Variant report

Variant	rs7766029
Chromosome Location	chr6:88847435-88847436
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 18 )
Associated
traits (count: 2 )

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

rs_ID	r²[population]
rs10485171	0.85[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs1049353	0.85[CHB][hapmap];0.88[JPT][hapmap];0.82[ASN][1000 genomes]
rs10944343	0.87[ASN][1000 genomes]
rs3857490	0.88[EUR][1000 genomes]
rs4707436	0.86[CHB][hapmap];0.91[CHD][hapmap];1.00[JPT][hapmap];0.86[YRI][hapmap];0.91[ASN][1000 genomes]
rs59299454	0.85[ASN][1000 genomes]
rs9344755	0.88[EUR][1000 genomes]
rs9450891	0.89[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:10 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv604120	chr6:88818965-89198994	Enhancers Flanking Bivalent TSS/Enh Flanking Active TSS Bivalent/Poised TSS Active TSS Weak transcription Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3' Strong transcription Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
2	nsv1015298	chr6:88830630-89075508	Bivalent/Poised TSS Flanking Active TSS Enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Weak transcription Active TSS Genic enhancers Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
3	nsv538355	chr6:88830630-89075508	Bivalent/Poised TSS Enhancers Weak transcription Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Flanking Active TSS ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
4	nsv1020107	chr6:88838931-88866748	Enhancers Flanking Active TSS Weak transcription Active TSS Genic enhancers Strong transcription Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
5	esv2763586	chr6:88838943-88867488	Enhancers Weak transcription Active TSS Strong transcription Flanking Active TSS Transcr. at gene 5' and 3' Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
6	nsv519365	chr6:88842154-88861698	Enhancers Weak transcription Flanking Active TSS Genic enhancers ZNF genes & repeats Strong transcription Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island lncRNA	1 gene(s)	inside rSNPs	diseases
7	nsv463944	chr6:88842154-88861698	Weak transcription Strong transcription Enhancers Flanking Active TSS Transcr. at gene 5' and 3' Genic enhancers Active TSS ZNF genes & repeats	TF binding region CpG island lncRNA	1 gene(s)	inside rSNPs	diseases
8	nsv463945	chr6:88842154-88861698	Enhancers Weak transcription Transcr. at gene 5' and 3' Flanking Active TSS Active TSS Genic enhancers ZNF genes & repeats Strong transcription	TF binding region CpG island lncRNA	1 gene(s)	inside rSNPs	diseases
9	nsv604121	chr6:88842154-88861698	Weak transcription Flanking Active TSS Enhancers ZNF genes & repeats Genic enhancers Strong transcription Transcr. at gene 5' and 3' Active TSS	TF binding region CpG island lncRNA	1 gene(s)	inside rSNPs	diseases
10	nsv1023549	chr6:88842545-88869048	Enhancers Weak transcription Active TSS ZNF genes & repeats Flanking Active TSS Strong transcription Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs7766029	SYNCRIP	cis	parietal	SCAN
rs7766029	MDN1	cis	parietal	SCAN

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:88843000-88853400	Weak transcription	Stomach Smooth Muscle	stomach
2	chr6:88847000-88847800	Weak transcription	Colon Smooth Muscle	Colon
3	chr6:88847000-88850800	Weak transcription	GM12878-XiMat	blood
4	chr6:88847200-88850000	Weak transcription	Primary B cells from peripheral blood	blood
5	chr6:88847400-88847600	Enhancers	Rectal Smooth Muscle	rectum

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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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