Variant report

Variant	rs28703034
Chromosome Location	chr5:68747047-68747048
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr5:68745489..68748200-chr5:68856022..68857612,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000183474	Chromatin interaction

Extended variants
information (count: 28 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:26)

rs_ID	r²[population]
rs10035835	0.82[AFR][1000 genomes];0.90[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs10038816	0.82[AFR][1000 genomes];0.86[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs10064264	0.82[AFR][1000 genomes];0.88[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs10068576	0.82[AFR][1000 genomes];0.87[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs10077458	0.82[AFR][1000 genomes];0.85[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs10078100	0.82[AFR][1000 genomes];0.89[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs1168404	0.82[ASN][1000 genomes]
rs1168409	0.82[AFR][1000 genomes];0.89[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs1177556	0.82[AFR][1000 genomes];0.90[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs1183278	0.87[AMR][1000 genomes];0.92[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs182447	0.83[EUR][1000 genomes]
rs2561160	0.84[EUR][1000 genomes]
rs2561169	0.92[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs2561172	0.82[AFR][1000 genomes];0.87[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs2561186	0.82[AFR][1000 genomes];0.89[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs28371924	0.84[EUR][1000 genomes]
rs299075	0.89[AFR][1000 genomes];0.91[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs299077	0.89[AFR][1000 genomes];0.93[AMR][1000 genomes];0.95[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs299078	0.81[EUR][1000 genomes]
rs299088	0.82[AFR][1000 genomes];0.90[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs299091	0.82[AFR][1000 genomes];0.91[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs299094	0.91[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs299098	0.82[AFR][1000 genomes];0.91[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs299099	0.82[AFR][1000 genomes];0.91[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs299102	0.82[AFR][1000 genomes];0.91[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs4252228	0.81[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:2 , 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

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs28703034	CCDC125	cis	Thyroid	GTEx
rs28703034	CCDC125	cis	lung	GTEx
rs28703034	MRPS36	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:16 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:68730400-68747400	Weak transcription	Rectal Mucosa Donor 31	rectum
2	chr5:68730400-68747400	Weak transcription	Sigmoid Colon	Sigmoid Colon
3	chr5:68732600-68747400	Weak transcription	Rectal Mucosa Donor 29	rectum
4	chr5:68732600-68750000	Weak transcription	HUES6 Cell Line	embryonic stem cell
5	chr5:68732600-68750400	Weak transcription	HUES64 Cell Line	embryonic stem cell
6	chr5:68734200-68747400	Weak transcription	Lung	lung
7	chr5:68734400-68749200	Weak transcription	Duodenum Mucosa	Duodenum
8	chr5:68745000-68747400	Enhancers	Fetal Intestine Small	intestine
9	chr5:68745200-68747600	Enhancers	Fetal Intestine Large	intestine
10	chr5:68745200-68750200	Enhancers	Stomach Mucosa	stomach
11	chr5:68745400-68747600	Enhancers	Pancreas	Pancrea
12	chr5:68745400-68747800	Enhancers	HepG2	liver
13	chr5:68746000-68747400	Enhancers	Liver	Liver
14	chr5:68746400-68747800	Weak transcription	A549	lung
15	chr5:68746800-68748000	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
16	chr5:68746800-68750400	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin

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