Variant report

Variant	rs16894533
Chromosome Location	chr6:28945522-28945523
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr6:28890727..28894097-chr6:28943047..28947323,5	MCF-7	breast:
2	chr6:28907253..28915101-chr6:28945522..28952393,17	K562	blood:
3	chr6:28905933..28927444-chr6:28943937..28954526,53	K562	blood:
4	chr6:28888560..28894615-chr6:28945306..28952099,20	K562	blood:

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-C6orf100-14	chr6:28945252-28945547	NONHSAT108499

Variant related genes	Relation type
ENSG00000204713	Chromatin interaction
ENSG00000204709	Chromatin interaction

Extended variants
information (count: 35 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:24)

rs_ID	r²[population]
rs10484544	0.81[AMR][1000 genomes];0.88[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs12663679	0.83[AMR][1000 genomes];0.90[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs12663717	0.83[AFR][1000 genomes];0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12665108	0.83[EUR][1000 genomes]
rs16894540	0.83[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs16894554	0.81[AMR][1000 genomes];0.88[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2269554	0.81[AMR][1000 genomes];0.88[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2394546	0.81[EUR][1000 genomes]
rs28796930	0.85[EUR][1000 genomes]
rs3116845	0.87[EUR][1000 genomes]
rs3130719	0.88[EUR][1000 genomes]
rs56080800	0.87[ASN][1000 genomes]
rs56131223	0.81[AMR][1000 genomes];0.89[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs57232568	0.81[AMR][1000 genomes];0.84[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs57332439	0.88[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs58065505	0.86[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs58836159	0.90[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs58912940	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs61554786	0.82[AMR][1000 genomes];0.90[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs62407578	0.83[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs62407581	0.83[AFR][1000 genomes];0.99[AMR][1000 genomes];0.94[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs62407603	0.81[AMR][1000 genomes];0.88[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs62407619	0.88[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs736467	0.81[EUR][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	nsv427748	chr6:28831888-28999434	Weak transcription Flanking Active TSS Enhancers Active TSS ZNF genes & repeats Strong transcription Bivalent/Poised TSS Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	62 gene(s)	inside rSNPs	diseases
2	nsv830622	chr6:28861667-29015804	Flanking Active TSS Active TSS Bivalent/Poised TSS Enhancers Bivalent Enhancer Weak transcription Flanking Bivalent TSS/Enh Strong transcription Transcr. at gene 5' and 3' ZNF genes & repeats Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	59 gene(s)	inside rSNPs	diseases
3	nsv1023540	chr6:28922691-29326018	Active TSS Bivalent/Poised TSS Enhancers Strong transcription Flanking Active TSS Weak transcription Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	46 gene(s)	inside rSNPs	diseases
4	nsv538169	chr6:28922691-29326018	Bivalent Enhancer Weak transcription Active TSS Flanking Active TSS Bivalent/Poised TSS Enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Strong transcription Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	46 gene(s)	inside rSNPs	diseases
5	nsv869541	chr6:28922692-29326017	Flanking Active TSS Bivalent/Poised TSS Enhancers Bivalent Enhancer Active TSS Strong transcription ZNF genes & repeats Weak transcription Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	46 gene(s)	inside rSNPs	diseases
6	nsv916439	chr6:28922697-29326087	Weak transcription Active TSS Flanking Active TSS Enhancers Bivalent Enhancer Strong transcription Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	46 gene(s)	inside rSNPs	diseases
7	nsv462668	chr6:28922719-29342775	Enhancers Flanking Active TSS Weak transcription Active TSS Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	46 gene(s)	inside rSNPs	diseases
8	nsv601213	chr6:28922719-29342775	Weak transcription Enhancers Flanking Bivalent TSS/Enh Active TSS Flanking Active TSS Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3' Genic enhancers Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	46 gene(s)	inside rSNPs	diseases
9	nsv1015796	chr6:28923980-29342825	Enhancers Flanking Bivalent TSS/Enh Flanking Active TSS Active TSS Weak transcription ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Strong transcription Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	45 gene(s)	inside rSNPs	diseases
10	nsv462669	chr6:28936556-29337500	Weak transcription Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Enhancers ZNF genes & repeats Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3' Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	45 gene(s)	inside rSNPs	diseases
11	nsv601214	chr6:28936556-29337500	Enhancers ZNF genes & repeats Active TSS Flanking Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Weak transcription Strong transcription Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	45 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:91 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:28943200-28945800	Weak transcription	HepG2	liver
2	chr6:28944800-28945600	Active TSS	ES-I3 Cell Line	embryonic stem cell
3	chr6:28944800-28945600	Bivalent/Poised TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
4	chr6:28944800-28945600	Bivalent/Poised TSS	HUES64 Cell Line	embryonic stem cell
5	chr6:28944800-28945600	Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
6	chr6:28944800-28945600	Enhancers	K562	blood
7	chr6:28944800-28945800	Active TSS	H1 Cell Line	embryonic stem cell
8	chr6:28944800-28945800	Bivalent/Poised TSS	iPS-18 Cell Line	embryonic stem cell
9	chr6:28944800-28945800	Active TSS	iPS DF 6.9 Cell Line	embryonic stem cell
10	chr6:28944800-28945800	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
11	chr6:28944800-28945800	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Female	--
12	chr6:28944800-28945800	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
13	chr6:28944800-28945800	Active TSS	Brain Anterior Caudate	brain
14	chr6:28944800-28945800	Active TSS	NHDF-Ad	bronchial
15	chr6:28944800-28946000	Enhancers	Primary T killer memory cells from peripheral blood	blood
16	chr6:28944800-28946200	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
17	chr6:28944800-28946400	Flanking Active TSS	Monocytes-CD14+_RO01746	blood
18	chr6:28945000-28945600	Active TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
19	chr6:28945000-28945600	Bivalent/Poised TSS	HUES48 Cell Line	embryonic stem cell
20	chr6:28945000-28945600	Active TSS	IMR90 fetal lung fibroblasts Cell Line	lung
21	chr6:28945000-28945600	Active TSS	ES-UCSF4 Cell Line	embryonic stem cell
22	chr6:28945000-28945600	Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
23	chr6:28945000-28945600	Flanking Bivalent TSS/Enh	Primary T cells fromperipheralblood	blood
24	chr6:28945000-28945600	Flanking Active TSS	Primary T cells effector/memory enriched fromperipheralblood	blood
25	chr6:28945000-28945600	Flanking Bivalent TSS/Enh	Primary Natural Killer cells fromperipheralblood	blood
26	chr6:28945000-28945600	Flanking Bivalent TSS/Enh	Cortex derived primary cultured neurospheres	brain
27	chr6:28945000-28945600	Active TSS	Ganglion Eminence derived primary cultured neurospheres	brain
28	chr6:28945000-28945600	Active TSS	Foreskin Fibroblast Primary Cells skin02	Skin
29	chr6:28945000-28945600	Bivalent/Poised TSS	Brain Germinal Matrix	brain
30	chr6:28945000-28945600	Active TSS	Brain Hippocampus Middle	brain
31	chr6:28945000-28945600	Active TSS	Brain Inferior Temporal Lobe	brain
32	chr6:28945000-28945600	Active TSS	Brain Dorsolateral Prefrontal Cortex	brain
33	chr6:28945000-28945600	Active TSS	Duodenum Mucosa	Duodenum
34	chr6:28945000-28945600	Active TSS	Placenta Amnion	Placenta Amnion
35	chr6:28945000-28945800	Active TSS	H9 Cell Line	embryonic stem cell
36	chr6:28945000-28945800	Bivalent/Poised TSS	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
37	chr6:28945000-28945800	Active TSS	HUES6 Cell Line	embryonic stem cell
38	chr6:28945000-28945800	Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
39	chr6:28945000-28945800	Flanking Active TSS	Primary neutrophils fromperipheralblood	blood
40	chr6:28945000-28945800	Flanking Bivalent TSS/Enh	Primary B cells from cord blood	blood
41	chr6:28945000-28945800	Active TSS	Primary T killer naive cells fromperipheralblood	blood
42	chr6:28945000-28945800	Active TSS	Foreskin Melanocyte Primary Cells skin01	Skin
43	chr6:28945000-28945800	Flanking Active TSS	Placenta	Placenta
44	chr6:28945000-28945800	Bivalent/Poised TSS	Psoas Muscle	Psoas
45	chr6:28945000-28945800	Active TSS	Rectal Mucosa Donor 29	rectum
46	chr6:28945000-28945800	Flanking Active TSS	HUVEC	blood vessel
47	chr6:28945000-28946000	Bivalent/Poised TSS	Primary T cells from cord blood	blood
48	chr6:28945000-28946000	Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
49	chr6:28945000-28946200	Flanking Active TSS	Foreskin Melanocyte Primary Cells skin03	Skin
50	chr6:28945000-28946400	Enhancers	HMEC	breast

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