Variant report

Variant	rs17610154
Chromosome Location	chr5:1944263-1944264
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 22 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:11)

rs_ID	r²[population]
rs11133926	1.00[CHD][hapmap]
rs11737953	1.00[CEU][hapmap];1.00[CHD][hapmap];0.93[MEX][hapmap];0.90[TSI][hapmap];0.93[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11744276	1.00[CEU][hapmap];0.93[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17538144	1.00[ASN][1000 genomes]
rs17539841	1.00[CHD][hapmap]
rs17610178	1.00[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2353003	1.00[CHD][hapmap]
rs34515565	0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35823958	0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6860447	1.00[CHD][hapmap]
rs71595084	0.81[AMR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:11 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv817407	chr5:1495354-2191460	Weak transcription Strong transcription Enhancers Flanking Active TSS Bivalent/Poised TSS Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA	107 gene(s)	inside rSNPs	diseases
2	nsv869236	chr5:1719263-2259100	Flanking Active TSS Active TSS Bivalent/Poised TSS Bivalent Enhancer Enhancers Weak transcription ZNF genes & repeats Genic enhancers Strong transcription Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	66 gene(s)	inside rSNPs	diseases
3	nsv915846	chr5:1891098-2167677	Active TSS Genic enhancers Enhancers Weak transcription ZNF genes & repeats Bivalent Enhancer Flanking Active TSS Bivalent/Poised TSS Strong transcription Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	21 gene(s)	inside rSNPs	diseases
4	nsv881650	chr5:1892995-1944487	Enhancers Bivalent/Poised TSS Bivalent Enhancer Flanking Active TSS Flanking Bivalent TSS/Enh Weak transcription Active TSS ZNF genes & repeats Strong transcription Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases
5	nsv880653	chr5:1892995-1946697	Enhancers Flanking Bivalent TSS/Enh Flanking Active TSS Bivalent/Poised TSS Weak transcription Bivalent Enhancer Active TSS ZNF genes & repeats Strong transcription Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases
6	nsv880381	chr5:1895829-1946697	Enhancers Flanking Active TSS Weak transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer Active TSS Strong transcription ZNF genes & repeats Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases
7	nsv1026930	chr5:1898993-2126061	Bivalent/Poised TSS Flanking Active TSS Enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Weak transcription Genic enhancers Strong transcription ZNF genes & repeats Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	21 gene(s)	inside rSNPs	diseases
8	nsv508344	chr5:1905222-1976860	Enhancers Active TSS Weak transcription ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Flanking Active TSS Strong transcription Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	15 gene(s)	inside rSNPs	diseases
9	nsv881562	chr5:1907974-1976187	Enhancers Weak transcription Genic enhancers Bivalent Enhancer ZNF genes & repeats Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Flanking Active TSS Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	15 gene(s)	inside rSNPs	diseases
10	nsv880964	chr5:1912921-1953161	Weak transcription ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh Enhancers Active TSS Flanking Active TSS Bivalent Enhancer Strong transcription Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases
11	nsv980962	chr5:1932426-1945863	Enhancers Weak transcription ZNF genes & repeats Strong transcription Active TSS Flanking Active TSS Genic enhancers Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs17610154	SLC12A7	cis	cerebellum	SCAN

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:1932000-1950800	Weak transcription	Gastric	stomach
2	chr5:1932200-1945600	Weak transcription	Right Ventricle	heart
3	chr5:1932200-1946400	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
4	chr5:1935400-1945600	Weak transcription	Left Ventricle	heart
5	chr5:1935600-1950800	Weak transcription	Pancreas	Pancrea
6	chr5:1938200-1948200	Weak transcription	HMEC	breast
7	chr5:1939000-1965600	Weak transcription	Brain Angular Gyrus	brain
8	chr5:1942600-1946600	Weak transcription	Brain Cingulate Gyrus	brain
9	chr5:1942600-1947200	Strong transcription	Breast Myoepithelial Primary Cells	Breast
10	chr5:1942600-1947200	Weak transcription	Duodenum Smooth Muscle	Duodenum
11	chr5:1942600-1953800	Weak transcription	Ovary	ovary
12	chr5:1943400-1944400	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
13	chr5:1944000-1945400	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
14	chr5:1944000-1945600	Weak transcription	Esophagus	oesophagus
15	chr5:1944000-1946600	Enhancers	Fetal Heart	heart
16	chr5:1944200-1944800	Enhancers	NHEK	skin
17	chr5:1944200-1945200	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
18	chr5:1944200-1945600	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
19	chr5:1944200-1945800	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell

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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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