Variant report

Variant	rs28410552
Chromosome Location	chr1:85603644-85603645
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	chr1:85599313..85601260-chr1:85603584..85606556,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000266110	Chromatin interaction

Extended variants
information (count: 34 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:31)

rs_ID	r²[population]
rs12021868	1.00[AFR][1000 genomes]
rs12022814	1.00[AFR][1000 genomes];0.82[EUR][1000 genomes]
rs12023751	1.00[AFR][1000 genomes]
rs12028707	1.00[AFR][1000 genomes]
rs12034359	1.00[AFR][1000 genomes]
rs12034501	1.00[AFR][1000 genomes]
rs12036276	1.00[AFR][1000 genomes]
rs12039804	1.00[AFR][1000 genomes]
rs12040408	1.00[AFR][1000 genomes]
rs12041155	1.00[AFR][1000 genomes]
rs12043409	1.00[AFR][1000 genomes]
rs12045141	1.00[AFR][1000 genomes]
rs1674179	0.80[EUR][1000 genomes]
rs17099217	1.00[AFR][1000 genomes];0.88[AMR][1000 genomes];0.92[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs17121656	1.00[AFR][1000 genomes];0.88[AMR][1000 genomes];0.90[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs17121745	1.00[AFR][1000 genomes];0.88[AMR][1000 genomes];0.92[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs17121935	1.00[AFR][1000 genomes];0.88[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs17121978	0.88[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2305930	1.00[AFR][1000 genomes];0.88[AMR][1000 genomes];0.92[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2305931	1.00[AFR][1000 genomes];0.88[AMR][1000 genomes];0.92[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs41289039	1.00[AFR][1000 genomes];0.86[EUR][1000 genomes]
rs56191061	1.00[AFR][1000 genomes]
rs57222060	1.00[AFR][1000 genomes];0.88[AMR][1000 genomes];0.85[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs57516443	1.00[AFR][1000 genomes]
rs58068482	1.00[AFR][1000 genomes]
rs58246117	1.00[AFR][1000 genomes]
rs58604582	1.00[AFR][1000 genomes]
rs58659750	1.00[AFR][1000 genomes];0.84[EUR][1000 genomes]
rs59030463	1.00[AFR][1000 genomes];0.83[AMR][1000 genomes];0.90[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs59248240	1.00[AFR][1000 genomes]
rs60866399	1.00[AFR][1000 genomes];0.88[AMR][1000 genomes];0.88[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1006994	chr1:85454304-86327679	Active TSS Enhancers Weak transcription Flanking Active TSS Strong transcription Flanking Bivalent TSS/Enh Genic enhancers ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	72 gene(s)	inside rSNPs	diseases
2	esv34165	chr1:85542040-85846249	Flanking Active TSS Active TSS Weak transcription Enhancers Transcr. at gene 5' and 3' Strong transcription Genic enhancers Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	30 gene(s)	inside rSNPs	diseases
3	nsv830459	chr1:85589585-85786311	Weak transcription Enhancers Genic enhancers Flanking Active TSS Active TSS Strong transcription Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	27 gene(s)	inside rSNPs	diseases

No data

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:85594800-85614400	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
2	chr1:85598400-85608400	Weak transcription	Pancreas	Pancrea
3	chr1:85598600-85608600	Weak transcription	Left Ventricle	heart
4	chr1:85599400-85604400	Enhancers	Fetal Intestine Large	intestine
5	chr1:85599600-85603800	Enhancers	Fetal Intestine Small	intestine
6	chr1:85600200-85604000	Enhancers	Liver	Liver
7	chr1:85600600-85603800	Enhancers	Primary neutrophils fromperipheralblood	blood
8	chr1:85601000-85608400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
9	chr1:85601200-85604000	Enhancers	Rectal Mucosa Donor 31	rectum
10	chr1:85602400-85604200	Enhancers	Duodenum Mucosa	Duodenum
11	chr1:85602600-85603800	Enhancers	Brain Germinal Matrix	brain
12	chr1:85602600-85604000	Enhancers	Pancreatic Islets	Pancreatic Islet
13	chr1:85602800-85603800	Enhancers	Gastric	stomach
14	chr1:85602800-85604000	Enhancers	Fetal Heart	heart
15	chr1:85603000-85603800	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
16	chr1:85603000-85604000	Enhancers	Stomach Smooth Muscle	stomach
17	chr1:85603200-85604000	Enhancers	Cortex derived primary cultured neurospheres	brain
18	chr1:85603200-85604800	Enhancers	Placenta	Placenta
19	chr1:85603400-85603800	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
20	chr1:85603400-85603800	Enhancers	Breast Myoepithelial Primary Cells	Breast
21	chr1:85603400-85603800	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
22	chr1:85603400-85603800	Enhancers	Ovary	ovary
23	chr1:85603400-85603800	Flanking Active TSS	A549	lung
24	chr1:85603400-85603800	Flanking Active TSS	HepG2	liver
25	chr1:85603400-85604000	Enhancers	Rectal Smooth Muscle	rectum
26	chr1:85603400-85604000	Enhancers	Stomach Mucosa	stomach
27	chr1:85603600-85603800	Flanking Active TSS	Fetal Brain Female	brain
28	chr1:85603600-85603800	Flanking Active TSS	Fetal Kidney	kidney
29	chr1:85603600-85603800	Enhancers	Fetal Lung	lung
30	chr1:85603600-85603800	Enhancers	Right Atrium	heart
31	chr1:85603600-85603800	Enhancers	Sigmoid Colon	Sigmoid Colon
32	chr1:85603600-85604000	Enhancers	Rectal Mucosa Donor 29	rectum
33	chr1:85603600-85608400	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung

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