Variant report

Variant	rs11772239
Chromosome Location	chr7:140014556-140014557
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr7:140014544..140017368-chr7:140028842..140031384,2	MCF-7	breast:
2	chr7:139873831..139877475-chr7:140012242..140019161,9	MCF-7	breast:
3	chr7:140003129..140009929-chr7:140011645..140017997,10	MCF-7	breast:
4	chr7:139874735..139878684-chr7:140013731..140018103,7	MCF-7	breast:

Variant related genes	Relation type
ENSG00000006459	Chromatin interaction
ENSG00000260231	Chromatin interaction

Extended variants
information (count: 13 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:11)

rs_ID	r²[population]
rs12538711	0.81[CHB][hapmap];0.81[JPT][hapmap]
rs12672394	0.80[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs12673119	0.95[ASN][1000 genomes]
rs12703730	0.80[JPT][hapmap]
rs12703742	0.89[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34473504	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35828749	0.96[ASN][1000 genomes]
rs4725679	0.85[ASN][1000 genomes]
rs4726766	0.80[AMR][1000 genomes];0.99[ASN][1000 genomes]
rs6970317	0.86[CHB][hapmap];0.97[CHD][hapmap];0.88[MEX][hapmap];0.87[ASN][1000 genomes]
rs7792748	0.91[CHB][hapmap];0.97[CHD][hapmap];0.83[GIH][hapmap];1.00[JPT][hapmap];0.84[MEX][hapmap];0.89[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	nsv889247	chr7:139855216-140033631	Weak transcription Flanking Active TSS Active TSS Enhancers ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS Genic enhancers Strong transcription Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	18 gene(s)	inside rSNPs	diseases
2	nsv1026255	chr7:139944473-140043299	Flanking Active TSS Enhancers Weak transcription Bivalent/Poised TSS Strong transcription Genic enhancers Active TSS Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	9 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs11772239	SLC37A3	cis	cerebellum	SCAN
rs11772239	CHRM2	cis	parietal	SCAN
rs11772239	TRPV5	cis	cerebellum	SCAN

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr7:140004600-140015400	Weak transcription	Sigmoid Colon	Sigmoid Colon
2	chr7:140006000-140015400	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
3	chr7:140008400-140014800	Weak transcription	Stomach Mucosa	stomach
4	chr7:140009400-140014800	Weak transcription	Colonic Mucosa	Colon
5	chr7:140009400-140015000	Enhancers	Primary monocytes fromperipheralblood	blood
6	chr7:140011600-140015600	Weak transcription	NHDF-Ad	bronchial
7	chr7:140011600-140016400	Enhancers	Primary B cells from cord blood	blood
8	chr7:140012400-140014600	Weak transcription	Rectal Smooth Muscle	rectum
9	chr7:140013200-140014600	Weak transcription	Duodenum Mucosa	Duodenum
10	chr7:140013200-140015000	Weak transcription	Esophagus	oesophagus
11	chr7:140013200-140015000	Weak transcription	Gastric	stomach
12	chr7:140013200-140015600	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
13	chr7:140013200-140017800	Weak transcription	Primary hematopoietic stem cells	blood
14	chr7:140013600-140018600	Flanking Active TSS	Monocytes-CD14+_RO01746	blood
15	chr7:140013800-140015400	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
16	chr7:140013800-140015600	Flanking Active TSS	Primary neutrophils fromperipheralblood	blood
17	chr7:140013800-140016800	Enhancers	Liver	Liver
18	chr7:140014000-140015800	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
19	chr7:140014000-140016000	Flanking Active TSS	HepG2	liver
20	chr7:140014200-140014600	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
21	chr7:140014200-140014600	Enhancers	HMEC	breast
22	chr7:140014400-140014600	Enhancers	Ovary	ovary
23	chr7:140014400-140014600	Active TSS	Stomach Smooth Muscle	stomach
24	chr7:140014400-140015000	Enhancers	Brain Cingulate Gyrus	brain
25	chr7:140014400-140015200	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
26	chr7:140014400-140015400	Flanking Active TSS	Breast Myoepithelial Primary Cells	Breast
27	chr7:140014400-140015600	Enhancers	A549	lung
28	chr7:140014400-140015800	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
29	chr7:140014400-140015800	Enhancers	Lung	lung
30	chr7:140014400-140016000	Flanking Active TSS	Colon Smooth Muscle	Colon

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