Variant report

Variant	rs4428502
Chromosome Location	chr6:53634851-53634852
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	chr6:53617168..53619456-chr6:53632557..53635306,2	MCF-7	breast:

Extended variants
information (count: 32 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:30)

rs_ID	r²[population]
rs10456164	0.82[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs10456166	0.83[ASN][1000 genomes]
rs10456167	0.83[ASN][1000 genomes]
rs10456671	0.81[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs12193312	0.82[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs12197259	0.80[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs13191282	0.95[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs13195168	0.89[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs13196802	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13206978	0.94[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13211007	0.80[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs13219456	0.97[AFR][1000 genomes];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3000995	0.95[AFR][1000 genomes];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3003502	0.96[AFR][1000 genomes];0.96[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4302662	0.82[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs4409173	0.92[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs4416674	0.81[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs4443499	0.81[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs4469293	0.80[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs4479931	0.81[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs4555913	0.81[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs4574642	0.82[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs4715423	0.96[AFR][1000 genomes];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6458955	0.88[AFR][1000 genomes];0.86[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs6909833	0.81[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs6930030	0.81[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs6930035	0.81[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs7745277	0.82[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs7755196	0.81[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs7755522	0.88[EUR][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	nsv1034955	chr6:53447607-53931055	Enhancers Bivalent Enhancer Weak transcription Flanking Active TSS Flanking Bivalent TSS/Enh Active TSS Strong transcription Bivalent/Poised TSS ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	35 gene(s)	inside rSNPs	diseases
2	nsv1021506	chr6:53600338-53770482	Flanking Active TSS Weak transcription Enhancers Active TSS Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats Strong transcription Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	16 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs4428502	LRRC1	Cis_1M	lymphoblastoid	RTeQTL
rs4428502	KLHL31	cis	Skin Sun Exposed Lower leg	GTEx

Chromatin state (count:14 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:53601600-53638000	Weak transcription	Primary hematopoietic stem cells	blood
2	chr6:53618800-53635800	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
3	chr6:53632000-53636000	Weak transcription	Aorta	Aorta
4	chr6:53632000-53639600	Weak transcription	Placenta Amnion	Placenta Amnion
5	chr6:53632200-53635400	Weak transcription	Fetal Heart	heart
6	chr6:53632200-53639000	Weak transcription	Gastric	stomach
7	chr6:53633600-53636800	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
8	chr6:53633600-53636800	Weak transcription	HSMMtube	muscle
9	chr6:53634400-53636800	Enhancers	Fetal Intestine Small	intestine
10	chr6:53634600-53635200	Enhancers	Fetal Intestine Large	intestine
11	chr6:53634600-53637400	Enhancers	NHEK	skin
12	chr6:53634800-53635400	Enhancers	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
13	chr6:53634800-53637600	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
14	chr6:53634800-53638200	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin

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