Variant report

Variant	rs2852227
Chromosome Location	chr11:120589179-120589180
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr11:120588756..120591317-chr11:120596716..120599050,2	K562	blood:
2	chr11:120586309..120588238-chr11:120588252..120589968,2	MCF-7	breast:
3	chr11:120196443..120199058-chr11:120588153..120590155,2	MCF-7	breast:
4	chr11:120584157..120585682-chr11:120588505..120590152,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000181264	Chromatin interaction

Extended variants
information (count: 40 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:32)

rs_ID	r²[population]
rs11217980	0.80[ASN][1000 genomes]
rs11217987	0.81[CEU][hapmap];0.80[MEX][hapmap]
rs11217988	0.81[CEU][hapmap];0.80[ASN][1000 genomes]
rs11217989	0.81[CEU][hapmap];0.88[CHB][hapmap];0.97[CHD][hapmap];0.92[GIH][hapmap];1.00[JPT][hapmap];0.87[MEX][hapmap];0.85[TSI][hapmap];0.81[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12270261	1.00[CEU][hapmap]
rs12270409	0.81[CEU][hapmap]
rs12272864	1.00[CEU][hapmap]
rs12274300	0.81[CEU][hapmap];0.80[ASN][1000 genomes]
rs12276440	0.89[CEU][hapmap]
rs12278795	1.00[CEU][hapmap]
rs12280296	1.00[CEU][hapmap]
rs12281464	0.90[CEU][hapmap]
rs12281614	0.81[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12291927	1.00[CEU][hapmap]
rs12293393	1.00[CEU][hapmap]
rs12294858	0.82[CEU][hapmap]
rs12295113	1.00[CEU][hapmap]
rs12295200	1.00[CEU][hapmap]
rs17124211	0.89[CEU][hapmap];0.83[EUR][1000 genomes]
rs2846109	1.00[CEU][hapmap]
rs2852225	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.99[AFR][1000 genomes];0.91[AMR][1000 genomes];0.95[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs28781001	0.80[ASN][1000 genomes]
rs3133855	0.86[YRI][hapmap]
rs4567478	0.81[CEU][hapmap]
rs7102869	1.00[CEU][hapmap]
rs7103228	0.81[CEU][hapmap];0.80[MEX][hapmap]
rs7103418	0.90[CEU][hapmap]
rs7119619	0.81[CEU][hapmap];0.80[ASN][1000 genomes]
rs7120727	0.81[AFR][1000 genomes];0.91[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7944756	0.90[CEU][hapmap]
rs9630199	0.89[CEU][hapmap]
rs9630200	0.89[CEU][hapmap]

Variant overlapped rSNPs/rCNVs (count:8 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1054407	chr11:120535570-120630114	Enhancers Bivalent Enhancer Weak transcription Flanking Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Active TSS ZNF genes & repeats Strong transcription Genic enhancers	Chromatin interactive region	3 gene(s)	inside rSNPs	diseases
2	nsv1053607	chr11:120540795-120802006	Enhancers Strong transcription Weak transcription Bivalent Enhancer Flanking Active TSS ZNF genes & repeats Active TSS Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
3	esv3693392	chr11:120549745-120628012	Enhancers Bivalent Enhancer Weak transcription Active TSS Bivalent/Poised TSS Flanking Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Strong transcription Genic enhancers	Chromatin interactive region	3 gene(s)	inside rSNPs	diseases
4	nsv1041465	chr11:120582595-120630114	Bivalent/Poised TSS Enhancers Bivalent Enhancer Weak transcription Flanking Active TSS Flanking Bivalent TSS/Enh Active TSS Genic enhancers ZNF genes & repeats	Chromatin interactive region	1 gene(s)	inside rSNPs	n/a
5	nsv541180	chr11:120582595-120630114	Enhancers Flanking Active TSS Weak transcription Bivalent Enhancer Bivalent/Poised TSS Active TSS Flanking Bivalent TSS/Enh Genic enhancers ZNF genes & repeats	Chromatin interactive region	1 gene(s)	inside rSNPs	n/a
6	nsv1038264	chr11:120582595-120799335	Enhancers Weak transcription Bivalent Enhancer ZNF genes & repeats Flanking Active TSS Strong transcription Bivalent/Poised TSS Active TSS Flanking Bivalent TSS/Enh Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
7	nsv541181	chr11:120582595-120799335	Enhancers Weak transcription Flanking Active TSS ZNF genes & repeats Active TSS Bivalent Enhancer Strong transcription Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
8	nsv832286	chr11:120585843-120745846	Enhancers Weak transcription Bivalent Enhancer Flanking Active TSS Active TSS Bivalent/Poised TSS Strong transcription ZNF genes & repeats Flanking Bivalent TSS/Enh Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs2852227	C2CD2L	cis	parietal	SCAN
rs2852227	TMEM136	cis	cerebellum	SCAN
rs2852227	VPS11	cis	parietal	SCAN

Chromatin state (count:21 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr11:120585800-120590000	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
2	chr11:120586200-120590000	Weak transcription	Brain Inferior Temporal Lobe	brain
3	chr11:120586400-120593200	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
4	chr11:120586600-120590400	Weak transcription	Fetal Intestine Large	intestine
5	chr11:120587200-120589600	Enhancers	Breast Myoepithelial Primary Cells	Breast
6	chr11:120587600-120590000	Weak transcription	iPS-15b Cell Line	embryonic stem cell
7	chr11:120587800-120589200	Enhancers	HUES6 Cell Line	embryonic stem cell
8	chr11:120587800-120589600	Genic enhancers	iPS DF 19.11 Cell Line	embryonic stem cell
9	chr11:120587800-120589600	Bivalent Enhancer	Foreskin Keratinocyte Primary Cells skin03	Skin
10	chr11:120587800-120590600	Enhancers	H1 Cell Line	embryonic stem cell
11	chr11:120587800-120591000	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
12	chr11:120588000-120590200	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
13	chr11:120588400-120591000	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
14	chr11:120588400-120591000	Enhancers	iPS DF 6.9 Cell Line	embryonic stem cell
15	chr11:120588600-120589200	Enhancers	iPS-18 Cell Line	embryonic stem cell
16	chr11:120588600-120589400	Enhancers	ES-WA7 Cell Line	embryonic stem cell
17	chr11:120588600-120589400	Weak transcription	Ovary	ovary
18	chr11:120588800-120591000	Enhancers	HUES48 Cell Line	embryonic stem cell
19	chr11:120589000-120589200	Weak transcription	HUES64 Cell Line	embryonic stem cell
20	chr11:120589000-120590000	Weak transcription	ES-I3 Cell Line	embryonic stem cell
21	chr11:120589000-120590800	Weak transcription	iPS-20b Cell Line	embryonic stem cell

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