Variant report

Variant	rs11236452
Chromosome Location	chr11:75249886-75249887
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr11:75247004..75250213-chr11:75275515..75278123,3	MCF-7	breast:
2	chr11:75248740..75251271-chr11:75278768..75280519,2	K562	blood:
3	chr11:75249028..75251434-chr11:75272260..75274448,3	MCF-7	breast:
4	chr11:75185179..75187092-chr11:75248204..75250033,2	K562	blood:

Variant related genes	Relation type
ENSG00000149257	Chromatin interaction

Extended variants
information (count: 26 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:24)

rs_ID	r²[population]
rs10899091	0.92[ASW][hapmap];0.92[CEU][hapmap];0.88[CHD][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.87[AMR][1000 genomes];0.87[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs10899092	0.87[AMR][1000 genomes];0.87[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs11236448	0.86[ASN][1000 genomes]
rs11236449	1.00[CEU][hapmap];1.00[CHB][hapmap];0.92[CHD][hapmap];1.00[GIH][hapmap];0.92[JPT][hapmap];1.00[MEX][hapmap];0.95[TSI][hapmap];0.90[AMR][1000 genomes];0.93[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs11236454	0.90[AMR][1000 genomes];0.87[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs12291026	0.92[ASW][hapmap];0.92[CEU][hapmap];0.88[CHD][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.87[AMR][1000 genomes];0.87[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs12361128	0.86[ASN][1000 genomes]
rs12362081	0.91[CEU][hapmap];1.00[CHB][hapmap];0.83[JPT][hapmap];0.87[AMR][1000 genomes];0.81[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs12362890	0.87[AMR][1000 genomes];0.81[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs1783551	0.81[EUR][1000 genomes]
rs1938800	0.88[CHD][hapmap];0.82[TSI][hapmap];0.90[ASN][1000 genomes]
rs55702115	0.90[AMR][1000 genomes];0.87[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs56232370	0.87[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs618202	0.85[TSI][hapmap];0.82[EUR][1000 genomes]
rs662358	0.82[EUR][1000 genomes]
rs7109103	0.94[AMR][1000 genomes];0.87[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs7110149	0.94[AMR][1000 genomes];0.87[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs7128888	0.92[ASW][hapmap];0.92[CEU][hapmap];0.88[CHD][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.94[AMR][1000 genomes];0.87[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs7129014	0.92[CEU][hapmap];0.94[AMR][1000 genomes];0.87[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs7129150	0.82[CEU][hapmap];0.94[AMR][1000 genomes];0.87[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs72989929	0.84[AMR][1000 genomes];0.81[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs72989989	0.90[AMR][1000 genomes];0.93[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs7938523	0.97[AMR][1000 genomes];0.93[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs947844	0.91[CEU][hapmap];1.00[CHB][hapmap];0.92[CHD][hapmap];1.00[GIH][hapmap];0.92[JPT][hapmap];1.00[MEX][hapmap];0.95[TSI][hapmap];0.84[AMR][1000 genomes];0.90[EUR][1000 genomes];0.83[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:2 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv3381903	chr11:75123498-75587233	Bivalent Enhancer Strong transcription Enhancers Bivalent/Poised TSS Genic enhancers Weak transcription ZNF genes & repeats Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	81 gene(s)	inside rSNPs	diseases
2	nsv897923	chr11:75129007-75302855	Active TSS Weak transcription Bivalent Enhancer Enhancers Transcr. at gene 5' and 3' Flanking Active TSS Bivalent/Poised TSS Genic enhancers Strong transcription Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	56 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs11236452	NGFRAP1	trans	lymphoblastoid	seeQTL

Chromatin state (count:30 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr11:75237800-75258800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
2	chr11:75243600-75250600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
3	chr11:75243600-75258400	Weak transcription	iPS-15b Cell Line	embryonic stem cell
4	chr11:75245200-75250000	Enhancers	Primary T cells fromperipheralblood	blood
5	chr11:75245800-75250400	Weak transcription	HSMMtube	muscle
6	chr11:75245800-75254600	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
7	chr11:75246400-75265800	Weak transcription	Right Atrium	heart
8	chr11:75246600-75250000	Weak transcription	Fetal Muscle Trunk	muscle
9	chr11:75246600-75251400	Enhancers	K562	blood
10	chr11:75246600-75252200	Weak transcription	Fetal Intestine Small	intestine
11	chr11:75248200-75250000	Enhancers	Primary hematopoietic stem cells	blood
12	chr11:75248400-75250800	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
13	chr11:75248400-75255000	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
14	chr11:75248600-75250400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
15	chr11:75248600-75250400	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
16	chr11:75248600-75250400	Weak transcription	Placenta	Placenta
17	chr11:75248600-75251000	Weak transcription	Fetal Thymus	thymus
18	chr11:75248800-75250000	Enhancers	Primary neutrophils fromperipheralblood	blood
19	chr11:75248800-75250000	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
20	chr11:75248800-75254600	Weak transcription	HUES6 Cell Line	embryonic stem cell
21	chr11:75248800-75258800	Weak transcription	ES-I3 Cell Line	embryonic stem cell
22	chr11:75249200-75251600	Enhancers	Fetal Adrenal Gland	Adrenal Gland
23	chr11:75249400-75250000	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
24	chr11:75249400-75251600	Enhancers	Ovary	ovary
25	chr11:75249600-75251200	Enhancers	Fetal Heart	heart
26	chr11:75249600-75252400	Weak transcription	A549	lung
27	chr11:75249600-75252400	Weak transcription	Hela-S3	cervix
28	chr11:75249600-75252600	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
29	chr11:75249800-75250000	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
30	chr11:75249800-75250600	Weak transcription	Spleen	Spleen

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