Variant report

Variant	rs11111921
Chromosome Location	chr12:104573504-104573505
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr12:104530177..104533540-chr12:104569302..104573926,9	MCF-7	breast:
2	chr12:104571599..104574180-chr12:104689003..104690549,2	MCF-7	breast:
3	chr12:104571824..104574318-chr12:104580582..104582719,2	MCF-7	breast:
4	chr12:104566313..104569865-chr12:104572688..104576807,3	K562	blood:
5	chr12:104528363..104533397-chr12:104570131..104576145,10	MCF-7	breast:

Variant related genes	Relation type
ENSG00000120837	Chromatin interaction

Extended variants
information (count: 20 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:15)

rs_ID	r²[population]
rs11111913	0.82[AMR][1000 genomes];0.90[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs11111938	0.86[ASW][hapmap];1.00[CEU][hapmap];0.91[CHB][hapmap];0.93[CHD][hapmap];0.90[JPT][hapmap];0.81[LWK][hapmap];0.92[MEX][hapmap];0.93[TSI][hapmap];0.82[YRI][hapmap];0.88[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs11111945	1.00[CEU][hapmap];0.91[CHB][hapmap];0.84[CHD][hapmap];0.90[JPT][hapmap];1.00[TSI][hapmap];0.85[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs11536084	0.85[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs2629745	0.83[CEU][hapmap]
rs2629755	0.85[MEX][hapmap]
rs4628754	0.89[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4964635	0.83[AMR][1000 genomes];0.92[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs6539125	1.00[CEU][hapmap];0.86[CHB][hapmap];0.98[CHD][hapmap];0.95[JPT][hapmap];0.92[MEX][hapmap];0.89[TSI][hapmap];0.86[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7310815	1.00[CEU][hapmap];0.91[CHB][hapmap];0.98[CHD][hapmap];0.83[GIH][hapmap];0.90[JPT][hapmap];0.94[TSI][hapmap];0.88[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs7311546	0.88[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs7312300	0.93[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7487242	0.85[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs7954970	1.00[CEU][hapmap];0.95[CHB][hapmap];0.89[JPT][hapmap];0.88[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs7966740	0.89[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:5 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1045725	chr12:104524153-104614108	Enhancers Weak transcription Genic enhancers ZNF genes & repeats Flanking Active TSS Flanking Bivalent TSS/Enh Active TSS Bivalent/Poised TSS Strong transcription Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	32 gene(s)	inside rSNPs	n/a
2	nsv541586	chr12:104524153-104614108	Enhancers Active TSS Weak transcription Genic enhancers Flanking Active TSS Strong transcription Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	32 gene(s)	inside rSNPs	n/a
3	esv1842062	chr12:104531180-104638773	Weak transcription Flanking Active TSS Enhancers Flanking Bivalent TSS/Enh Active TSS Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	33 gene(s)	inside rSNPs	n/a
4	nsv899493	chr12:104548613-104703228	Flanking Active TSS Active TSS Enhancers Strong transcription Weak transcription Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	30 gene(s)	inside rSNPs	diseases
5	nsv899494	chr12:104561521-104806232	Flanking Active TSS Weak transcription Genic enhancers Active TSS Enhancers Strong transcription Transcr. at gene 5' and 3' Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	34 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs11111921	PMCH	cis	cerebellum	SCAN

Chromatin state (count:33 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:104571000-104576600	Enhancers	Breast Myoepithelial Primary Cells	Breast
2	chr12:104572200-104574200	Weak transcription	Aorta	Aorta
3	chr12:104572200-104574400	Weak transcription	Adipose Nuclei	Adipose
4	chr12:104572200-104574400	Weak transcription	Duodenum Smooth Muscle	Duodenum
5	chr12:104572200-104574400	Weak transcription	Skeletal Muscle Female	skeletal muscle
6	chr12:104572200-104574800	Weak transcription	Fetal Muscle Leg	muscle
7	chr12:104572200-104575200	Weak transcription	Fetal Lung	lung
8	chr12:104572200-104575600	Weak transcription	Fetal Muscle Trunk	muscle
9	chr12:104572200-104575800	Weak transcription	Skeletal Muscle Male	skeletal muscle
10	chr12:104572200-104576000	Weak transcription	Right Atrium	heart
11	chr12:104572400-104573600	Enhancers	A549	lung
12	chr12:104572400-104574600	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
13	chr12:104572400-104574600	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
14	chr12:104572400-104575000	Weak transcription	NH-A	brain
15	chr12:104572400-104575000	Weak transcription	NHDF-Ad	bronchial
16	chr12:104572400-104575200	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
17	chr12:104572400-104576000	Weak transcription	Ovary	ovary
18	chr12:104572600-104574000	Weak transcription	Stomach Smooth Muscle	stomach
19	chr12:104572600-104574200	Weak transcription	HMEC	breast
20	chr12:104572600-104574200	Weak transcription	NHLF	lung
21	chr12:104572600-104574800	Weak transcription	Placenta	Placenta
22	chr12:104572600-104575200	Weak transcription	HSMMtube	muscle
23	chr12:104572600-104576200	Weak transcription	Psoas Muscle	Psoas
24	chr12:104572800-104573800	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
25	chr12:104572800-104574200	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
26	chr12:104572800-104574200	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
27	chr12:104572800-104574200	Weak transcription	Muscle Satellite Cultured Cells	--
28	chr12:104572800-104574200	Weak transcription	Osteobl	bone
29	chr12:104572800-104574400	Weak transcription	Rectal Smooth Muscle	rectum
30	chr12:104573000-104574000	Weak transcription	Hela-S3	cervix
31	chr12:104573200-104573600	Weak transcription	Colon Smooth Muscle	Colon
32	chr12:104573400-104573600	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
33	chr12:104573400-104573600	Enhancers	Spleen	Spleen

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