Variant report

Variant	rs7924472
Chromosome Location	chr11:86003498-86003499
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	CTCF	chr11:86003380-86003530	HCM	heart:	n/a	n/a
2	RAD21	chr11:86002214-86003608	SK-N-SH	brain:	n/a	chr11:86003015-86003034
3	SMC3	chr11:86002620-86003557	SK-N-SH	brain:	n/a	chr11:86003019-86003033
4	ZNF384	chr11:86002483-86003515	GM12878	blood:	n/a	n/a
5	CTCF	chr11:86003440-86003590	WI-38	lung:	n/a	n/a
6	CTCF	chr11:86002647-86003740	SK-N-SH	brain:	n/a	chr11:86003017-86003035 chr11:86003012-86003033 chr11:86003019-86003032 chr11:86003023-86003032
7	CUX1	chr11:86003361-86003498	GM12878	blood:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr11:85993708..85996490-chr11:86003264..86007905,4	K562	blood:
2	chr11:86001868..86005047-chr11:86005098..86008545,3	K562	blood:
3	chr11:85997706..86000207-chr11:86001867..86004535,3	MCF-7	breast:
4	chr11:85971469..85973576-chr11:86002289..86004505,2	MCF-7	breast:
5	chr11:85990195..85992374-chr11:86002425..86005252,2	K562	blood:
6	chr11:85989760..85992310-chr11:86001977..86004661,2	MCF-7	breast:

Variant related genes	Relation type
SETP17	TF binding region
ENSG00000254783	Chromatin interaction
ENSG00000255222	Chromatin interaction

Extended variants
information (count: 38 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:36)

rs_ID	r²[population]
rs10751137	1.00[CEU][hapmap];0.89[CHB][hapmap];0.93[JPT][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs10792841	0.93[AMR][1000 genomes];0.91[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs10792842	0.88[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.93[AMR][1000 genomes];0.91[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs10792843	1.00[ASW][hapmap];0.92[CEU][hapmap];0.90[CHB][hapmap];0.90[CHD][hapmap];0.98[GIH][hapmap];0.93[JPT][hapmap];1.00[LWK][hapmap];0.94[MEX][hapmap];0.98[MKK][hapmap];0.95[TSI][hapmap];1.00[YRI][hapmap];0.81[AFR][1000 genomes];0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs10792844	0.86[ASW][hapmap];0.90[YRI][hapmap]
rs10898448	0.93[ASN][1000 genomes]
rs10898449	0.96[ASN][1000 genomes]
rs10898452	0.91[EUR][1000 genomes]
rs10898457	1.00[ASW][hapmap];0.88[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];0.94[MEX][hapmap];0.98[MKK][hapmap];0.95[TSI][hapmap];0.91[YRI][hapmap];0.91[AMR][1000 genomes];0.91[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs10898458	0.88[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];0.95[TSI][hapmap];0.84[AMR][1000 genomes];0.91[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs10898459	0.92[CEU][hapmap];0.89[GIH][hapmap];0.95[TSI][hapmap];0.96[EUR][1000 genomes]
rs10898461	0.95[EUR][1000 genomes]
rs10898462	0.94[EUR][1000 genomes]
rs10898463	0.92[CEU][hapmap];0.96[EUR][1000 genomes]
rs11234594	0.93[AMR][1000 genomes];0.91[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs11234596	0.84[ASN][1000 genomes]
rs12223670	0.86[ASW][hapmap];0.90[YRI][hapmap]
rs12284085	0.84[AMR][1000 genomes];0.90[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1466804	0.91[EUR][1000 genomes]
rs1497725	0.84[AMR][1000 genomes];0.92[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs1497726	0.84[AMR][1000 genomes];0.91[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1874694	0.87[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2270680	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.84[AMR][1000 genomes];0.92[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2270681	0.92[CEU][hapmap];0.88[CHB][hapmap];0.90[CHD][hapmap];0.89[GIH][hapmap];0.86[JPT][hapmap];0.90[TSI][hapmap];0.84[AMR][1000 genomes];0.97[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs3758881	1.00[CEU][hapmap];0.90[CHB][hapmap];0.93[JPT][hapmap];0.88[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs6592279	0.92[CEU][hapmap];0.89[GIH][hapmap];0.95[TSI][hapmap];0.96[EUR][1000 genomes]
rs7101712	0.92[CEU][hapmap];0.90[CHB][hapmap];0.93[JPT][hapmap];0.81[AMR][1000 genomes];0.96[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs7120070	0.84[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs7120222	0.88[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.88[AMR][1000 genomes];0.89[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7122629	0.84[ASW][hapmap];0.89[YRI][hapmap]
rs7942971	0.88[CEU][hapmap];0.91[EUR][1000 genomes]
rs7950820	0.84[AMR][1000 genomes];0.91[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7951030	0.88[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];0.96[GIH][hapmap];1.00[JPT][hapmap];0.89[MEX][hapmap];0.95[TSI][hapmap];0.84[AMR][1000 genomes];0.91[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7951188	0.84[AMR][1000 genomes];0.91[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs974144	1.00[ASW][hapmap];0.88[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];0.94[MEX][hapmap];0.98[MKK][hapmap];0.95[TSI][hapmap];1.00[YRI][hapmap];0.81[AFR][1000 genomes];0.93[AMR][1000 genomes];0.91[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs991435	0.88[CEU][hapmap];0.89[GIH][hapmap];0.95[TSI][hapmap];0.89[EUR][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	nsv832223	chr11:85845315-86015957	Enhancers Weak transcription Active TSS Flanking Active TSS Strong transcription Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	36 gene(s)	inside rSNPs	diseases
2	nsv508643	chr11:85988577-86047719	Strong transcription Weak transcription Flanking Active TSS ZNF genes & repeats Active TSS Enhancers Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	11 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs7924472	C11orf73	Cis_1M	lymphoblastoid	RTeQTL
rs7924472	CCDC81	cis	cerebellum	SCAN
rs7924472	EED	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:22 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr11:85957400-86008000	Weak transcription	Psoas Muscle	Psoas
2	chr11:85995600-86012600	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
3	chr11:85995600-86012800	Weak transcription	Rectal Smooth Muscle	rectum
4	chr11:85995800-86012600	Weak transcription	Brain Inferior Temporal Lobe	brain
5	chr11:85995800-86013200	Weak transcription	Esophagus	oesophagus
6	chr11:85995800-86013200	Weak transcription	Sigmoid Colon	Sigmoid Colon
7	chr11:85996000-86012800	Weak transcription	Skeletal Muscle Female	skeletal muscle
8	chr11:85996000-86013000	Weak transcription	Fetal Intestine Large	intestine
9	chr11:86000200-86003800	Weak transcription	Primary T helper cells fromperipheralblood	blood
10	chr11:86000400-86005400	Enhancers	GM12878-XiMat	blood
11	chr11:86001000-86004400	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
12	chr11:86001000-86004800	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
13	chr11:86001200-86005200	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
14	chr11:86002400-86005400	Enhancers	Primary T helper 17 cells PMA-I stimulated	--
15	chr11:86002600-86004600	Enhancers	Primary T helper cells PMA-I stimulated	--
16	chr11:86002600-86005400	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
17	chr11:86002800-86004600	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
18	chr11:86002800-86004600	Enhancers	Primary T regulatory cells fromperipheralblood	blood
19	chr11:86003000-86004200	Enhancers	Primary T helper naive cells from peripheral blood	blood
20	chr11:86003000-86012600	Weak transcription	ES-I3 Cell Line	embryonic stem cell
21	chr11:86003200-86013000	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
22	chr11:86003400-86004600	Enhancers	Primary T cells fromperipheralblood	blood

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