Variant report

Variant	rs1934792
Chromosome Location	chr6:54178822-54178823
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 16 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:13)

rs_ID	r²[population]
rs12192061	1.00[CHB][hapmap];0.95[CHD][hapmap];0.85[JPT][hapmap];0.91[ASN][1000 genomes]
rs12202919	0.96[ASN][1000 genomes]
rs12211623	1.00[CHB][hapmap];0.85[JPT][hapmap];0.91[ASN][1000 genomes]
rs1353707	0.95[CHB][hapmap];0.95[JPT][hapmap];0.95[ASN][1000 genomes]
rs2297983	1.00[CHB][hapmap];0.95[CHD][hapmap];0.85[JPT][hapmap];0.91[ASN][1000 genomes]
rs2297986	1.00[CHB][hapmap];0.95[CHD][hapmap];0.84[JPT][hapmap];0.91[ASN][1000 genomes]
rs2840121	1.00[CHB][hapmap];0.95[JPT][hapmap];0.95[ASN][1000 genomes]
rs3777655	1.00[CHB][hapmap];0.94[JPT][hapmap];0.95[ASN][1000 genomes]
rs3798276	1.00[CHB][hapmap];0.98[CHD][hapmap];0.95[JPT][hapmap];0.95[ASN][1000 genomes]
rs6909083	0.87[CEU][hapmap];0.87[GIH][hapmap];0.84[EUR][1000 genomes]
rs9370286	1.00[CHB][hapmap];0.98[CHD][hapmap];0.95[JPT][hapmap];0.97[ASN][1000 genomes]
rs9370288	1.00[CHB][hapmap];0.95[CHD][hapmap];0.85[JPT][hapmap];0.91[ASN][1000 genomes]
rs9370289	0.86[CHB][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:2)

SNP	Gene	Cis/trans	Tissue	Source
rs1934792	GCLC	cis	parietal	SCAN
rs1934792	TINAG	Cis_1M	lymphoblastoid	RTeQTL

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	chr6:54178800-54179000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived

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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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