Variant report

Variant	rs11773294
Chromosome Location	chr7:16839835-16839836
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 19 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:13)

rs_ID	r²[population]
rs10244119	1.00[ASN][1000 genomes]
rs10499477	0.82[ASW][hapmap];1.00[GIH][hapmap];0.92[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];0.80[AFR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11760249	0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11767782	0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11768938	1.00[ASN][1000 genomes]
rs13238103	1.00[ASN][1000 genomes]
rs28945078	1.00[ASN][1000 genomes]
rs35944096	1.00[ASN][1000 genomes]
rs55919881	1.00[ASN][1000 genomes]
rs55975927	1.00[ASN][1000 genomes]
rs62440996	1.00[ASN][1000 genomes]
rs6968651	1.00[ASN][1000 genomes]
rs71540774	1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:6 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1028125	chr7:16529160-16847225	Weak transcription Strong transcription Flanking Active TSS Enhancers ZNF genes & repeats Active TSS Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	40 gene(s)	inside rSNPs	diseases
2	nsv887761	chr7:16834361-17732490	Enhancers Genic enhancers Weak transcription Flanking Active TSS Active TSS Strong transcription ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	34 gene(s)	inside rSNPs	diseases
3	nsv887762	chr7:16834361-17746628	Enhancers Genic enhancers Flanking Active TSS Active TSS Strong transcription Weak transcription Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	34 gene(s)	inside rSNPs	diseases
4	nsv887763	chr7:16834361-17750811	Weak transcription Active TSS Enhancers Strong transcription Flanking Active TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	34 gene(s)	inside rSNPs	diseases
5	nsv887764	chr7:16839835-17218800	Weak transcription Enhancers Active TSS Flanking Active TSS Genic enhancers Strong transcription Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	16 gene(s)	inside rSNPs	diseases
6	nsv887765	chr7:16839835-17750811	Enhancers Active TSS Flanking Active TSS Weak transcription ZNF genes & repeats Strong transcription Bivalent Enhancer Bivalent/Poised TSS Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	34 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs11773294	SNX13	cis	cerebellum	SCAN

Chromatin state (count:19 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr7:16814400-16843800	Weak transcription	Small Intestine	intestine
2	chr7:16823600-16843600	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
3	chr7:16832400-16840000	Strong transcription	Rectal Mucosa Donor 29	rectum
4	chr7:16834000-16842400	Weak transcription	Gastric	stomach
5	chr7:16835000-16844200	Weak transcription	Psoas Muscle	Psoas
6	chr7:16835800-16840000	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
7	chr7:16838200-16841200	Weak transcription	Colonic Mucosa	Colon
8	chr7:16838400-16840000	Weak transcription	Fetal Stomach	stomach
9	chr7:16839200-16841000	Genic enhancers	Fetal Intestine Large	intestine
10	chr7:16839200-16842600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
11	chr7:16839600-16841000	Genic enhancers	Rectal Mucosa Donor 31	rectum
12	chr7:16839600-16841000	Genic enhancers	A549	lung
13	chr7:16839600-16841200	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
14	chr7:16839600-16841200	Genic enhancers	Fetal Intestine Small	intestine
15	chr7:16839800-16840000	Genic enhancers	Stomach Mucosa	stomach
16	chr7:16839800-16840200	Enhancers	Placenta Amnion	Placenta Amnion
17	chr7:16839800-16840400	Strong transcription	Sigmoid Colon	Sigmoid Colon
18	chr7:16839800-16840600	Genic enhancers	Duodenum Mucosa	Duodenum
19	chr7:16839800-16841200	Enhancers	Hela-S3	cervix

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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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