Variant report

Variant	rs28652974
Chromosome Location	chr5:68790440-68790441
allele	G/T
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:8)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

(count:8 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr5:68709515..68715463-chr5:68785927..68791978,14	MCF-7	breast:
2	chr5:68724609..68726158-chr5:68789945..68791911,2	MCF-7	breast:
3	chr5:68787536..68790695-chr5:68794621..68799046,5	MCF-7	breast:
4	chr5:68786861..68791714-chr5:68792845..68799561,13	MCF-7	breast:
5	chr5:68785201..68788163-chr5:68788393..68790569,2	MCF-7	breast:
6	chr20:45988009..45989760-chr5:68788980..68791296,2	MCF-7	breast:
7	chr5:68708231..68714128-chr5:68786986..68792913,14	MCF-7	breast:
8	chr5:68740205..68742889-chr5:68789458..68791816,2	MCF-7	breast:

No data

Variant related genes	Relation type
ENSG00000152939	Chromatin interaction
ENSG00000197822	Chromatin interaction
ENSG00000249295	Chromatin interaction

Extended variants
information (count: 9 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:6)

rs_ID	r²[population]
rs28469160	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[ASN][1000 genomes]
rs28666036	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[ASN][1000 genomes]
rs61705994	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[ASN][1000 genomes]
rs73116828	0.86[AFR][1000 genomes];0.89[AMR][1000 genomes]
rs73116892	0.91[AFR][1000 genomes];0.89[AMR][1000 genomes]
rs73116901	0.87[AFR][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	nsv1018410	chr5:68692244-68822384	Weak transcription Flanking Bivalent TSS/Enh Strong transcription Enhancers ZNF genes & repeats Bivalent/Poised TSS Active TSS Genic enhancers Flanking Active TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	15 gene(s)	inside rSNPs	diseases
2	nsv1023116	chr5:68744307-68867282	Weak transcription Active TSS Flanking Active TSS Enhancers Flanking Bivalent TSS/Enh Genic enhancers Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS Strong transcription Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	12 gene(s)	inside rSNPs	diseases
3	nsv1034024	chr5:68760271-69118123	Active TSS Weak transcription Enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Strong transcription Genic enhancers Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	15 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:44 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:68787400-68791200	Active TSS	ES-I3 Cell Line	embryonic stem cell
2	chr5:68787600-68790600	Active TSS	H1 Cell Line	embryonic stem cell
3	chr5:68787600-68790600	Active TSS	iPS-15b Cell Line	embryonic stem cell
4	chr5:68787600-68790800	Active TSS	Pancreatic Islets	Pancreatic Islet
5	chr5:68787800-68790600	Active TSS	Pancreas	Pancrea
6	chr5:68787800-68791400	Active TSS	ES-WA7 Cell Line	embryonic stem cell
7	chr5:68788000-68790600	Active TSS	Gastric	stomach
8	chr5:68788000-68790600	Bivalent/Poised TSS	Rectal Smooth Muscle	rectum
9	chr5:68788000-68791000	Bivalent/Poised TSS	Fetal Intestine Large	intestine
10	chr5:68788200-68790600	Active TSS	Rectal Mucosa Donor 31	rectum
11	chr5:68788200-68791800	Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
12	chr5:68789200-68790800	Active TSS	Lung	lung
13	chr5:68789200-68791000	Active TSS	iPS-20b Cell Line	embryonic stem cell
14	chr5:68789400-68790600	Active TSS	Stomach Mucosa	stomach
15	chr5:68789400-68790800	Bivalent/Poised TSS	Rectal Mucosa Donor 29	rectum
16	chr5:68789600-68790600	Bivalent/Poised TSS	iPS-18 Cell Line	embryonic stem cell
17	chr5:68789800-68790600	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
18	chr5:68789800-68790600	Bivalent/Poised TSS	Fetal Kidney	kidney
19	chr5:68789800-68790800	Flanking Active TSS	Liver	Liver
20	chr5:68790000-68790600	Bivalent Enhancer	Foreskin Fibroblast Primary Cells skin01	Skin
21	chr5:68790000-68790600	Enhancers	Placenta	Placenta
22	chr5:68790000-68790600	Flanking Active TSS	HepG2	liver
23	chr5:68790000-68790800	Bivalent/Poised TSS	Fetal Stomach	stomach
24	chr5:68790000-68791400	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
25	chr5:68790000-68792600	Weak transcription	HSMM	muscle
26	chr5:68790000-68798200	Weak transcription	Placenta Amnion	Placenta Amnion
27	chr5:68790200-68790600	Active TSS	Esophagus	oesophagus
28	chr5:68790200-68790800	Enhancers	iPS DF 6.9 Cell Line	embryonic stem cell
29	chr5:68790200-68790800	Active TSS	Duodenum Mucosa	Duodenum
30	chr5:68790200-68791200	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
31	chr5:68790200-68791600	Flanking Active TSS	HUES48 Cell Line	embryonic stem cell
32	chr5:68790200-68792600	Weak transcription	H9 Cell Line	embryonic stem cell
33	chr5:68790200-68795800	Weak transcription	Colonic Mucosa	Colon
34	chr5:68790200-68797400	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
35	chr5:68790200-68797400	Weak transcription	HMEC	breast
36	chr5:68790200-68797400	Weak transcription	HUVEC	blood vessel
37	chr5:68790200-68824600	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
38	chr5:68790400-68790600	Flanking Active TSS	HUES6 Cell Line	embryonic stem cell
39	chr5:68790400-68790800	Flanking Active TSS	HUES64 Cell Line	embryonic stem cell
40	chr5:68790400-68790800	Flanking Active TSS	Fetal Intestine Small	intestine
41	chr5:68790400-68790800	Flanking Active TSS	GM12878-XiMat	blood
42	chr5:68790400-68791000	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
43	chr5:68790400-68791400	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
44	chr5:68790400-68791600	Enhancers	A549	lung

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