Variant report

Variant	rs11630029
Chromosome Location	chr15:59916050-59916051
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 20 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:15)

rs_ID	r²[population]
rs11071459	0.92[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs11629842	0.82[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs11853644	0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs12439405	0.99[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs12899060	0.88[AMR][1000 genomes]
rs12906018	0.86[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs2170062	0.81[AFR][1000 genomes]
rs2414636	0.93[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2414638	0.87[AFR][1000 genomes]
rs28581634	0.91[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs34626301	0.99[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs62014429	0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs62015260	0.83[AFR][1000 genomes]
rs6494124	0.92[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs8026652	0.84[AMR][1000 genomes];0.88[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:5 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv527307	chr15:59103328-60018487	Enhancers Genic enhancers Weak transcription Flanking Bivalent TSS/Enh Strong transcription Flanking Active TSS Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	145 gene(s)	inside rSNPs	diseases
2	nsv1044442	chr15:59765724-59955587	Weak transcription Enhancers Active TSS ZNF genes & repeats Strong transcription Flanking Active TSS Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	14 gene(s)	inside rSNPs	diseases
3	nsv542403	chr15:59765724-59955587	Enhancers Weak transcription Active TSS Flanking Active TSS Bivalent Enhancer Genic enhancers Strong transcription 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 miRNA target site	14 gene(s)	inside rSNPs	diseases
4	nsv569605	chr15:59855226-59956553	Strong transcription Active TSS Enhancers Weak transcription Transcr. at gene 5' and 3' Flanking Active TSS Bivalent Enhancer Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	12 gene(s)	inside rSNPs	diseases
5	nsv533240	chr15:59858093-59998176	Flanking Active TSS Strong transcription Enhancers Weak transcription Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS Genic enhancers ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	30 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs11630029	GTF2A2	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:13 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:59905200-59931600	Weak transcription	Fetal Stomach	stomach
2	chr15:59905200-59946200	Weak transcription	Gastric	stomach
3	chr15:59909000-59930200	Weak transcription	Fetal Intestine Large	intestine
4	chr15:59911400-59929800	Weak transcription	Duodenum Smooth Muscle	Duodenum
5	chr15:59912000-59932600	Weak transcription	Colonic Mucosa	Colon
6	chr15:59912200-59928400	Weak transcription	Rectal Mucosa Donor 29	rectum
7	chr15:59912200-59935000	Weak transcription	Fetal Intestine Small	intestine
8	chr15:59914800-59916200	Weak transcription	Rectal Mucosa Donor 31	rectum
9	chr15:59914800-59937800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
10	chr15:59915000-59919400	Strong transcription	Duodenum Mucosa	Duodenum
11	chr15:59915200-59922200	Weak transcription	Stomach Mucosa	stomach
12	chr15:59915400-59920600	Strong transcription	A549	lung
13	chr15:59915800-59916800	Weak transcription	Sigmoid Colon	Sigmoid Colon

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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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