Variant report

Variant	rs2868128
Chromosome Location	chr4:81943068-81943069
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	chr4:81942639..81943385-chr7:30269373..30270144,2	MCF-7	breast:

Extended variants
information (count: 34 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:29)

rs_ID	r²[population]
rs10014087	0.90[ASN][1000 genomes]
rs10031561	0.82[CHB][hapmap]
rs10516736	0.82[TSI][hapmap]
rs1106107	0.82[CHB][hapmap]
rs11099457	0.91[ASN][1000 genomes]
rs13138132	0.82[ASN][1000 genomes]
rs1353386	0.82[ASN][1000 genomes]
rs1353387	0.89[CHB][hapmap];0.82[ASN][1000 genomes]
rs1390319	0.89[CHB][hapmap];0.81[MEX][hapmap];0.82[MKK][hapmap];0.84[TSI][hapmap];0.81[ASN][1000 genomes]
rs1390320	0.82[ASN][1000 genomes]
rs1495644	0.85[AMR][1000 genomes];0.83[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs17005020	0.86[EUR][1000 genomes]
rs17005022	0.82[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1994990	0.82[CHB][hapmap];0.81[MEX][hapmap]
rs2055178	0.82[ASN][1000 genomes]
rs28416900	0.91[ASN][1000 genomes]
rs28420618	0.91[ASN][1000 genomes]
rs2868126	0.82[CHB][hapmap];0.81[MKK][hapmap]
rs4693151	0.82[AMR][1000 genomes];0.84[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs4693767	0.83[AMR][1000 genomes];0.81[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs4693781	0.85[AMR][1000 genomes];0.84[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs4693791	0.86[EUR][1000 genomes]
rs6814223	0.85[EUR][1000 genomes]
rs6823242	0.85[AMR][1000 genomes];0.84[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs6827935	0.84[EUR][1000 genomes]
rs6845445	0.86[TSI][hapmap]
rs7676223	0.85[AMR][1000 genomes];0.82[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs963322	0.89[ASN][1000 genomes]
rs963856	0.83[AMR][1000 genomes];0.82[EUR][1000 genomes];0.88[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:5 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv999729	chr4:81802554-82627820	Genic enhancers Enhancers Weak transcription Flanking Active TSS Active TSS Strong transcription Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	7 gene(s)	inside rSNPs	diseases
2	nsv537156	chr4:81802554-82627820	Flanking Active TSS Strong transcription Enhancers Weak transcription Genic enhancers Active TSS ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	7 gene(s)	inside rSNPs	diseases
3	esv3412549	chr4:81834479-81951850	Flanking Active TSS Bivalent Enhancer Enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Weak transcription Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
4	nsv1006466	chr4:81888983-82009675	Enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Weak transcription Bivalent/Poised TSS Active TSS Strong transcription Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
5	nsv521480	chr4:81941456-81943068	Active TSS Flanking Active TSS Enhancers Weak transcription	Chromatin interactive region	n/a	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs2868128	NCRNA00247	cis	cerebellum	SCAN

Chromatin state (count:10 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:81940000-81944200	Enhancers	Fetal Intestine Large	intestine
2	chr4:81940800-81944200	Enhancers	Fetal Intestine Small	intestine
3	chr4:81941800-81943200	Weak transcription	Duodenum Mucosa	Duodenum
4	chr4:81942600-81943200	Active TSS	Rectal Mucosa Donor 29	rectum
5	chr4:81942600-81943200	Active TSS	Stomach Smooth Muscle	stomach
6	chr4:81942600-81943800	Enhancers	Duodenum Smooth Muscle	Duodenum
7	chr4:81942800-81943400	Enhancers	Rectal Smooth Muscle	rectum
8	chr4:81942800-81943600	Enhancers	Stomach Mucosa	stomach
9	chr4:81942800-81944000	Enhancers	Colon Smooth Muscle	Colon
10	chr4:81943000-81943600	Flanking Active TSS	Rectal Mucosa Donor 31	rectum

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