Variant report

Variant	rs2797786
Chromosome Location	chr6:37501967-37501968
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 7 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:4)

rs_ID	r²[population]
rs1573133	0.93[EUR][1000 genomes]
rs2776885	0.91[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs2797777	1.00[CEU][hapmap];0.95[CHB][hapmap];0.93[MEX][hapmap];0.85[TSI][hapmap];0.91[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs2797781	0.95[CEU][hapmap];1.00[CHB][hapmap];0.89[JPT][hapmap];0.91[AMR][1000 genomes];0.93[EUR][1000 genomes];0.81[ASN][1000 genomes]

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	esv2752124	chr6:37416219-37680622	Weak transcription Enhancers Flanking Active TSS Genic enhancers Strong transcription Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	22 gene(s)	inside rSNPs	diseases
2	nsv1016310	chr6:37473075-37528469	Enhancers Weak transcription Bivalent/Poised TSS Flanking Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Genic enhancers Active TSS ZNF genes & repeats Strong transcription Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	8 gene(s)	inside rSNPs	diseases
3	nsv1028825	chr6:37495154-38278320	Enhancers Active TSS Weak transcription Bivalent/Poised TSS Flanking Active TSS Bivalent Enhancer Strong transcription Flanking Bivalent TSS/Enh ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	19 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs2797786	FTSJD2	cis	parietal	SCAN
rs2797786	DEF6	cis	cerebellum	SCAN

Chromatin state (count:15 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:37489400-37502000	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
2	chr6:37489600-37502000	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
3	chr6:37490800-37502000	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
4	chr6:37491000-37503000	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
5	chr6:37493800-37514000	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
6	chr6:37495200-37503000	Weak transcription	Primary T helper cells PMA-I stimulated	--
7	chr6:37495600-37502200	Weak transcription	Primary T helper cells fromperipheralblood	blood
8	chr6:37496800-37503200	Weak transcription	GM12878-XiMat	blood
9	chr6:37499600-37502800	Enhancers	Fetal Brain Male	brain
10	chr6:37500000-37502800	Weak transcription	Primary T helper naive cells from peripheral blood	blood
11	chr6:37500800-37503400	Bivalent Enhancer	H9 Derived Neuron Cultured Cells	ES cell derived
12	chr6:37501400-37503600	Bivalent Enhancer	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
13	chr6:37501600-37503400	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
14	chr6:37501800-37502000	Bivalent Enhancer	Cortex derived primary cultured neurospheres	brain
15	chr6:37501800-37502800	Enhancers	Fetal Brain Female	brain

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dbSNP/dbVar ID: rs12345 /nsv7879
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chromosomal regions: chr1:12345-34567

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