Variant report

Variant	rs16873828
Chromosome Location	chr7:25357772-25357773
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 10 )
Associated
traits (count: 1 )

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

rs_ID	r²[population]
rs17306270	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs56180026	0.81[EUR][1000 genomes]
rs7799626	0.85[EUR][1000 genomes]
rs7805812	0.81[EUR][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	nsv606424	chr7:24982529-25466521	Genic enhancers Flanking Active TSS Active TSS Enhancers Weak transcription Bivalent Enhancer Strong transcription Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	79 gene(s)	inside rSNPs	diseases
2	nsv606426	chr7:25254125-25621579	Enhancers Bivalent Enhancer Flanking Active TSS Weak transcription Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	13 gene(s)	inside rSNPs	diseases
3	nsv1028018	chr7:25351950-25371700	Weak transcription Enhancers Active TSS ZNF genes & repeats Flanking Active TSS	TF binding region Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	n/a
4	nsv464409	chr7:25352809-25371700	Enhancers Weak transcription Active TSS ZNF genes & repeats Flanking Active TSS	TF binding region Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	n/a
5	nsv464410	chr7:25354077-25371700	Enhancers Weak transcription ZNF genes & repeats Flanking Active TSS Active TSS	TF binding region Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	n/a
6	nsv606427	chr7:25354077-25371700	Weak transcription Enhancers ZNF genes & repeats Active TSS Flanking Active TSS	TF binding region Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	n/a

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs16873828	HOXA2	cis	cerebellum	SCAN

Chromatin state (count:16 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr7:25351000-25358400	Weak transcription	Pancreatic Islets	Pancreatic Islet
2	chr7:25351600-25358200	Weak transcription	H9 Cell Line	embryonic stem cell
3	chr7:25353800-25358400	Enhancers	Fetal Adrenal Gland	Adrenal Gland
4	chr7:25354000-25360000	Weak transcription	Sigmoid Colon	Sigmoid Colon
5	chr7:25354400-25357800	Weak transcription	Brain Anterior Caudate	brain
6	chr7:25355000-25360000	Weak transcription	Breast Myoepithelial Primary Cells	Breast
7	chr7:25355200-25358200	Weak transcription	Ovary	ovary
8	chr7:25355200-25358600	Weak transcription	Liver	Liver
9	chr7:25355400-25361000	Weak transcription	Rectal Mucosa Donor 29	rectum
10	chr7:25356200-25360000	Weak transcription	Duodenum Mucosa	Duodenum
11	chr7:25356200-25360800	Weak transcription	Fetal Intestine Large	intestine
12	chr7:25356400-25361000	Weak transcription	Fetal Lung	lung
13	chr7:25357200-25357800	Enhancers	ES-I3 Cell Line	embryonic stem cell
14	chr7:25357200-25358000	Enhancers	HUES6 Cell Line	embryonic stem cell
15	chr7:25357200-25358400	Weak transcription	Fetal Intestine Small	intestine
16	chr7:25357600-25360000	Weak transcription	Pancreas	Pancrea

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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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