Variant report

Variant	rs62341886
Chromosome Location	chr4:173911114-173911115
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-HMGB2-11	chr4:173908348-173911353	NONHSAT099211

Extended variants
information (count: 33 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:31)

rs_ID	r²[population]
rs10003998	0.84[EUR][1000 genomes]
rs10014915	0.81[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs12641678	0.81[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs12644630	0.99[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs17254079	0.81[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs17254611	0.84[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17254681	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs2610188	0.83[ASN][1000 genomes]
rs2610191	0.83[ASN][1000 genomes]
rs2653844	0.81[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs28380538	0.91[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28483480	0.88[EUR][1000 genomes]
rs28485277	0.85[EUR][1000 genomes]
rs28524136	0.81[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs28582871	0.84[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28671519	0.87[EUR][1000 genomes]
rs28705797	0.81[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28800549	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28890012	0.86[AFR][1000 genomes];0.84[AMR][1000 genomes];0.81[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4547777	0.89[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs55936404	0.81[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs56110146	0.83[ASN][1000 genomes]
rs62341884	0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62341887	1.00[ASN][1000 genomes]
rs62341919	0.82[EUR][1000 genomes]
rs62341920	0.80[EUR][1000 genomes]
rs6852770	0.83[ASN][1000 genomes]
rs7663630	0.88[EUR][1000 genomes]
rs7682619	0.88[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs7693329	0.88[EUR][1000 genomes]
rs9997573	0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[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	nsv948856	chr4:173388217-173967546	Enhancers Weak transcription Flanking Active TSS Bivalent Enhancer Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh	Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
2	nsv949126	chr4:173466221-174051451	Enhancers Weak transcription Active TSS ZNF genes & repeats Flanking Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:13 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:173903800-173918000	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
2	chr4:173904200-173935200	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
3	chr4:173907400-173913200	Weak transcription	Hela-S3	cervix
4	chr4:173907600-173911200	Weak transcription	HUVEC	blood vessel
5	chr4:173907800-173917000	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
6	chr4:173909800-173911400	Enhancers	Fetal Intestine Large	intestine
7	chr4:173910200-173911800	Enhancers	Fetal Intestine Small	intestine
8	chr4:173910200-173916200	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
9	chr4:173910400-173911200	Weak transcription	Colonic Mucosa	Colon
10	chr4:173910400-173920200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
11	chr4:173911000-173911200	Enhancers	Rectal Mucosa Donor 29	rectum
12	chr4:173911000-173912600	Weak transcription	Rectal Mucosa Donor 31	rectum
13	chr4:173911000-173913800	Weak transcription	Duodenum Mucosa	Duodenum

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