Variant report

Variant	rs73878325
Chromosome Location	chr3:161128787-161128788
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:0)
CpG islands
(count:0)
Chromatin interactive
region (count:15)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

(count:15 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr3:161034414..161036485-chr3:161127790..161130788,3	MCF-7	breast:
2	chr3:161003253..161016100-chr3:161121496..161137189,33	MCF-7	breast:
3	chr3:161127684..161130255-chr3:161157024..161159447,2	MCF-7	breast:
4	chr3:160943414..160948630-chr3:161124537..161130455,7	MCF-7	breast:
5	chr3:160821506..160824217-chr3:161128356..161130934,2	MCF-7	breast:
6	chr3:160934874..160951087-chr3:161118055..161142485,77	MCF-7	breast:
7	chr3:160937705..160941241-chr3:161127569..161134417,11	MCF-7	breast:
8	chr19:51869577..51872275-chr3:161126868..161129523,2	MCF-7	breast:
9	chr3:161041936..161043684-chr3:161128783..161133001,3	MCF-7	breast:
10	chr3:161007555..161015806-chr3:161127103..161142651,19	MCF-7	breast:
11	chr21:41759432..41760978-chr3:161127056..161129807,2	MCF-7	breast:
12	chr20:46156869..46158917-chr3:161128342..161130279,2	MCF-7	breast:
13	chr3:160809924..160811857-chr3:161127749..161129534,3	MCF-7	breast:
14	chr3:160747461..160750414-chr3:161128370..161130411,2	MCF-7	breast:
15	chr3:160818015..160820994-chr3:161127414..161132752,10	MCF-7	breast:

No data

Variant related genes	Relation type
ENSG00000160318	Chromatin interaction
ENSG00000269403	Chromatin interaction
ENSG00000105379	Chromatin interaction
ENSG00000271052	Chromatin interaction
ENSG00000169255	Chromatin interaction
ENSG00000169251	Chromatin interaction

Extended variants
information (count: 36 )
Associated
traits (count: 0)

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

rs_ID	r²[population]
rs12632537	0.84[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12634006	0.91[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs16832203	0.96[EUR][1000 genomes]
rs57175632	0.82[ASN][1000 genomes]
rs57278490	0.87[EUR][1000 genomes]
rs57496534	0.87[EUR][1000 genomes]
rs57803909	0.87[EUR][1000 genomes]
rs58350275	0.87[EUR][1000 genomes]
rs58550445	0.82[AFR][1000 genomes]
rs58557417	0.80[EUR][1000 genomes]
rs58562874	0.87[EUR][1000 genomes]
rs59541314	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs59761692	0.91[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs59964190	0.87[EUR][1000 genomes]
rs60172527	0.82[ASN][1000 genomes]
rs60400555	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs60612225	0.87[EUR][1000 genomes]
rs60684226	0.87[EUR][1000 genomes]
rs61048679	1.00[AMR][1000 genomes]
rs61217744	0.91[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs73021435	0.82[ASN][1000 genomes]
rs73878307	0.89[AFR][1000 genomes];1.00[AMR][1000 genomes];0.91[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs73878308	0.91[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs73878311	0.91[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs73878313	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs73878321	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs73878322	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs73878324	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73878328	0.84[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7625217	0.87[EUR][1000 genomes]
rs873183	0.91[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs896080	0.91[EUR][1000 genomes];0.85[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	nsv931072	chr3:160669567-161159779	Enhancers Strong transcription Weak transcription Flanking Active TSS Active TSS Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	98 gene(s)	inside rSNPs	diseases
2	nsv533237	chr3:161019834-161804660	Enhancers Flanking Bivalent TSS/Enh Flanking Active TSS Weak transcription Bivalent/Poised TSS Bivalent Enhancer Active TSS ZNF genes & repeats Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	91 gene(s)	inside rSNPs	diseases
3	nsv829772	chr3:161047817-161202554	Bivalent Enhancer Bivalent/Poised TSS Enhancers Flanking Active TSS Strong transcription Weak transcription Flanking Bivalent TSS/Enh Active TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	88 gene(s)	inside rSNPs	diseases
4	nsv877710	chr3:161087857-161245414	Enhancers Weak transcription Bivalent Enhancer Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Active TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	84 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:17 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:161123200-161132000	Enhancers	Stomach Mucosa	stomach
2	chr3:161124000-161133400	Weak transcription	Fetal Lung	lung
3	chr3:161124800-161131000	Weak transcription	Muscle Satellite Cultured Cells	--
4	chr3:161124800-161131000	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
5	chr3:161125600-161129600	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
6	chr3:161125600-161137000	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
7	chr3:161126200-161131000	Weak transcription	Gastric	stomach
8	chr3:161127600-161131000	Weak transcription	Pancreatic Islets	Pancreatic Islet
9	chr3:161128000-161131600	Weak transcription	HUVEC	blood vessel
10	chr3:161128000-161133200	Weak transcription	ES-I3 Cell Line	embryonic stem cell
11	chr3:161128000-161133400	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
12	chr3:161128200-161129200	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
13	chr3:161128200-161129200	Weak transcription	Hela-S3	cervix
14	chr3:161128200-161133200	Weak transcription	NHEK	skin
15	chr3:161128200-161133600	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
16	chr3:161128200-161134000	Weak transcription	Esophagus	oesophagus
17	chr3:161128400-161129600	Weak transcription	HMEC	breast

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