Variant report

Variant	rs6722217
Chromosome Location	chr2:48994898-48994899
allele	A/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 14 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:8)

rs_ID	r²[population]
rs12998409	0.86[AMR][1000 genomes]
rs4074647	0.91[AMR][1000 genomes]
rs4074648	0.92[AMR][1000 genomes]
rs4603819	0.89[AFR][1000 genomes];0.97[AMR][1000 genomes];0.89[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs4953625	0.86[AMR][1000 genomes];0.85[ASN][1000 genomes]
rs7563144	0.86[AMR][1000 genomes];0.88[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs7563465	0.87[AFR][1000 genomes];0.88[AMR][1000 genomes];0.88[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs9798043	0.88[AMR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:6 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1010494	chr2:48767055-49027310	Enhancers Weak transcription Strong transcription ZNF genes & repeats Flanking Active TSS Bivalent/Poised TSS Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	8 gene(s)	inside rSNPs	diseases
2	nsv1002793	chr2:48771220-49466550	ZNF genes & repeats Enhancers Weak transcription Bivalent Enhancer Strong transcription Genic enhancers Active TSS Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	11 gene(s)	inside rSNPs	diseases
3	nsv1004965	chr2:48796170-49443587	Bivalent Enhancer Enhancers Weak transcription Strong transcription ZNF genes & repeats Genic enhancers Active TSS Flanking Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	10 gene(s)	inside rSNPs	diseases
4	nsv535684	chr2:48796170-49443587	Enhancers Weak transcription Active TSS Flanking Active TSS Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh Strong transcription Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	10 gene(s)	inside rSNPs	diseases
5	nsv498119	chr2:48808834-49422647	Weak transcription Enhancers Flanking Bivalent TSS/Enh Strong transcription Bivalent Enhancer Flanking Active TSS ZNF genes & repeats Bivalent/Poised TSS Active TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	10 gene(s)	inside rSNPs	diseases
6	nsv833992	chr2:48814223-48998037	Flanking Bivalent TSS/Enh Enhancers Weak transcription Strong transcription Bivalent/Poised TSS Bivalent Enhancer Flanking Active TSS ZNF genes & repeats Genic enhancers Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	6 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs6722217	LHCGR	cis	Esophagus Muscularis	GTEx

Chromatin state (count:17 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:48994200-48995000	Weak transcription	HUES64 Cell Line	embryonic stem cell
2	chr2:48994200-48995200	Enhancers	HUES48 Cell Line	embryonic stem cell
3	chr2:48994200-48995200	Enhancers	iPS DF 19.11 Cell Line	embryonic stem cell
4	chr2:48994200-48995200	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
5	chr2:48994200-48995400	Enhancers	iPS-20b Cell Line	embryonic stem cell
6	chr2:48994200-48996200	Enhancers	iPS-15b Cell Line	embryonic stem cell
7	chr2:48994200-48996600	Enhancers	Placenta	Placenta
8	chr2:48994400-48995200	Enhancers	iPS-18 Cell Line	embryonic stem cell
9	chr2:48994400-48995200	Enhancers	iPS DF 6.9 Cell Line	embryonic stem cell
10	chr2:48994400-48996200	Enhancers	ES-I3 Cell Line	embryonic stem cell
11	chr2:48994400-48996200	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
12	chr2:48994600-48995000	Enhancers	H1 Cell Line	embryonic stem cell
13	chr2:48994600-48995800	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
14	chr2:48994600-48998000	Weak transcription	Adipose Nuclei	Adipose
15	chr2:48994600-49080200	Weak transcription	Stomach Smooth Muscle	stomach
16	chr2:48994800-48995200	Flanking Active TSS	HUES6 Cell Line	embryonic stem cell
17	chr2:48994800-48995400	Enhancers	ES-WA7 Cell Line	embryonic stem cell

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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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