Variant report

Variant	rs2214409
Chromosome Location	chr4:106032945-106032946
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 21 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:16)

rs_ID	r²[population]
rs10856976	1.00[JPT][hapmap]
rs12509636	1.00[CHB][hapmap];0.85[CHD][hapmap];1.00[JPT][hapmap]
rs168989	0.86[CHB][hapmap]
rs17429675	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.92[AFR][1000 genomes];0.93[ASN][1000 genomes]
rs17429682	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.92[AFR][1000 genomes];0.93[ASN][1000 genomes]
rs17429745	0.92[AFR][1000 genomes];0.93[ASN][1000 genomes]
rs17501550	0.92[AFR][1000 genomes];0.93[ASN][1000 genomes]
rs1844655	0.86[CHB][hapmap]
rs195149	0.86[CHB][hapmap]
rs4698931	0.85[CHB][hapmap];0.92[CHD][hapmap];1.00[JPT][hapmap]
rs4699151	0.86[CHB][hapmap]
rs4699153	1.00[JPT][hapmap]
rs56883672	0.91[AFR][1000 genomes];0.91[ASN][1000 genomes]
rs62331120	0.80[AFR][1000 genomes];0.84[ASN][1000 genomes]
rs62331124	0.94[AFR][1000 genomes];0.95[ASN][1000 genomes]
rs72617743	0.91[AFR][1000 genomes];0.86[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:5 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv461609	chr4:105869548-106366209	Weak transcription Strong transcription Genic enhancers Enhancers ZNF genes & repeats Active TSS Transcr. at gene 5' and 3' Flanking Active TSS Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	37 gene(s)	inside rSNPs	diseases
2	nsv470063	chr4:105869548-106366209	Transcr. at gene 5' and 3' Strong transcription Weak transcription Enhancers Flanking Active TSS ZNF genes & repeats Genic enhancers Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	37 gene(s)	inside rSNPs	diseases
3	nsv595007	chr4:105869548-106366209	Weak transcription ZNF genes & repeats Strong transcription Flanking Active TSS Enhancers Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS Genic enhancers Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	37 gene(s)	inside rSNPs	diseases
4	nsv830024	chr4:105884350-106037816	Flanking Active TSS Enhancers Weak transcription ZNF genes & repeats Active TSS Bivalent Enhancer Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases
5	nsv830025	chr4:105988876-106137946	Enhancers Weak transcription Active TSS ZNF genes & repeats Strong transcription Flanking Active TSS Genic enhancers Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	26 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs2214409	AGXT2L1	cis	parietal	SCAN

Chromatin state (count:5 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:106028400-106033000	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
2	chr4:106028600-106033600	Weak transcription	Primary hematopoietic stem cells short term culture	blood
3	chr4:106032600-106038000	Enhancers	Primary neutrophils fromperipheralblood	blood
4	chr4:106032600-106038400	Enhancers	Primary monocytes fromperipheralblood	blood
5	chr4:106032800-106034600	Enhancers	Monocytes-CD14+_RO01746	blood

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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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