Variant report

Variant	rs2523983
Chromosome Location	chr6:30082221-30082222
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr6:30080946..30082589-chr6:30093243..30095341,2	MCF-7	breast:

Extended variants
information (count: 28 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:27)

rs_ID	r²[population]
rs1034326	1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs1034327	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1541269	0.82[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs2239529	0.87[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2245420	0.87[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs2249099	0.81[AFR][1000 genomes];0.87[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs2427749	0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2517595	0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2517596	0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2517597	0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2517598	0.87[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs2523976	0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2523977	0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2523979	0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2523981	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2523982	0.97[AFR][1000 genomes];0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2523984	0.87[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs2523985	0.87[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs2523986	0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2523987	0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2523988	0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2523989	0.86[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2523992	0.83[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2844790	0.92[EUR][1000 genomes]
rs2844791	0.80[EUR][1000 genomes]
rs2844792	0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2844793	0.91[AFR][1000 genomes];0.88[EUR][1000 genomes];0.92[ASN][1000 genomes]

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

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv884055	chr6:30078275-30087776	Enhancers Bivalent Enhancer Weak transcription Flanking Bivalent TSS/Enh Active TSS Flanking Active TSS Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs2523983	HLA-C	Cis_chr	lymphoblastoid	RTeQTL

Chromatin state (count:11 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:30080200-30082400	Enhancers	HepG2	liver
2	chr6:30080800-30082800	Enhancers	Fetal Intestine Large	intestine
3	chr6:30080800-30082800	Enhancers	Fetal Intestine Small	intestine
4	chr6:30081200-30082400	Enhancers	Sigmoid Colon	Sigmoid Colon
5	chr6:30081400-30082400	Enhancers	Hela-S3	cervix
6	chr6:30081800-30082600	Enhancers	Stomach Mucosa	stomach
7	chr6:30082000-30089400	Weak transcription	Duodenum Mucosa	Duodenum
8	chr6:30082200-30082600	Enhancers	A549	lung
9	chr6:30082200-30083400	Weak transcription	GM12878-XiMat	blood
10	chr6:30082200-30086400	Weak transcription	Rectal Mucosa Donor 31	rectum
11	chr6:30082200-30087400	Weak transcription	Rectal Mucosa Donor 29	rectum

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