Variant report

Variant	rs1819409
Chromosome Location	chr11:49079350-49079351
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 47 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:26)

rs_ID	r²[population]
rs10839217	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.94[GIH][hapmap];1.00[JPT][hapmap];1.00[TSI][hapmap]
rs10839230	0.95[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs11040241	1.00[CHB][hapmap];0.92[JPT][hapmap]
rs11040255	1.00[CEU][hapmap];1.00[CHB][hapmap];0.84[JPT][hapmap]
rs11040261	1.00[CEU][hapmap];0.89[CHB][hapmap];0.94[CHD][hapmap];1.00[GIH][hapmap];0.85[JPT][hapmap];1.00[TSI][hapmap];0.93[EUR][1000 genomes]
rs11826051	0.95[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs12271751	0.85[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1847640	0.89[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap]
rs202672	0.89[EUR][1000 genomes]
rs202673	0.87[EUR][1000 genomes]
rs202681	0.81[EUR][1000 genomes]
rs202687	0.91[EUR][1000 genomes]
rs202689	0.90[EUR][1000 genomes]
rs202696	0.83[EUR][1000 genomes]
rs202698	0.83[EUR][1000 genomes]
rs202701	0.87[EUR][1000 genomes]
rs202705	0.87[EUR][1000 genomes]
rs202713	1.00[CEU][hapmap];0.89[CHB][hapmap];0.85[JPT][hapmap];0.86[EUR][1000 genomes]
rs202719	0.90[EUR][1000 genomes]
rs202724	0.90[EUR][1000 genomes]
rs369803	0.90[EUR][1000 genomes]
rs58846727	0.85[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs595139	0.92[EUR][1000 genomes]
rs648728	0.90[EUR][1000 genomes]
rs689329	0.85[EUR][1000 genomes]
rs7932738	1.00[CEU][hapmap];1.00[CHB][hapmap];0.88[CHD][hapmap];0.88[GIH][hapmap];0.92[JPT][hapmap];0.86[TSI][hapmap]

Variant overlapped rSNPs/rCNVs (count:21 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv2759824	chr11:48303671-49185190	Weak transcription Active TSS ZNF genes & repeats Enhancers Bivalent/Poised TSS Strong transcription Flanking Bivalent TSS/Enh Bivalent Enhancer Flanking Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	36 gene(s)	inside rSNPs	diseases
2	esv1828260	chr11:48735614-49162948	Bivalent Enhancer Weak transcription Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Flanking Active TSS Enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	18 gene(s)	inside rSNPs	diseases
3	nsv427886	chr11:48850348-49185190	Flanking Bivalent TSS/Enh ZNF genes & repeats Weak transcription Active TSS Strong transcription Enhancers Bivalent/Poised TSS Flanking Active TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	19 gene(s)	inside rSNPs	diseases
4	esv2758268	chr11:48856977-49185190	Weak transcription ZNF genes & repeats Enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Active TSS Strong transcription Flanking Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	19 gene(s)	inside rSNPs	diseases
5	nsv469956	chr11:48922645-49862647	Weak transcription Enhancers Flanking Active TSS Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3' Strong transcription Genic enhancers Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	25 gene(s)	inside rSNPs	diseases
6	nsv897481	chr11:48987539-49111467	ZNF genes & repeats Enhancers	TF binding region CpG island lncRNA	8 gene(s)	inside rSNPs	diseases
7	nsv832145	chr11:49002873-49185190	ZNF genes & repeats Weak transcription Enhancers Strong transcription Bivalent/Poised TSS	TF binding region CpG island lncRNA	13 gene(s)	inside rSNPs	diseases
8	nsv897482	chr11:49003921-49111467	ZNF genes & repeats Enhancers	TF binding region CpG island lncRNA	8 gene(s)	inside rSNPs	diseases
9	nsv897483	chr11:49003921-49120367	ZNF genes & repeats Enhancers	TF binding region CpG island lncRNA	8 gene(s)	inside rSNPs	diseases
10	nsv1054955	chr11:49007476-49138758	Enhancers ZNF genes & repeats	TF binding region CpG island lncRNA	10 gene(s)	inside rSNPs	diseases
11	nsv975174	chr11:49039206-49083950	ZNF genes & repeats	TF binding region CpG island	3 gene(s)	inside rSNPs	diseases
12	nsv897484	chr11:49042866-49162948	ZNF genes & repeats Enhancers Bivalent/Poised TSS	TF binding region CpG island lncRNA	9 gene(s)	inside rSNPs	diseases
13	esv3507647	chr11:49072476-49105274	Enhancers	TF binding region CpG island lncRNA	3 gene(s)	inside rSNPs	diseases
14	esv3507648	chr11:49072476-49105274	Enhancers	TF binding region CpG island lncRNA	3 gene(s)	inside rSNPs	diseases
15	esv3497082	chr11:49077426-49105124	Enhancers	TF binding region CpG island lncRNA	3 gene(s)	inside rSNPs	diseases
16	esv3497081	chr11:49077536-49104203	Enhancers	TF binding region CpG island lncRNA	3 gene(s)	inside rSNPs	diseases
17	esv3497083	chr11:49077536-49104203	Enhancers	TF binding region CpG island lncRNA	3 gene(s)	inside rSNPs	diseases
18	nsv1051896	chr11:49078859-49120388	Enhancers	TF binding region CpG island lncRNA	4 gene(s)	inside rSNPs	diseases
19	esv2421548	chr11:49078871-49103690	Enhancers	TF binding region CpG island lncRNA	3 gene(s)	inside rSNPs	diseases
20	esv2760191	chr11:49078871-49103690	Enhancers	TF binding region CpG island lncRNA	3 gene(s)	inside rSNPs	diseases
21	nsv554346	chr11:49079350-49095165	Inactive region	TF binding region CpG island lncRNA	2 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs1819409	SLC35C1	cis	cerebellum	SCAN
rs1819409	OR4C3	cis	parietal	SCAN

Chromatin state (count:0 , 50 per page) page:

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dbSNP/dbVar ID: rs12345 /nsv7879
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