Variant report

Variant	rs1340660
Chromosome Location	chr6:54172879-54172880
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 21 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:18)

rs_ID	r²[population]
rs10948810	0.86[CEU][hapmap];1.00[JPT][hapmap];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1150873	1.00[JPT][hapmap]
rs12191165	0.85[AFR][1000 genomes];1.00[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12193042	0.81[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12199953	0.81[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12201064	1.00[ASN][1000 genomes]
rs12201103	0.86[CEU][hapmap];1.00[JPT][hapmap];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12208501	1.00[JPT][hapmap];0.81[EUR][1000 genomes]
rs12212836	0.92[CEU][hapmap];1.00[JPT][hapmap];0.81[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1417390	1.00[JPT][hapmap]
rs16885246	1.00[JPT][hapmap]
rs2136134	0.90[AMR][1000 genomes]
rs2211241	0.84[AFR][1000 genomes];0.90[AMR][1000 genomes]
rs2297980	0.92[CEU][hapmap];1.00[JPT][hapmap];0.81[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2754813	1.00[JPT][hapmap]
rs2792644	1.00[JPT][hapmap]
rs73442548	0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs843827	1.00[JPT][hapmap]

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:11 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:54168800-54176400	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
2	chr6:54171800-54173800	Enhancers	HepG2	liver
3	chr6:54171800-54176600	Active TSS	Rectal Mucosa Donor 29	rectum
4	chr6:54172200-54176200	Active TSS	Fetal Kidney	kidney
5	chr6:54172400-54176600	Active TSS	Duodenum Mucosa	Duodenum
6	chr6:54172600-54173000	Flanking Active TSS	Fetal Intestine Small	intestine
7	chr6:54172600-54175200	Active TSS	Rectal Smooth Muscle	rectum
8	chr6:54172600-54176200	Active TSS	Colonic Mucosa	Colon
9	chr6:54172800-54173000	Flanking Active TSS	Fetal Intestine Large	intestine
10	chr6:54172800-54173600	Enhancers	A549	lung
11	chr6:54172800-54176600	Active TSS	Rectal Mucosa Donor 31	rectum

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

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