Variant report

Variant	rs13227417
Chromosome Location	chr7:7888862-7888863
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 30 )
Associated
traits (count: 1 )

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

rs_ID	r²[population]
rs11972179	0.85[AFR][1000 genomes];0.85[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs11973875	0.81[CEU][hapmap];0.85[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs11982917	0.88[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs17494879	0.91[CEU][hapmap];0.88[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs17494974	0.81[CEU][hapmap];0.83[MKK][hapmap];0.85[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs17560422	0.83[CEU][hapmap]
rs17560750	0.89[CEU][hapmap];0.88[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs17562193	0.85[AFR][1000 genomes];0.85[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs34716105	0.88[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs34965254	0.85[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs35002430	0.82[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs35191635	0.88[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs55643119	0.82[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs56299844	0.85[AFR][1000 genomes];0.85[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs741048	0.85[AMR][1000 genomes];0.85[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:15 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1026758	chr7:7187491-8075259	Weak transcription Enhancers Strong transcription Flanking Active TSS Genic enhancers Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	84 gene(s)	inside rSNPs	diseases
2	nsv1032670	chr7:7535515-8017077	Active TSS Weak transcription Enhancers Flanking Active TSS Strong transcription ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	59 gene(s)	inside rSNPs	diseases
3	nsv887478	chr7:7670718-7917360	Enhancers Active TSS Weak transcription Flanking Active TSS ZNF genes & repeats Genic enhancers Strong transcription Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	35 gene(s)	inside rSNPs	diseases
4	nsv887480	chr7:7681131-7917360	Weak transcription Strong transcription Enhancers Active TSS Flanking Active TSS Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	16 gene(s)	inside rSNPs	diseases
5	nsv887485	chr7:7692483-7917360	Enhancers Weak transcription Strong transcription Active TSS Flanking Active TSS ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	12 gene(s)	inside rSNPs	diseases
6	esv2752177	chr7:7729247-8177689	Weak transcription Enhancers Transcr. at gene 5' and 3' Strong transcription Active TSS Flanking Active TSS ZNF genes & repeats Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	31 gene(s)	inside rSNPs	diseases
7	nsv1026564	chr7:7734846-7897847	Enhancers Weak transcription Flanking Active TSS Active TSS Bivalent Enhancer ZNF genes & repeats Strong transcription Genic enhancers Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	12 gene(s)	inside rSNPs	diseases
8	nsv887489	chr7:7770203-7913311	Enhancers Flanking Active TSS Weak transcription ZNF genes & repeats Strong transcription Active TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	12 gene(s)	inside rSNPs	diseases
9	nsv1027770	chr7:7797431-7957507	Weak transcription Enhancers Flanking Active TSS Active TSS ZNF genes & repeats Strong transcription Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases
10	nsv538722	chr7:7797431-7957507	Weak transcription Enhancers Active TSS Flanking Active TSS Strong transcription ZNF genes & repeats Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases
11	nsv887490	chr7:7801684-7908970	Weak transcription Enhancers ZNF genes & repeats Flanking Active TSS Active TSS Genic enhancers Strong transcription	TF binding region CpG island Chromatin interactive region	10 gene(s)	inside rSNPs	diseases
12	nsv523479	chr7:7821594-7909899	ZNF genes & repeats Weak transcription Active TSS Enhancers Flanking Active TSS Strong transcription Genic enhancers	Chromatin interactive region	8 gene(s)	inside rSNPs	diseases
13	nsv917172	chr7:7854632-8807385	Weak transcription Flanking Active TSS Enhancers Strong transcription Active TSS Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	56 gene(s)	inside rSNPs	diseases
14	nsv1030180	chr7:7860424-8059221	Flanking Active TSS ZNF genes & repeats Weak transcription Active TSS Enhancers Bivalent/Poised TSS Bivalent Enhancer Strong transcription Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	25 gene(s)	inside rSNPs	diseases
15	nsv1027123	chr7:7870047-7926288	Weak transcription Enhancers ZNF genes & repeats Flanking Active TSS Strong transcription Active TSS	Chromatin interactive region	4 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs13227417	TNRC18	cis	parietal	SCAN

Chromatin state (count:18 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr7:7870000-7900400	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
2	chr7:7884200-7891000	Weak transcription	Placenta Amnion	Placenta Amnion
3	chr7:7884800-7894000	Weak transcription	Thymus	Thymus
4	chr7:7885000-7892000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
5	chr7:7887200-7889400	Enhancers	Primary T killer naive cells fromperipheralblood	blood
6	chr7:7887400-7889000	Weak transcription	Small Intestine	intestine
7	chr7:7887600-7889000	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
8	chr7:7887600-7891000	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
9	chr7:7888200-7890800	Weak transcription	Primary T helper cells PMA-I stimulated	--
10	chr7:7888200-7890800	Weak transcription	Dnd41	blood
11	chr7:7888200-7891000	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
12	chr7:7888200-7894200	Weak transcription	Primary T helper cells fromperipheralblood	blood
13	chr7:7888400-7891000	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
14	chr7:7888400-7892000	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
15	chr7:7888800-7889000	Enhancers	Primary T helper naive cells from peripheral blood	blood
16	chr7:7888800-7889200	Enhancers	Hela-S3	cervix
17	chr7:7888800-7891000	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
18	chr7:7888800-7894000	Weak transcription	Primary T cells from cord blood	blood

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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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