Variant report

Variant	rs55929411
Chromosome Location	chr3:24546344-24546345
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr3:24537125..24539078-chr3:24545572..24547994,2	MCF-7	breast:
2	chr3:24544311..24546900-chr3:24549591..24551326,2	K562	blood:
3	chr3:24542552..24545017-chr3:24545304..24547564,2	MCF-7	breast:
4	chr3:24535073..24541427-chr3:24545752..24549370,7	MCF-7	breast:

Variant related genes	Relation type
ENSG00000228791	Chromatin interaction
ENSG00000272554	Chromatin interaction
ENSG00000151090	Chromatin interaction

Extended variants
information (count: 23 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:19)

rs_ID	r²[population]
rs13078191	0.81[ASN][1000 genomes]
rs17014772	1.00[EUR][1000 genomes]
rs1865710	0.81[ASN][1000 genomes]
rs1865711	0.85[ASN][1000 genomes]
rs56035340	0.82[AFR][1000 genomes]
rs56783261	0.85[ASN][1000 genomes]
rs57622980	1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs57751578	0.83[ASN][1000 genomes]
rs58388581	0.85[ASN][1000 genomes]
rs58932894	0.85[ASN][1000 genomes]
rs61063562	0.85[ASN][1000 genomes]
rs61078139	0.82[AFR][1000 genomes]
rs61078516	1.00[EUR][1000 genomes]
rs6764938	1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs6765048	1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs73152119	0.81[ASN][1000 genomes]
rs73823340	0.85[ASN][1000 genomes]
rs73823348	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73823356	1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv834641	chr3:24465862-24633738	Enhancers Bivalent Enhancer Active TSS Weak transcription Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Strong transcription Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	19 gene(s)	inside rSNPs	diseases
2	nsv834642	chr3:24475558-24640593	Enhancers Flanking Bivalent TSS/Enh Weak transcription Bivalent Enhancer Flanking Active TSS Bivalent/Poised TSS Strong transcription Active TSS Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA	19 gene(s)	inside rSNPs	diseases
3	nsv1012975	chr3:24500706-24615644	Enhancers Flanking Active TSS Bivalent Enhancer Active TSS Weak transcription Flanking Bivalent TSS/Enh Strong transcription Bivalent/Poised TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	18 gene(s)	inside rSNPs	diseases
4	nsv999384	chr3:24525345-24656873	Enhancers Weak transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS Flanking Active TSS Active TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA miRNA	18 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:29 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:24537400-24546400	Weak transcription	Sigmoid Colon	Sigmoid Colon
2	chr3:24538200-24547000	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
3	chr3:24538200-24552000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
4	chr3:24538200-24560600	Weak transcription	Aorta	Aorta
5	chr3:24538400-24549000	Weak transcription	Breast Myoepithelial Primary Cells	Breast
6	chr3:24539000-24547400	Weak transcription	Duodenum Mucosa	Duodenum
7	chr3:24539000-24560200	Weak transcription	HepG2	liver
8	chr3:24540600-24549000	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
9	chr3:24541000-24549000	Weak transcription	ES-I3 Cell Line	embryonic stem cell
10	chr3:24542800-24547400	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
11	chr3:24542800-24548800	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
12	chr3:24542800-24549400	Weak transcription	HSMM	muscle
13	chr3:24543800-24546400	Enhancers	Fetal Intestine Large	intestine
14	chr3:24543800-24549200	Weak transcription	HUES64 Cell Line	embryonic stem cell
15	chr3:24544000-24547000	Enhancers	Primary B cells from cord blood	blood
16	chr3:24544200-24547800	Enhancers	Fetal Intestine Small	intestine
17	chr3:24544200-24548200	Enhancers	Primary B cells from peripheral blood	blood
18	chr3:24544800-24546400	Weak transcription	Rectal Mucosa Donor 29	rectum
19	chr3:24544800-24548600	Weak transcription	Muscle Satellite Cultured Cells	--
20	chr3:24544800-24549000	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
21	chr3:24544800-24549000	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
22	chr3:24545000-24548800	Weak transcription	NHEK	skin
23	chr3:24545000-24549000	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
24	chr3:24545000-24549000	Weak transcription	HMEC	breast
25	chr3:24545200-24546400	Weak transcription	K562	blood
26	chr3:24545800-24547800	Enhancers	Stomach Mucosa	stomach
27	chr3:24546000-24548600	Weak transcription	Monocytes-CD14+_RO01746	blood
28	chr3:24546000-24548800	Weak transcription	Primary monocytes fromperipheralblood	blood
29	chr3:24546200-24547000	Enhancers	Rectal Mucosa Donor 31	rectum

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