Variant report

Variant	rs11125091
Chromosome Location	chr2:47009746-47009747
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr2:46842690..46844852-chr2:47008012..47010268,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000151665	Chromatin interaction
ENSG00000119878	Chromatin interaction

Extended variants
information (count: 10 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:4)

rs_ID	r²[population]
rs11125089	1.00[CHB][hapmap];1.00[JPT][hapmap];0.98[ASN][1000 genomes]
rs6718658	0.83[JPT][hapmap]
rs6756738	1.00[CHB][hapmap];1.00[JPT][hapmap];0.97[ASN][1000 genomes]
rs72804410	0.85[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:6 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1014425	chr2:46670179-47033417	Enhancers Strong transcription Flanking Active TSS Weak transcription Active TSS Genic enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	31 gene(s)	inside rSNPs	diseases
2	nsv535678	chr2:46670179-47033417	Enhancers Weak transcription Flanking Active TSS Active TSS Genic enhancers ZNF genes & repeats Strong transcription Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	31 gene(s)	inside rSNPs	diseases
3	nsv873996	chr2:46670941-47065227	Strong transcription Enhancers Weak transcription Active TSS ZNF genes & repeats Genic enhancers Flanking Active TSS 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 target site	35 gene(s)	inside rSNPs	diseases
4	nsv817517	chr2:46819371-47715140	Enhancers Weak transcription Genic enhancers Bivalent Enhancer Flanking Active TSS Strong transcription Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	152 gene(s)	inside rSNPs	diseases
5	nsv457352	chr2:47004788-47325973	Active TSS Enhancers Genic enhancers Strong transcription Weak transcription Flanking Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	37 gene(s)	inside rSNPs	diseases
6	nsv581749	chr2:47004788-47325973	Flanking Active TSS Enhancers Genic enhancers Strong transcription Weak transcription Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	37 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs11125091	CRIPT	cis	parietal	SCAN

Chromatin state (count:27 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:47005200-47010000	Enhancers	Fetal Lung	lung
2	chr2:47005400-47012400	Enhancers	Breast Myoepithelial Primary Cells	Breast
3	chr2:47005600-47010000	Enhancers	Left Ventricle	heart
4	chr2:47005800-47009800	Enhancers	Skeletal Muscle Female	skeletal muscle
5	chr2:47006400-47009800	Enhancers	Fetal Stomach	stomach
6	chr2:47006400-47009800	Enhancers	Right Ventricle	heart
7	chr2:47006600-47009800	Enhancers	Fetal Muscle Leg	muscle
8	chr2:47006600-47009800	Enhancers	Lung	lung
9	chr2:47006600-47009800	Enhancers	Right Atrium	heart
10	chr2:47006800-47009800	Enhancers	Spleen	Spleen
11	chr2:47006800-47010000	Enhancers	Psoas Muscle	Psoas
12	chr2:47006800-47010000	Enhancers	Rectal Smooth Muscle	rectum
13	chr2:47007400-47010000	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
14	chr2:47008000-47011800	Weak transcription	A549	lung
15	chr2:47008200-47009800	Enhancers	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
16	chr2:47008200-47010000	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
17	chr2:47008200-47021000	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
18	chr2:47008400-47009800	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
19	chr2:47008400-47010000	Enhancers	Fetal Adrenal Gland	Adrenal Gland
20	chr2:47008400-47010800	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
21	chr2:47008800-47009800	Enhancers	Colon Smooth Muscle	Colon
22	chr2:47009000-47009800	Enhancers	Stomach Smooth Muscle	stomach
23	chr2:47009000-47011800	Weak transcription	Placenta Amnion	Placenta Amnion
24	chr2:47009200-47009800	Weak transcription	Fetal Muscle Trunk	muscle
25	chr2:47009400-47009800	Enhancers	HUES64 Cell Line	embryonic stem cell
26	chr2:47009600-47009800	Enhancers	Pancreas	Pancrea
27	chr2:47009600-47010800	Weak transcription	Ovary	ovary

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