Variant report

Variant	rs16867858
Chromosome Location	chr6:27529509-27529510
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr6:27098876..27101009-chr6:27528408..27531042,2	K562	blood:

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-ZNF184-4	chr6:27529140-27529523	NONHSAT108387

Variant related genes	Relation type
ENSG00000196787	Chromatin interaction
ENSG00000124635	Chromatin interaction

Extended variants
information (count: 41 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:29)

rs_ID	r²[population]
rs12111051	1.00[EUR][1000 genomes]
rs16867899	1.00[EUR][1000 genomes]
rs16867901	1.00[TSI][hapmap];1.00[EUR][1000 genomes]
rs16867911	1.00[MEX][hapmap];1.00[TSI][hapmap]
rs16899778	0.82[ASW][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap]
rs55768730	1.00[EUR][1000 genomes]
rs55965630	1.00[EUR][1000 genomes]
rs55987929	1.00[EUR][1000 genomes]
rs56221999	1.00[EUR][1000 genomes]
rs58359716	1.00[EUR][1000 genomes]
rs6456800	1.00[EUR][1000 genomes]
rs6904979	1.00[ASW][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.92[YRI][hapmap];1.00[EUR][1000 genomes]
rs73739106	1.00[AMR][1000 genomes]
rs73739117	1.00[EUR][1000 genomes]
rs73739122	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs73739150	1.00[EUR][1000 genomes]
rs73739606	1.00[EUR][1000 genomes]
rs73739685	1.00[EUR][1000 genomes]
rs73739750	1.00[EUR][1000 genomes]
rs73740805	1.00[EUR][1000 genomes]
rs73742455	1.00[EUR][1000 genomes]
rs766093	1.00[TSI][hapmap]
rs7758568	1.00[TSI][hapmap]
rs7765353	1.00[MEX][hapmap];1.00[TSI][hapmap]
rs7768826	1.00[MEX][hapmap];1.00[TSI][hapmap]
rs9295739	1.00[TSI][hapmap];1.00[EUR][1000 genomes]
rs9461396	1.00[EUR][1000 genomes]
rs9468189	1.00[EUR][1000 genomes]
rs9468190	1.00[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
rs16867858	Hs.158943	cis	multi-tissue	Pritchard

Chromatin state (count:27 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:27526600-27533400	Weak transcription	GM12878-XiMat	blood
2	chr6:27527000-27529800	Weak transcription	K562	blood
3	chr6:27528400-27530200	Bivalent/Poised TSS	iPS-15b Cell Line	embryonic stem cell
4	chr6:27528800-27530000	Active TSS	H1 Cell Line	embryonic stem cell
5	chr6:27528800-27530200	Active TSS	H9 Cell Line	embryonic stem cell
6	chr6:27528800-27530200	Active TSS	iPS DF 19.11 Cell Line	embryonic stem cell
7	chr6:27528800-27530400	Bivalent/Poised TSS	HUES6 Cell Line	embryonic stem cell
8	chr6:27529000-27530000	Bivalent/Poised TSS	iPS-20b Cell Line	embryonic stem cell
9	chr6:27529000-27530000	Active TSS	iPS DF 6.9 Cell Line	embryonic stem cell
10	chr6:27529000-27530000	Active TSS	ES-UCSF4 Cell Line	embryonic stem cell
11	chr6:27529000-27530200	Bivalent/Poised TSS	HUES64 Cell Line	embryonic stem cell
12	chr6:27529000-27530200	Bivalent/Poised TSS	iPS-18 Cell Line	embryonic stem cell
13	chr6:27529000-27530400	Active TSS	HUES48 Cell Line	embryonic stem cell
14	chr6:27529200-27529600	Bivalent/Poised TSS	ES-I3 Cell Line	embryonic stem cell
15	chr6:27529200-27529600	Bivalent/Poised TSS	ES-WA7 Cell Line	embryonic stem cell
16	chr6:27529200-27529800	Active TSS	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
17	chr6:27529200-27529800	Bivalent Enhancer	Foreskin Fibroblast Primary Cells skin01	Skin
18	chr6:27529200-27530000	Bivalent/Poised TSS	Foreskin Keratinocyte Primary Cells skin02	Skin
19	chr6:27529200-27530200	Bivalent/Poised TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
20	chr6:27529200-27530400	Active TSS	A549	lung
21	chr6:27529400-27529600	Bivalent Enhancer	Foreskin Melanocyte Primary Cells skin03	Skin
22	chr6:27529400-27529600	Flanking Bivalent TSS/Enh	HepG2	liver
23	chr6:27529400-27529600	Flanking Active TSS	HMEC	breast
24	chr6:27529400-27529600	Bivalent/Poised TSS	NHEK	skin
25	chr6:27529400-27529800	Flanking Bivalent TSS/Enh	Foreskin Keratinocyte Primary Cells skin03	Skin
26	chr6:27529400-27530000	Bivalent/Poised TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
27	chr6:27529400-27530200	Bivalent/Poised TSS	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived

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