Variant report

Variant	rs6955594
Chromosome Location	chr7:124644291-124644292
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 27 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:18)

rs_ID	r²[population]
rs6466976	1.00[YRI][hapmap]
rs6466977	1.00[LWK][hapmap];1.00[MKK][hapmap];1.00[YRI][hapmap]
rs6466983	0.89[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs6466984	0.89[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs6947018	1.00[YRI][hapmap]
rs6947227	1.00[YRI][hapmap]
rs6958244	1.00[YRI][hapmap]
rs6968124	0.83[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs6970006	1.00[YRI][hapmap]
rs7778361	1.00[ASW][hapmap];0.87[LWK][hapmap];1.00[MKK][hapmap];1.00[YRI][hapmap]
rs7780541	1.00[AMR][1000 genomes]
rs7780893	1.00[ASW][hapmap];1.00[LWK][hapmap];1.00[MKK][hapmap];1.00[YRI][hapmap];0.83[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs7784734	0.89[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs7786212	0.82[YRI][hapmap]
rs7790680	1.00[YRI][hapmap]
rs7791015	0.82[YRI][hapmap]
rs7800277	0.89[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs7805443	1.00[YRI][hapmap];0.83[AFR][1000 genomes];1.00[AMR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:9 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv429809	chr7:123937674-124835925	Enhancers Strong transcription Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Weak transcription Flanking Active TSS Bivalent Enhancer Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	49 gene(s)	inside rSNPs	diseases
2	nsv1016655	chr7:124575684-124684279	Enhancers Flanking Active TSS ZNF genes & repeats Active TSS Weak transcription	TF binding region CpG island Chromatin interactive region lncRNA	14 gene(s)	inside rSNPs	diseases
3	nsv1032336	chr7:124590688-124673373	Enhancers Weak transcription Flanking Active TSS Active TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases
4	nsv1025873	chr7:124591433-124668423	Enhancers Weak transcription Flanking Active TSS ZNF genes & repeats Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases
5	esv2761363	chr7:124591433-124673373	Enhancers Flanking Active TSS Weak transcription Active TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases
6	nsv1034654	chr7:124591433-124673373	Weak transcription Enhancers Active TSS Flanking Active TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases
7	nsv889139	chr7:124600505-124767295	Enhancers Weak transcription Flanking Bivalent TSS/Enh Flanking Active TSS Active TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	23 gene(s)	inside rSNPs	diseases
8	esv3394090	chr7:124602150-124900799	Enhancers Flanking Active TSS ZNF genes & repeats Weak transcription Active TSS Strong transcription Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	35 gene(s)	inside rSNPs	diseases
9	nsv608343	chr7:124610346-124674022	Enhancers Weak transcription Active TSS Flanking Active TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs6955594	GALM	trans	lymphoblastoid	seeQTL
rs6955594	KIF7	trans	lymphoblastoid	seeQTL
rs6955594	OAF	trans	lymphoblastoid	seeQTL

Chromatin state (count:2 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr7:124644000-124644400	Enhancers	Fetal Brain Male	brain
2	chr7:124644200-124644600	Enhancers	Brain Germinal Matrix	brain

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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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