Variant report

Variant	rs12215012
Chromosome Location	chr6:27507494-27507495
allele	C/G
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:18)

rs_ID	r²[population]
rs10807029	0.82[EUR][1000 genomes]
rs10946935	0.90[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs10946936	0.90[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs10946940	0.86[EUR][1000 genomes]
rs12208078	0.90[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs13201411	0.90[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4272217	0.80[ASN][1000 genomes]
rs4713112	0.88[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs62401383	0.85[EUR][1000 genomes]
rs6456799	0.82[EUR][1000 genomes]
rs67734963	0.87[AFR][1000 genomes];0.82[AMR][1000 genomes];0.88[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs6915266	0.87[AFR][1000 genomes];0.88[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs6915987	0.81[EUR][1000 genomes]
rs6921256	0.81[EUR][1000 genomes]
rs6933926	0.83[ASN][1000 genomes]
rs6934437	0.82[ASN][1000 genomes]
rs7764081	0.82[ASN][1000 genomes]
rs9393830	0.80[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:12 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1022797	chr6:27396961-27864277	Enhancers Weak transcription Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Flanking Active TSS Active TSS ZNF genes & repeats Strong transcription Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	390 gene(s)	inside rSNPs	diseases
2	nsv830617	chr6:27424769-27598595	Active TSS Enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats Weak transcription Bivalent/Poised TSS Flanking Active TSS Strong transcription Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	35 gene(s)	inside rSNPs	diseases
3	nsv462665	chr6:27458013-27547792	Weak transcription Active TSS Enhancers Flanking Active TSS Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	23 gene(s)	inside rSNPs	diseases
4	nsv601203	chr6:27458013-27547792	Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh Enhancers Bivalent Enhancer Weak transcription Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	23 gene(s)	inside rSNPs	diseases
5	nsv1030256	chr6:27477726-27605842	Bivalent Enhancer Active TSS Enhancers Flanking Bivalent TSS/Enh Weak transcription Bivalent/Poised TSS Flanking Active TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	25 gene(s)	inside rSNPs	diseases
6	nsv1025862	chr6:27480227-27605321	Active TSS Bivalent Enhancer Enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Weak transcription Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	25 gene(s)	inside rSNPs	diseases
7	nsv1017347	chr6:27483816-27605842	Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Active TSS Bivalent Enhancer Weak transcription Enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	25 gene(s)	inside rSNPs	diseases
8	nsv1025572	chr6:27487852-27604454	Active TSS Weak transcription Enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS Flanking Active TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	25 gene(s)	inside rSNPs	diseases
9	nsv538167	chr6:27487852-27604454	Flanking Bivalent TSS/Enh Flanking Active TSS Bivalent Enhancer Active TSS Bivalent/Poised TSS Enhancers Weak transcription ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	25 gene(s)	inside rSNPs	diseases
10	nsv883509	chr6:27492906-27586181	Bivalent Enhancer Flanking Active TSS Enhancers Bivalent/Poised TSS Weak transcription Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	24 gene(s)	inside rSNPs	diseases
11	nsv1018107	chr6:27503525-27596736	Flanking Active TSS Bivalent Enhancer Enhancers Active TSS Bivalent/Poised TSS Weak transcription Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	24 gene(s)	inside rSNPs	diseases
12	nsv538168	chr6:27503525-27596736	Enhancers Bivalent/Poised TSS Active TSS Weak transcription Flanking Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	24 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs12215012	AL022393.7	cis	Muscle Skeletal	GTEx

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:27501400-27511600	Weak transcription	HMEC	breast
2	chr6:27501800-27508600	Weak transcription	K562	blood
3	chr6:27506200-27507600	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
4	chr6:27506600-27507600	Active TSS	iPS-15b Cell Line	embryonic stem cell
5	chr6:27506600-27508000	Active TSS	HUES64 Cell Line	embryonic stem cell
6	chr6:27507000-27507600	Active TSS	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
7	chr6:27507000-27507600	Active TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
8	chr6:27507000-27507600	Active TSS	iPS-18 Cell Line	embryonic stem cell
9	chr6:27507000-27507600	Active TSS	iPS-20b Cell Line	embryonic stem cell
10	chr6:27507000-27507800	Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
11	chr6:27507000-27507800	Active TSS	HUES48 Cell Line	embryonic stem cell
12	chr6:27507000-27508000	Active TSS	HUES6 Cell Line	embryonic stem cell
13	chr6:27507000-27508000	Active TSS	A549	lung
14	chr6:27507000-27509200	Active TSS	H9 Cell Line	embryonic stem cell
15	chr6:27507000-27510000	Active TSS	ES-I3 Cell Line	embryonic stem cell
16	chr6:27507200-27507800	Active TSS	Placenta	Placenta
17	chr6:27507400-27507600	Flanking Active TSS	H1 Cell Line	embryonic stem cell
18	chr6:27507400-27507600	Flanking Bivalent TSS/Enh	Foreskin Keratinocyte Primary Cells skin03	Skin

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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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