Variant report

Variant	rs3798275
Chromosome Location	chr6:54190938-54190939
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 73 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:70)

rs_ID	r²[population]
rs12055413	1.00[AMR][1000 genomes]
rs12055863	1.00[AMR][1000 genomes]
rs12175364	1.00[AMR][1000 genomes]
rs12175696	0.85[AMR][1000 genomes]
rs12176182	1.00[AMR][1000 genomes]
rs16885263	0.85[AMR][1000 genomes];0.86[ASN][1000 genomes]
rs2047431	0.82[CHB][hapmap];0.85[AMR][1000 genomes];1.00[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2291824	1.00[AMR][1000 genomes];0.86[ASN][1000 genomes]
rs2297984	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35506389	0.85[AMR][1000 genomes]
rs3777637	1.00[AMR][1000 genomes];0.86[ASN][1000 genomes]
rs3777638	1.00[AMR][1000 genomes];0.86[ASN][1000 genomes]
rs3777639	1.00[AMR][1000 genomes];0.86[ASN][1000 genomes]
rs3777641	1.00[AMR][1000 genomes];0.86[ASN][1000 genomes]
rs3777653	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3777657	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs55888793	0.85[AMR][1000 genomes]
rs57943356	1.00[EUR][1000 genomes]
rs60021603	1.00[AMR][1000 genomes];0.86[ASN][1000 genomes]
rs60701944	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6902373	0.85[AMR][1000 genomes]
rs9296746	0.85[AMR][1000 genomes]
rs9349701	0.85[AMR][1000 genomes]
rs9349703	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9349704	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs9349707	1.00[AMR][1000 genomes];0.86[ASN][1000 genomes]
rs9357796	0.85[AMR][1000 genomes]
rs9357797	0.85[AMR][1000 genomes]
rs9357798	0.85[AMR][1000 genomes]
rs9357799	0.85[AMR][1000 genomes]
rs9357800	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9357803	1.00[AMR][1000 genomes]
rs9367555	0.85[AMR][1000 genomes]
rs9367557	0.85[AMR][1000 genomes]
rs9367560	0.85[AMR][1000 genomes]
rs9367563	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9367564	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs9367567	1.00[AMR][1000 genomes];0.86[ASN][1000 genomes]
rs9367571	1.00[AMR][1000 genomes]
rs9370277	0.85[AMR][1000 genomes]
rs9370278	0.85[AMR][1000 genomes]
rs9370280	0.85[AMR][1000 genomes]
rs9370285	0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9370287	0.82[CHB][hapmap];0.85[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9370293	1.00[AMR][1000 genomes]
rs9370294	1.00[AMR][1000 genomes]
rs9370297	1.00[AMR][1000 genomes]
rs9370298	1.00[AMR][1000 genomes]
rs9382312	0.85[AMR][1000 genomes]
rs9382317	0.85[AMR][1000 genomes]
rs9382320	0.85[AMR][1000 genomes]
rs9382322	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9382324	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs9382327	1.00[AMR][1000 genomes];0.86[ASN][1000 genomes]
rs9382328	1.00[AMR][1000 genomes];0.86[ASN][1000 genomes]
rs9382339	1.00[AMR][1000 genomes]
rs9382340	1.00[AMR][1000 genomes]
rs9395925	0.85[AMR][1000 genomes]
rs9395932	0.85[AMR][1000 genomes]
rs9395933	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9395938	1.00[AMR][1000 genomes];0.86[ASN][1000 genomes]
rs9395940	1.00[AMR][1000 genomes];0.86[ASN][1000 genomes]
rs9395941	1.00[AMR][1000 genomes];0.86[ASN][1000 genomes]
rs9395945	1.00[AMR][1000 genomes];0.86[ASN][1000 genomes]
rs9395946	1.00[AMR][1000 genomes];0.86[ASN][1000 genomes]
rs9395952	1.00[AMR][1000 genomes]
rs9395955	1.00[AMR][1000 genomes]
rs9395956	1.00[AMR][1000 genomes]
rs9395960	1.00[AMR][1000 genomes]
rs9395963	1.00[AMR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1067663	chr6:53796341-54449718	Enhancers Active TSS Weak transcription Strong transcription Flanking Active TSS Bivalent Enhancer Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	14 gene(s)	inside rSNPs	diseases
2	nsv529158	chr6:53796341-54449718	Weak transcription Enhancers ZNF genes & repeats Active TSS Flanking Active TSS Strong transcription Genic enhancers Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	14 gene(s)	inside rSNPs	diseases
3	nsv885888	chr6:54132353-54266032	Enhancers Weak transcription Flanking Active TSS Active TSS Strong transcription ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:6 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:54176600-54191800	Weak transcription	Rectal Mucosa Donor 29	rectum
2	chr6:54176600-54191800	Weak transcription	Rectal Mucosa Donor 31	rectum
3	chr6:54178200-54191600	Weak transcription	Fetal Intestine Large	intestine
4	chr6:54181000-54200400	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
5	chr6:54186400-54192400	Weak transcription	Sigmoid Colon	Sigmoid Colon
6	chr6:54189200-54191800	Weak transcription	Fetal Intestine Small	intestine

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