Variant report

Variant	rs11929841
Chromosome Location	chr4:103930245-103930246
allele	A/G
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:12)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

No data

(count:12 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr4:103635554..103636497-chr4:103929867..103930385,2	MCF-7	breast:
2	chr4:103930026..103930930-chr4:104021908..104022769,2	K562	blood:
3	chr4:103541677..103542319-chr4:103930001..103930835,2	MCF-7	breast:
4	chr4:103930055..103930910-chr4:104011447..104012271,2	MCF-7	breast:
5	chr4:103352380..103353182-chr4:103929736..103930540,2	K562	blood:
6	chr4:103541561..103542496-chr4:103929971..103930975,6	K562	blood:
7	chr4:103929746..103932464-chr4:103934730..103936768,2	MCF-7	breast:
8	chr4:103925655..103927320-chr4:103927745..103930358,2	MCF-7	breast:
9	chr4:103748007..103750644-chr4:103928520..103930455,2	K562	blood:
10	chr4:103541811..103542577-chr4:103929931..103930910,7	MCF-7	breast:
11	chr4:103544609..103545517-chr4:103930008..103930946,3	MCF-7	breast:
12	chr4:103929312..103930892-chr4:103937396..103939916,2	MCF-7	breast:

No data

No data

No data

Variant related genes	Relation type
ENSG00000246560	Chromatin interaction
ENSG00000109332	Chromatin interaction
ENSG00000248161	Chromatin interaction
ENSG00000138821	Chromatin interaction

Extended variants
information (count: 22 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:16)

rs_ID	r²[population]
rs10006474	0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs10013062	0.90[AMR][1000 genomes];0.89[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs10516495	0.82[AMR][1000 genomes];0.88[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs10516496	0.90[AMR][1000 genomes];0.94[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs11946020	0.97[AMR][1000 genomes];0.94[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs13150953	0.90[AMR][1000 genomes];0.94[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs13151569	0.90[AMR][1000 genomes];0.94[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2866416	0.88[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs34475639	0.87[AMR][1000 genomes];0.92[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs4698875	0.89[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4698876	0.99[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4699048	1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6533039	0.81[EUR][1000 genomes]
rs6816370	0.89[AMR][1000 genomes];0.95[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs6843738	0.89[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7665026	0.99[AMR][1000 genomes];0.96[EUR][1000 genomes];0.92[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:6 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv2757946	chr4:103780705-104057321	Strong transcription Active TSS Enhancers Weak transcription ZNF genes & repeats Flanking Active TSS Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	36 gene(s)	inside rSNPs	diseases
2	esv2759270	chr4:103780705-104057321	ZNF genes & repeats Strong transcription Weak transcription Active TSS Bivalent Enhancer Enhancers Flanking Active TSS Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	36 gene(s)	inside rSNPs	diseases
3	nsv461598	chr4:103807720-103953389	Enhancers Active TSS Flanking Active TSS Weak transcription ZNF genes & repeats Strong transcription Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	18 gene(s)	inside rSNPs	diseases
4	nsv594978	chr4:103807720-103953389	Weak transcription Active TSS Enhancers Flanking Active TSS ZNF genes & repeats Strong transcription Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	18 gene(s)	inside rSNPs	diseases
5	nsv879684	chr4:103887561-103939894	Weak transcription Enhancers Flanking Active TSS Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
6	esv3429917	chr4:103915319-104207455	ZNF genes & repeats Weak transcription Enhancers Strong transcription Flanking Active TSS Active TSS Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	20 gene(s)	inside rSNPs	diseases

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs11929841	BDH2	Cis_1M	lymphoblastoid	RTeQTL
rs11929841	LRRC37A15P	cis	Thyroid	GTEx
rs11929841	MANBA	Cis_1M	lymphoblastoid	RTeQTL
rs11929841	KRT8P46	cis	lung	GTEx

Chromatin state (count:2 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:103924800-103932400	Weak transcription	Lung	lung
2	chr4:103930200-103930400	Enhancers	Rectal Mucosa Donor 31	rectum

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Input of quick search could be:

dbSNP/dbVar ID: rs12345 /nsv7879
a single nucleotide as 0-based coordinates: chr1:12345
chromosomal regions: chr1:12345-34567

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