Variant report

Variant	rs12199067
Chromosome Location	chr6:114762507-114762508
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 84 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:73)

rs_ID	r²[population]
rs1028300	1.00[ASN][1000 genomes]
rs10456892	1.00[CHD][hapmap];0.88[GIH][hapmap];0.85[TSI][hapmap];1.00[ASN][1000 genomes]
rs10457277	1.00[ASN][1000 genomes]
rs10457278	1.00[ASN][1000 genomes]
rs10457279	1.00[ASN][1000 genomes]
rs11153480	1.00[ASN][1000 genomes]
rs11153482	0.81[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs11153483	0.86[CEU][hapmap]
rs11754047	1.00[ASN][1000 genomes]
rs11756498	1.00[ASN][1000 genomes]
rs12189772	1.00[ASN][1000 genomes]
rs12190227	1.00[ASN][1000 genomes]
rs12190524	1.00[ASN][1000 genomes]
rs12190621	1.00[ASN][1000 genomes]
rs12192586	1.00[ASN][1000 genomes]
rs12192949	1.00[ASN][1000 genomes]
rs12194343	1.00[ASN][1000 genomes]
rs12194780	1.00[ASN][1000 genomes]
rs12196148	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12196343	1.00[ASN][1000 genomes]
rs12196684	1.00[ASN][1000 genomes]
rs12196717	1.00[ASN][1000 genomes]
rs12197768	1.00[ASN][1000 genomes]
rs12199428	1.00[ASN][1000 genomes]
rs12202564	1.00[ASN][1000 genomes]
rs12203102	1.00[ASN][1000 genomes]
rs12203297	0.87[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12203473	1.00[ASN][1000 genomes]
rs12203936	1.00[ASN][1000 genomes]
rs12206111	1.00[ASN][1000 genomes]
rs12206217	1.00[ASN][1000 genomes]
rs12207886	0.86[CEU][hapmap]
rs12207904	1.00[ASN][1000 genomes]
rs12207919	1.00[ASN][1000 genomes]
rs12207939	0.86[CEU][hapmap]
rs12208021	1.00[ASN][1000 genomes]
rs12211335	0.81[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs12211634	1.00[ASN][1000 genomes]
rs12211637	1.00[ASN][1000 genomes]
rs12212330	1.00[ASN][1000 genomes]
rs12212361	1.00[ASN][1000 genomes]
rs12214339	1.00[ASN][1000 genomes]
rs12215457	0.93[EUR][1000 genomes]
rs12215919	1.00[ASN][1000 genomes]
rs12216093	1.00[ASN][1000 genomes]
rs13191892	1.00[ASN][1000 genomes]
rs13196504	1.00[ASN][1000 genomes]
rs13210832	1.00[ASN][1000 genomes]
rs13211232	1.00[ASN][1000 genomes]
rs13211367	1.00[ASN][1000 genomes]
rs13211773	1.00[ASN][1000 genomes]
rs13214864	0.87[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1337333	1.00[ASN][1000 genomes]
rs1415427	1.00[ASN][1000 genomes]
rs17076088	1.00[ASN][1000 genomes]
rs34144978	1.00[ASN][1000 genomes]
rs35103890	1.00[ASN][1000 genomes]
rs35633522	1.00[ASN][1000 genomes]
rs35713770	1.00[ASN][1000 genomes]
rs35898688	1.00[ASN][1000 genomes]
rs6568837	1.00[ASN][1000 genomes]
rs66605950	1.00[ASN][1000 genomes]
rs66786400	1.00[ASN][1000 genomes]
rs68097954	1.00[ASN][1000 genomes]
rs71566768	1.00[ASN][1000 genomes]
rs71566769	1.00[ASN][1000 genomes]
rs73546536	0.83[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9384899	1.00[ASN][1000 genomes]
rs9387204	1.00[ASN][1000 genomes]
rs9481447	1.00[ASN][1000 genomes]
rs9481453	0.80[EUR][1000 genomes]
rs9688966	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9689766	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][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	esv34434	chr6:114465305-115462799	Enhancers Weak transcription Bivalent/Poised TSS Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Active TSS Strong transcription Genic enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	36 gene(s)	inside rSNPs	diseases
2	nsv464024	chr6:114489321-114837181	Weak transcription Enhancers Flanking Active TSS Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3' Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	32 gene(s)	inside rSNPs	diseases
3	nsv604544	chr6:114489321-114837181	Enhancers Weak transcription Flanking Bivalent TSS/Enh Active TSS Bivalent/Poised TSS Flanking Active TSS Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3' Strong transcription Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	32 gene(s)	inside rSNPs	diseases
4	esv3692910	chr6:114597419-115480580	Flanking Active TSS Enhancers Bivalent/Poised TSS Active TSS Weak transcription Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer Strong transcription Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	25 gene(s)	inside rSNPs	diseases
5	nsv528128	chr6:114597657-115471129	Enhancers Weak transcription Flanking Active TSS Flanking Bivalent TSS/Enh Active TSS Strong transcription Genic enhancers Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	25 gene(s)	inside rSNPs	diseases
6	nsv818451	chr6:114597657-115471129	Enhancers Bivalent/Poised TSS Bivalent Enhancer Weak transcription Active TSS Transcr. at gene 5' and 3' Flanking Active TSS Strong transcription Flanking Bivalent TSS/Enh ZNF genes & repeats Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	25 gene(s)	inside rSNPs	diseases
7	nsv428494	chr6:114666307-114774841	Weak transcription Enhancers Flanking Active TSS Transcr. at gene 5' and 3' Active TSS Strong transcription Flanking Bivalent TSS/Enh Genic enhancers Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases
8	esv2758074	chr6:114666308-115526957	Enhancers Bivalent Enhancer Weak transcription Active TSS Transcr. at gene 5' and 3' Flanking Active TSS Strong transcription Genic enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	20 gene(s)	inside rSNPs	diseases
9	nsv1030191	chr6:114679497-115228028	Weak transcription Enhancers Active TSS Bivalent Enhancer Strong transcription Flanking Active TSS Transcr. at gene 5' and 3' Genic enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	19 gene(s)	inside rSNPs	diseases
10	nsv538424	chr6:114679497-115228028	Enhancers Flanking Active TSS Weak transcription Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Strong transcription Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	19 gene(s)	inside rSNPs	diseases
11	nsv1025817	chr6:114715204-115006108	Weak transcription Enhancers Bivalent Enhancer Flanking Active TSS Strong transcription Active TSS Transcr. at gene 5' and 3' Genic enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	17 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs12199067	HS3ST5	cis	parietal	SCAN
rs12199067	DCBLD1	cis	cerebellum	SCAN
rs12199067	MARCKS	cis	cerebellum	SCAN

Chromatin state (count:9 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:114752400-114767200	Weak transcription	HUES6 Cell Line	embryonic stem cell
2	chr6:114752800-114770400	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
3	chr6:114758400-114767000	Weak transcription	iPS-15b Cell Line	embryonic stem cell
4	chr6:114758600-114765800	Weak transcription	HUES64 Cell Line	embryonic stem cell
5	chr6:114762200-114762600	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
6	chr6:114762200-114762600	Enhancers	iPS-18 Cell Line	embryonic stem cell
7	chr6:114762200-114762800	Enhancers	HUES48 Cell Line	embryonic stem cell
8	chr6:114762400-114762600	Enhancers	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
9	chr6:114762400-114762600	Enhancers	Psoas Muscle	Psoas

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