Variant report

Variant	rs1340670
Chromosome Location	chr6:54183439-54183440
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 15 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:12)

rs_ID	r²[population]
rs1058768	0.96[CEU][hapmap];0.81[GIH][hapmap];0.82[TSI][hapmap];0.81[EUR][1000 genomes]
rs1316575	0.90[CHD][hapmap];0.81[JPT][hapmap];0.83[TSI][hapmap]
rs1353708	0.95[CHB][hapmap];0.86[JPT][hapmap];0.91[ASN][1000 genomes]
rs1508642	0.96[CEU][hapmap];0.89[GIH][hapmap];0.96[MEX][hapmap];0.87[TSI][hapmap];0.92[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs1995768	1.00[CHB][hapmap];0.95[CHD][hapmap];0.86[JPT][hapmap];0.93[ASN][1000 genomes]
rs3756808	0.88[CHD][hapmap];0.84[GIH][hapmap];0.81[JPT][hapmap];0.85[TSI][hapmap]
rs3777651	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[YRI][hapmap];0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3777652	1.00[CHB][hapmap];0.86[JPT][hapmap];0.93[ASN][1000 genomes]
rs3798278	0.92[ASN][1000 genomes]
rs4712061	0.93[CHD][hapmap];0.89[GIH][hapmap];0.86[JPT][hapmap];0.88[MEX][hapmap];0.83[TSI][hapmap]
rs9367562	1.00[CHB][hapmap];0.86[JPT][hapmap];0.92[ASN][1000 genomes]
rs9370283	0.81[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

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs1340670	TINAG	Cis_1M	lymphoblastoid	RTeQTL
rs1340670	IL17A	cis	parietal	SCAN
rs1340670	C6orf142	cis	cerebellum	SCAN
rs1340670	GSTA1	cis	parietal	SCAN

Chromatin state (count:5 , 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	chr6:54178200-54188400	Weak transcription	Fetal Intestine Small	intestine
4	chr6:54178200-54191600	Weak transcription	Fetal Intestine Large	intestine
5	chr6:54181000-54200400	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast

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Input of quick search could be:

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

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