Variant report

Variant	rs11231859
Chromosome Location	chr11:64488054-64488055
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr11:64485672..64488139-chr11:64489786..64491520,2	MCF-7	breast:
2	chr11:64126498..64128019-chr11:64487243..64489770,2	K562	blood:
3	chr11:64484197..64486078-chr11:64487763..64489732,2	K562	blood:
4	chr11:64479124..64481401-chr11:64485906..64488788,2	K562	blood:

Variant related genes	Relation type
ENSG00000110076	Chromatin interaction
ENSG00000162302	Chromatin interaction

Extended variants
information (count: 84 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:63)

rs_ID	r²[population]
rs10400348	0.83[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs10792444	0.84[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs10897524	0.92[GIH][hapmap];0.85[JPT][hapmap];0.93[TSI][hapmap];0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs10897525	0.83[MEX][hapmap]
rs11231853	0.86[CEU][hapmap];0.89[EUR][1000 genomes]
rs11231869	0.83[MEX][hapmap]
rs1143937	1.00[CEU][hapmap];0.83[MEX][hapmap]
rs1207181	0.85[AMR][1000 genomes];0.87[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs12223914	0.82[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs12417551	0.81[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs12575704	0.89[EUR][1000 genomes]
rs1633462	1.00[CEU][hapmap];0.80[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs17146121	0.89[CEU][hapmap];0.82[CHD][hapmap];0.89[GIH][hapmap];0.94[MEX][hapmap];0.93[TSI][hapmap];0.84[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs2003293	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2073797	0.88[EUR][1000 genomes]
rs2073798	0.81[GIH][hapmap];0.90[JPT][hapmap];0.94[MEX][hapmap];0.86[TSI][hapmap];0.88[EUR][1000 genomes]
rs2230414	0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2267918	1.00[CEU][hapmap];0.95[CHB][hapmap];0.98[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.94[MEX][hapmap];0.93[TSI][hapmap];0.90[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2284301	0.82[ASW][hapmap];1.00[CEU][hapmap];0.86[CHD][hapmap];0.92[GIH][hapmap];0.95[JPT][hapmap];0.97[LWK][hapmap];0.94[MEX][hapmap];0.93[TSI][hapmap];1.00[YRI][hapmap];0.93[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs2375335	0.81[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2959652	1.00[CEU][hapmap];0.81[GIH][hapmap];0.90[JPT][hapmap];0.94[MEX][hapmap];0.87[TSI][hapmap];0.81[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs3741398	1.00[CEU][hapmap];0.88[MEX][hapmap];0.93[TSI][hapmap];0.89[EUR][1000 genomes]
rs3809076	0.89[CEU][hapmap];0.84[CHD][hapmap];1.00[GIH][hapmap];0.85[JPT][hapmap];0.94[MEX][hapmap];1.00[TSI][hapmap];0.86[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs474707	0.81[CEU][hapmap];0.83[MEX][hapmap];0.87[TSI][hapmap];0.93[EUR][1000 genomes]
rs476037	0.89[CEU][hapmap];0.84[CHD][hapmap];0.89[GIH][hapmap];0.94[MEX][hapmap];0.86[TSI][hapmap];0.84[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs477549	1.00[CEU][hapmap];0.83[MEX][hapmap];0.82[TSI][hapmap];0.95[EUR][1000 genomes]
rs483962	1.00[CEU][hapmap];0.83[MEX][hapmap];0.87[TSI][hapmap];0.97[EUR][1000 genomes]
rs487105	1.00[CEU][hapmap];0.88[MEX][hapmap];0.93[TSI][hapmap];0.80[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs489192	1.00[CEU][hapmap];0.80[JPT][hapmap];0.94[MEX][hapmap];0.86[TSI][hapmap];0.86[EUR][1000 genomes]
rs490980	0.89[CEU][hapmap];0.88[EUR][1000 genomes]
rs494128	0.93[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs496914	1.00[CEU][hapmap];1.00[CHB][hapmap];0.98[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.94[MEX][hapmap];0.93[TSI][hapmap];0.86[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs523200	1.00[CEU][hapmap];0.89[MEX][hapmap];0.82[TSI][hapmap];0.93[EUR][1000 genomes]
rs523752	0.82[EUR][1000 genomes]
rs532747	0.92[GIH][hapmap];0.94[MEX][hapmap];0.93[TSI][hapmap];0.89[EUR][1000 genomes]
rs547066	0.84[GIH][hapmap];0.94[MEX][hapmap];0.93[TSI][hapmap];0.88[EUR][1000 genomes]
rs555974	0.88[EUR][1000 genomes]
rs569602	0.92[GIH][hapmap];0.90[JPT][hapmap];0.94[MEX][hapmap];0.93[TSI][hapmap];0.82[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs580374	0.88[AMR][1000 genomes];0.98[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs58483071	0.88[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs589691	1.00[CEU][hapmap];0.81[GIH][hapmap];0.90[JPT][hapmap];0.94[MEX][hapmap];0.82[TSI][hapmap];0.93[EUR][1000 genomes]
rs593394	0.80[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs606458	1.00[CEU][hapmap];0.89[MEX][hapmap];0.82[TSI][hapmap];0.87[EUR][1000 genomes]
rs607389	1.00[CEU][hapmap];0.85[EUR][1000 genomes]
rs620006	0.93[EUR][1000 genomes]
rs624975	0.90[CEU][hapmap];0.83[MEX][hapmap]
rs625172	0.81[GIH][hapmap];0.90[JPT][hapmap];0.94[MEX][hapmap];0.86[TSI][hapmap];0.88[EUR][1000 genomes]
rs630966	0.88[EUR][1000 genomes]
rs633923	0.93[EUR][1000 genomes]
rs637332	1.00[CEU][hapmap];0.83[MEX][hapmap];0.87[TSI][hapmap];0.97[EUR][1000 genomes]
rs667237	0.88[AMR][1000 genomes];0.93[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs669976	0.90[CEU][hapmap];0.83[MEX][hapmap]
rs674297	0.93[EUR][1000 genomes]
rs677298	1.00[CEU][hapmap]
rs680273	1.00[CEU][hapmap];0.89[MEX][hapmap];0.82[TSI][hapmap];0.90[EUR][1000 genomes]
rs683841	0.80[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs684720	0.86[EUR][1000 genomes]
rs686171	0.88[EUR][1000 genomes]
rs693235	0.90[CEU][hapmap];1.00[CHB][hapmap];0.98[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.94[MEX][hapmap];0.93[TSI][hapmap];0.88[AMR][1000 genomes];0.96[ASN][1000 genomes]
rs72643567	0.86[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs72643568	0.90[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs7938455	0.89[EUR][1000 genomes]
rs7939965	0.89[CEU][hapmap];0.82[CHD][hapmap];0.89[GIH][hapmap];0.94[MEX][hapmap];0.93[TSI][hapmap];0.89[EUR][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	nsv468596	chr11:64334114-64527080	Flanking Bivalent TSS/Enh Weak transcription Genic enhancers Active TSS Enhancers Bivalent Enhancer Flanking Active TSS Bivalent/Poised TSS Strong transcription Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	28 gene(s)	inside rSNPs	diseases
2	nsv555195	chr11:64334114-64527080	Bivalent Enhancer Weak transcription Strong transcription Flanking Bivalent TSS/Enh Enhancers Genic enhancers Flanking Active TSS Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	28 gene(s)	inside rSNPs	diseases
3	nsv897694	chr11:64334114-64584959	Weak transcription Bivalent/Poised TSS Bivalent Enhancer Enhancers Flanking Bivalent TSS/Enh Active TSS Strong transcription Genic enhancers ZNF genes & repeats Flanking Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	83 gene(s)	inside rSNPs	diseases
4	nsv818842	chr11:64345448-64546391	Bivalent Enhancer Enhancers Weak transcription Strong transcription Active TSS Genic enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	75 gene(s)	inside rSNPs	diseases
5	nsv528506	chr11:64345448-64701030	Strong transcription Weak transcription Enhancers Flanking Bivalent TSS/Enh Active TSS Genic enhancers Flanking Active TSS Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	1075 gene(s)	inside rSNPs	diseases
6	nsv555196	chr11:64357072-64559898	Enhancers Flanking Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Weak transcription Bivalent/Poised TSS Active TSS Strong transcription Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	77 gene(s)	inside rSNPs	diseases
7	nsv897695	chr11:64357072-64701030	Weak transcription Genic enhancers Enhancers Active TSS Transcr. at gene 5' and 3' Strong transcription Flanking Active TSS 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	1075 gene(s)	inside rSNPs	diseases
8	nsv1051350	chr11:64372906-64533632	Weak transcription Active TSS Enhancers Flanking Active TSS Bivalent/Poised TSS Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Strong transcription ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	33 gene(s)	inside rSNPs	diseases
9	nsv555198	chr11:64373899-64573589	Weak transcription Transcr. at gene 5' and 3' Genic enhancers Enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Flanking Active TSS Active TSS Strong transcription Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	80 gene(s)	inside rSNPs	diseases
10	esv1804443	chr11:64386453-64534785	Weak transcription Bivalent Enhancer Enhancers Flanking Active TSS Bivalent/Poised TSS Active TSS Flanking Bivalent TSS/Enh Strong transcription Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	33 gene(s)	inside rSNPs	diseases
11	nsv897697	chr11:64447420-64584959	Flanking Bivalent TSS/Enh Weak transcription Enhancers Flanking Active TSS Genic enhancers Bivalent Enhancer Active TSS Bivalent/Poised TSS Strong transcription Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	79 gene(s)	inside rSNPs	diseases
12	nsv897698	chr11:64447420-64621573	Active TSS Bivalent Enhancer Genic enhancers Enhancers Weak transcription Flanking Active TSS Strong transcription Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	82 gene(s)	inside rSNPs	diseases
13	nsv897699	chr11:64447420-64638041	Flanking Active TSS Active TSS Transcr. at gene 5' and 3' Strong transcription Enhancers Weak transcription Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	83 gene(s)	inside rSNPs	diseases
14	nsv897700	chr11:64447420-64701030	Flanking Active TSS Enhancers Active TSS Strong transcription Genic enhancers Transcr. at gene 5' and 3' Weak transcription Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	1071 gene(s)	inside rSNPs	diseases
15	nsv359	chr11:64477008-64502873	Bivalent/Poised TSS Flanking Active TSS Genic enhancers Enhancers Weak transcription Flanking Bivalent TSS/Enh Active TSS Bivalent Enhancer Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region	12 gene(s)	inside rSNPs	diseases
16	nsv555202	chr11:64477050-64573589	Strong transcription Bivalent/Poised TSS Enhancers Active TSS Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' Weak transcription Flanking Bivalent TSS/Enh Flanking Active TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	73 gene(s)	inside rSNPs	diseases
17	nsv468597	chr11:64477050-64584959	Enhancers Strong transcription Flanking Active TSS Flanking Bivalent TSS/Enh Genic enhancers Active TSS Weak transcription Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	77 gene(s)	inside rSNPs	diseases
18	nsv468598	chr11:64477050-64584959	Weak transcription Flanking Active TSS Strong transcription Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS Active TSS Enhancers Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	77 gene(s)	inside rSNPs	diseases
19	nsv555203	chr11:64477050-64584959	Strong transcription Genic enhancers Bivalent Enhancer Active TSS Enhancers Flanking Bivalent TSS/Enh Weak transcription Flanking Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	77 gene(s)	inside rSNPs	diseases
20	nsv1049744	chr11:64486615-64630149	Flanking Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer Active TSS Weak transcription Enhancers Genic enhancers Strong transcription Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	79 gene(s)	inside rSNPs	diseases
21	nsv832189	chr11:64487183-64620199	Weak transcription Transcr. at gene 5' and 3' Active TSS Enhancers Strong transcription Flanking Active TSS Genic enhancers Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	79 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs11231859	SF1	cis	lymphoblastoid	seeQTL
rs11231859	SF1	cis	multi-tissue	Pritchard
rs11231859	SF1	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:11 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr11:64480400-64489800	Enhancers	Fetal Brain Male	brain
2	chr11:64482600-64489000	Weak transcription	Brain Substantia Nigra	brain
3	chr11:64485600-64489000	Weak transcription	Brain Cingulate Gyrus	brain
4	chr11:64485800-64488200	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
5	chr11:64486000-64488400	Weak transcription	Spleen	Spleen
6	chr11:64486400-64488600	Weak transcription	Brain Inferior Temporal Lobe	brain
7	chr11:64487000-64490600	Weak transcription	K562	blood
8	chr11:64487400-64488200	Enhancers	iPS DF 19.11 Cell Line	embryonic stem cell
9	chr11:64487800-64489800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
10	chr11:64488000-64489600	Flanking Active TSS	Fetal Brain Female	brain
11	chr11:64488000-64490000	Flanking Active TSS	Brain Germinal Matrix	brain

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