Variant report

Variant	rs1738459
Chromosome Location	chr6:54796884-54796885
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 61 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:59)

rs_ID	r²[population]
rs1028423	0.87[AMR][1000 genomes];0.99[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs1056630	1.00[ASN][1000 genomes]
rs1503150	0.97[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs171226	0.87[AMR][1000 genomes];0.99[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs183011	0.87[AMR][1000 genomes];0.99[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2397176	0.92[ASN][1000 genomes]
rs239780	0.99[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs239787	0.82[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs239788	0.82[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs239789	0.90[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs239791	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs239793	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs239797	0.90[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs239798	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs239799	0.90[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs239802	0.90[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs239805	0.99[EUR][1000 genomes]
rs239807	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs239808	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs239810	0.90[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs239823	0.99[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs239824	0.99[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs239827	0.98[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs239828	0.85[ASN][1000 genomes]
rs239829	0.98[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs239830	0.98[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs239831	0.96[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs239832	0.99[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs239833	0.87[AMR][1000 genomes];0.98[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs239834	0.97[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs239835	0.98[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs239836	0.98[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs239838	0.87[AMR][1000 genomes];0.99[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs239839	0.99[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs239840	0.99[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs239841	0.99[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs239842	0.99[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs239843	0.99[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs239844	0.99[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs239845	0.99[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs239846	0.99[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs239847	0.99[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs239848	0.98[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs239849	0.99[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs239851	0.82[AMR][1000 genomes];0.98[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs239852	0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs239853	0.83[AMR][1000 genomes];1.00[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs2746440	0.90[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35620314	0.84[ASN][1000 genomes]
rs378853	0.82[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs398483	0.97[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs406149	0.87[AMR][1000 genomes];0.99[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs57835829	1.00[ASN][1000 genomes]
rs59689523	0.92[ASN][1000 genomes]
rs6917766	1.00[ASN][1000 genomes]
rs73431470	0.92[ASN][1000 genomes]
rs7749972	0.97[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7774568	0.84[ASN][1000 genomes]
rs9475077	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[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	nsv885900	chr6:54517968-54852462	Active TSS Bivalent Enhancer Enhancers Weak transcription Strong transcription Bivalent/Poised TSS Genic enhancers Flanking Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	13 gene(s)	inside rSNPs	diseases
2	esv2763553	chr6:54687979-54820487	Weak transcription Active TSS Transcr. at gene 5' and 3' Flanking Active TSS Enhancers Flanking Bivalent TSS/Enh Strong transcription Bivalent/Poised TSS Genic enhancers ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:16 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:54785600-54805000	Weak transcription	Rectal Mucosa Donor 29	rectum
2	chr6:54786800-54800000	Weak transcription	Hela-S3	cervix
3	chr6:54789800-54810200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
4	chr6:54790000-54800200	Weak transcription	Placenta Amnion	Placenta Amnion
5	chr6:54791400-54797000	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
6	chr6:54791400-54798000	Weak transcription	Fetal Intestine Large	intestine
7	chr6:54791400-54798600	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
8	chr6:54793200-54797400	Weak transcription	Rectal Mucosa Donor 31	rectum
9	chr6:54795200-54799600	Weak transcription	NHEK	skin
10	chr6:54795400-54799400	Strong transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
11	chr6:54795600-54797400	Weak transcription	HMEC	breast
12	chr6:54796400-54797000	Strong transcription	Breast Myoepithelial Primary Cells	Breast
13	chr6:54796400-54797400	Weak transcription	Fetal Kidney	kidney
14	chr6:54796800-54797000	ZNF genes & repeats	Esophagus	oesophagus
15	chr6:54796800-54797200	ZNF genes & repeats	Fetal Intestine Small	intestine
16	chr6:54796800-54798000	ZNF genes & repeats	Duodenum Mucosa	Duodenum

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