weak transcription Bivalent Enhancer Flanking Active TSS Enhancers Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs11229800	CD5	cis	cerebellum	SCAN
rs11229800	FAM111A	cis	parietal	SCAN
rs11229800	OR5AK2	cis	parietal	SCAN
rs11229800	C11orf31	cis	parietal	SCAN

Chromatin state (count:15 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr11:58858200-58869000	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
2	chr11:58860000-58864600	Genic enhancers	Primary B cells from peripheral blood	blood
3	chr11:58860000-58869000	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
4	chr11:58861400-58866400	Enhancers	iPS-18 Cell Line	embryonic stem cell
5	chr11:58863000-58867000	Enhancers	H1 Cell Line	embryonic stem cell
6	chr11:58863200-58864600	Weak transcription	ES-I3 Cell Line	embryonic stem cell
7	chr11:58863200-58866400	Enhancers	HUES48 Cell Line	embryonic stem cell
8	chr11:58863200-58866400	Enhancers	iPS-20b Cell Line	embryonic stem cell
9	chr11:58863200-58869600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
10	chr11:58863400-58866000	Weak transcription	HUES64 Cell Line	embryonic stem cell
11	chr11:58864000-58865200	Flanking Active TSS	Primary B cells from cord blood	blood
12	chr11:58864000-58867000	Enhancers	iPS-15b Cell Line	embryonic stem cell
13	chr11:58864200-58866000	Enhancers	HUES6 Cell Line	embryonic stem cell
14	chr11:58864400-58865200	Weak transcription	H9 Cell Line	embryonic stem cell
15	chr11:58864400-58866200	Flanking Active TSS	GM12878-XiMat	blood

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