Variant report

Variant	rs12301777
Chromosome Location	chr12:38938138-38938139
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-CPNE8-1	chr12:38938130-38938378	ENSG00000258119
2	lnc-CPNE8-1	chr12:38937979-38938333	ENSG00000258119
3	lnc-CPNE8-1	chr12:38937980-38938333	XLOC_010050

Extended variants
information (count: 42 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:25)

rs_ID	r²[population]
rs10881055	1.00[AMR][1000 genomes]
rs11169051	1.00[AMR][1000 genomes]
rs11183525	0.85[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs11183526	1.00[AMR][1000 genomes]
rs11183604	1.00[AMR][1000 genomes]
rs11183670	1.00[AMR][1000 genomes]
rs11504530	1.00[AMR][1000 genomes]
rs11831125	1.00[AMR][1000 genomes]
rs12299514	1.00[AMR][1000 genomes]
rs12305207	1.00[AMR][1000 genomes]
rs12308044	1.00[MEX][hapmap]
rs12309042	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs12310370	1.00[AMR][1000 genomes]
rs12311146	1.00[AMR][1000 genomes]
rs12316183	1.00[YRI][hapmap]
rs12316464	1.00[AMR][1000 genomes]
rs12317882	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs12319122	1.00[AMR][1000 genomes]
rs12320497	1.00[ASW][hapmap];1.00[MEX][hapmap];1.00[YRI][hapmap];1.00[AMR][1000 genomes]
rs13377614	1.00[AMR][1000 genomes]
rs61552146	1.00[AMR][1000 genomes]
rs7484905	1.00[AMR][1000 genomes]
rs7487322	1.00[AMR][1000 genomes]
rs7488546	1.00[AMR][1000 genomes]
rs9325221	1.00[AMR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:17 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv2422488	chr12:38103874-39070734	ZNF genes & repeats Active TSS Weak transcription Enhancers Flanking Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS Strong transcription Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	29 gene(s)	inside rSNPs	diseases
2	nsv898992	chr12:38106133-38959053	Enhancers ZNF genes & repeats Weak transcription Flanking Active TSS Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Strong transcription Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	24 gene(s)	inside rSNPs	diseases
3	nsv1047388	chr12:38169669-38949760	Bivalent Enhancer Flanking Active TSS Enhancers Weak transcription Active TSS ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh Strong transcription Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	24 gene(s)	inside rSNPs	diseases
4	nsv469356	chr12:38242029-39187408	Weak transcription Active TSS ZNF genes & repeats Enhancers Strong transcription Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	30 gene(s)	inside rSNPs	diseases
5	nsv558574	chr12:38242029-39187408	Strong transcription ZNF genes & repeats Enhancers Weak transcription Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Flanking Active TSS Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	30 gene(s)	inside rSNPs	diseases
6	nsv826332	chr12:38442547-38958438	Bivalent Enhancer Enhancers Flanking Active TSS Active TSS ZNF genes & repeats Weak transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS Strong transcription Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	24 gene(s)	inside rSNPs	diseases
7	nsv1046439	chr12:38453609-38956518	ZNF genes & repeats Flanking Active TSS Weak transcription Enhancers Flanking Bivalent TSS/Enh Active TSS Bivalent Enhancer Strong transcription Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	24 gene(s)	inside rSNPs	diseases
8	nsv541475	chr12:38453609-38956518	Enhancers Active TSS Bivalent/Poised TSS Weak transcription ZNF genes & repeats Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Strong transcription Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	24 gene(s)	inside rSNPs	diseases
9	nsv1039179	chr12:38453609-39029275	Enhancers ZNF genes & repeats Bivalent/Poised TSS Flanking Active TSS Weak transcription Active TSS Bivalent Enhancer Strong transcription Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	27 gene(s)	inside rSNPs	diseases
10	nsv541476	chr12:38453609-39029275	Active TSS Enhancers Flanking Bivalent TSS/Enh Flanking Active TSS ZNF genes & repeats Weak transcription Bivalent Enhancer Bivalent/Poised TSS Strong transcription Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	27 gene(s)	inside rSNPs	diseases
11	nsv1039538	chr12:38640895-39180750	Weak transcription Flanking Active TSS Strong transcription Active TSS Enhancers ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	18 gene(s)	inside rSNPs	diseases
12	nsv916679	chr12:38805678-38963660	Enhancers Weak transcription Flanking Active TSS Active TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
13	nsv1048325	chr12:38820721-38959645	Weak transcription Enhancers Active TSS Flanking Active TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
14	nsv1040304	chr12:38908242-38995786	Enhancers Flanking Active TSS Weak transcription Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases
15	nsv1046817	chr12:38909036-38995330	Enhancers Weak transcription Flanking Active TSS Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases
16	nsv469358	chr12:38919524-38989405	Enhancers Weak transcription Active TSS Flanking Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases
17	nsv558582	chr12:38919524-38989405	Enhancers Weak transcription Flanking Active TSS Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases

No data

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:38936000-38938400	Enhancers	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
2	chr12:38936200-38938400	Enhancers	HUES48 Cell Line	embryonic stem cell
3	chr12:38936400-38938600	Enhancers	ES-I3 Cell Line	embryonic stem cell
4	chr12:38936400-38939000	Enhancers	HUES6 Cell Line	embryonic stem cell
5	chr12:38936400-38939000	Enhancers	iPS-15b Cell Line	embryonic stem cell
6	chr12:38936800-38939000	Enhancers	HUES64 Cell Line	embryonic stem cell
7	chr12:38936800-38939000	Enhancers	iPS-18 Cell Line	embryonic stem cell
8	chr12:38937200-38938600	Enhancers	H9 Cell Line	embryonic stem cell
9	chr12:38937200-38938600	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
10	chr12:38937200-38939000	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
11	chr12:38937400-38939000	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
12	chr12:38937400-38941000	Weak transcription	Hela-S3	cervix
13	chr12:38937600-38938200	Weak transcription	H1 Cell Line	embryonic stem cell
14	chr12:38937800-38939000	Enhancers	Colon Smooth Muscle	Colon
15	chr12:38938000-38938200	Flanking Active TSS	iPS-20b Cell Line	embryonic stem cell
16	chr12:38938000-38938400	Active TSS	Duodenum Smooth Muscle	Duodenum

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