Variant report

Variant	rs8752
Chromosome Location	chr4:175412477-175412478
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 12 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:9)

rs_ID	r²[population]
rs11133041	0.88[CEU][hapmap];1.00[CHB][hapmap];0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs11724251	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.88[GIH][hapmap];0.95[JPT][hapmap];0.89[MEX][hapmap];0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs12641259	0.81[AMR][1000 genomes]
rs1426947	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.80[AFR][1000 genomes];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs17060573	0.89[CHB][hapmap];0.82[ASN][1000 genomes]
rs2612658	0.84[CEU][hapmap];0.84[CHB][hapmap];0.85[JPT][hapmap];0.85[ASN][1000 genomes]
rs41279511	0.99[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs56808147	0.80[AMR][1000 genomes]
rs7349744	0.94[CHB][hapmap];0.85[ASN][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	nsv869116	chr4:175231090-175801761	Flanking Active TSS Enhancers Genic enhancers Weak transcription Bivalent/Poised TSS Active TSS Strong transcription Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA	13 gene(s)	inside rSNPs	diseases
2	nsv525487	chr4:175400104-175470867	Enhancers Flanking Active TSS Weak transcription Strong transcription Active TSS Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
3	nsv881299	chr4:175403673-175415442	Enhancers Weak transcription ZNF genes & repeats Strong transcription Active TSS Flanking Active TSS Genic enhancers	TF binding region Chromatin interactive region	1 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs8752	HMGB2	cis	cerebellum	SCAN

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:175396000-175442800	Weak transcription	Esophagus	oesophagus
2	chr4:175406800-175412800	Weak transcription	Liver	Liver
3	chr4:175406800-175412800	Weak transcription	Duodenum Mucosa	Duodenum
4	chr4:175406800-175415200	Weak transcription	Fetal Intestine Large	intestine
5	chr4:175406800-175415800	Weak transcription	Fetal Intestine Small	intestine
6	chr4:175407000-175415000	Weak transcription	Primary T cells from cord blood	blood
7	chr4:175409200-175415000	Weak transcription	Fetal Thymus	thymus
8	chr4:175409400-175424000	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
9	chr4:175410000-175424600	Weak transcription	Fetal Stomach	stomach
10	chr4:175410000-175440800	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
11	chr4:175410400-175412600	Enhancers	Hela-S3	cervix
12	chr4:175410400-175418000	Weak transcription	Rectal Smooth Muscle	rectum
13	chr4:175410800-175412600	Weak transcription	Placenta	Placenta
14	chr4:175410800-175417400	Weak transcription	Primary hematopoietic stem cells short term culture	blood
15	chr4:175410800-175420800	Weak transcription	Lung	lung
16	chr4:175410800-175425400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
17	chr4:175410800-175430800	Weak transcription	Gastric	stomach
18	chr4:175410800-175440000	Weak transcription	HUES6 Cell Line	embryonic stem cell
19	chr4:175411000-175418200	Weak transcription	Rectal Mucosa Donor 29	rectum
20	chr4:175411400-175412600	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
21	chr4:175411600-175412600	Enhancers	Stomach Mucosa	stomach
22	chr4:175411600-175416600	Weak transcription	Colon Smooth Muscle	Colon
23	chr4:175412000-175412600	Enhancers	ES-I3 Cell Line	embryonic stem cell
24	chr4:175412000-175412800	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
25	chr4:175412000-175428400	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
26	chr4:175412200-175413800	Weak transcription	Primary hematopoietic stem cells	blood
27	chr4:175412400-175412600	Flanking Active TSS	A549	lung
28	chr4:175412400-175413800	Weak transcription	Muscle Satellite Cultured Cells	--
29	chr4:175412400-175417800	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived

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