Variant report

Variant	rs12953115
Chromosome Location	chr17:33797534-33797535
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-SLFN12L-2	chr17:33797088-33797647	NONHSAT053099

Extended variants
information (count: 54 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:48)

rs_ID	r²[population]
rs11650225	1.00[CHB][hapmap]
rs11655098	1.00[CHB][hapmap]
rs11656872	1.00[CHB][hapmap]
rs12449487	0.85[AMR][1000 genomes];0.86[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs12451876	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];0.96[TSI][hapmap];1.00[YRI][hapmap];0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12936256	0.88[EUR][1000 genomes]
rs12936954	0.86[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs12937961	0.88[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12939675	0.84[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs12940584	1.00[CHB][hapmap]
rs12943224	1.00[CHB][hapmap]
rs12943866	1.00[JPT][hapmap]
rs12949245	0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1350010	1.00[CHB][hapmap]
rs17606150	1.00[CHB][hapmap]
rs17669281	1.00[CHB][hapmap]
rs2304967	0.93[CEU][hapmap];0.84[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs34048495	0.80[AMR][1000 genomes];0.83[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs34121367	0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34620580	0.82[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs34646901	0.84[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs34656640	0.84[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs34734788	0.95[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34747751	0.94[EUR][1000 genomes]
rs34787927	0.81[EUR][1000 genomes]
rs35057074	1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3506	1.00[CHB][hapmap]
rs35210090	0.80[AMR][1000 genomes];0.86[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs35367381	0.84[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs35563348	0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35863546	0.80[AMR][1000 genomes];0.86[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs35927274	0.84[AFR][1000 genomes]
rs3744372	1.00[CEU][hapmap];0.85[GIH][hapmap];0.90[MEX][hapmap];0.89[TSI][hapmap];0.84[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs4239251	0.87[EUR][1000 genomes]
rs55668225	0.84[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs56033496	0.84[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs56061417	1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs67338337	0.84[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs67536209	0.82[EUR][1000 genomes]
rs7216628	1.00[CHB][hapmap]
rs72825999	0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs72826000	0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs8064887	0.84[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs8065289	0.84[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs8066132	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs8072477	1.00[CEU][hapmap];0.90[TSI][hapmap];0.86[EUR][1000 genomes]
rs8079653	0.84[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs8082478	0.84[AMR][1000 genomes];0.94[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	nsv1055936	chr17:33327166-33884184	Strong transcription Weak transcription Flanking Active TSS Bivalent/Poised TSS Enhancers Genic enhancers Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	112 gene(s)	inside rSNPs	diseases
2	nsv543317	chr17:33327166-33884184	Active TSS Weak transcription Enhancers Flanking Active TSS Strong transcription Bivalent Enhancer Bivalent/Poised TSS Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	112 gene(s)	inside rSNPs	diseases
3	nsv534371	chr17:33456878-34094068	Strong transcription Enhancers Weak transcription Bivalent Enhancer Flanking Active TSS Flanking Bivalent TSS/Enh Active TSS Bivalent/Poised TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	137 gene(s)	inside rSNPs	diseases
4	nsv574741	chr17:33552275-33827134	Bivalent/Poised TSS Active TSS Enhancers Flanking Active TSS Weak transcription ZNF genes & repeats Genic enhancers Flanking Bivalent TSS/Enh Strong transcription Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	72 gene(s)	inside rSNPs	diseases
5	nsv1056116	chr17:33691457-33815452	Weak transcription Bivalent/Poised TSS Flanking Active TSS Flanking Bivalent TSS/Enh Active TSS Enhancers Bivalent Enhancer Strong transcription ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	21 gene(s)	inside rSNPs	diseases
6	esv3432530	chr17:33738621-33802241	Flanking Active TSS Strong transcription Bivalent/Poised TSS Enhancers Bivalent Enhancer Weak transcription Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	15 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs12953115	EFCAB5	cis	cerebellum	SCAN

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr17:33791200-33801200	Weak transcription	Dnd41	blood
2	chr17:33794600-33797600	Enhancers	Primary T helper 17 cells PMA-I stimulated	--
3	chr17:33796000-33800400	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
4	chr17:33796000-33801000	Weak transcription	Primary T helper cells fromperipheralblood	blood
5	chr17:33796000-33801200	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
6	chr17:33796000-33803000	Weak transcription	Fetal Thymus	thymus
7	chr17:33796200-33801000	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
8	chr17:33796200-33801200	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
9	chr17:33796600-33800800	Weak transcription	Fetal Lung	lung
10	chr17:33796800-33800600	Weak transcription	Primary T helper cells PMA-I stimulated	--
11	chr17:33796800-33802000	Weak transcription	Primary T killer memory cells from peripheral blood	blood
12	chr17:33797000-33800800	Weak transcription	Primary T cells fromperipheralblood	blood
13	chr17:33797000-33800800	Weak transcription	Primary T helper naive cells from peripheral blood	blood
14	chr17:33797200-33797600	ZNF genes & repeats	Primary Natural Killer cells fromperipheralblood	blood
15	chr17:33797400-33800800	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
16	chr17:33797400-33801000	Weak transcription	Primary T helper naive cells fromperipheralblood	blood

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