Variant report

Variant	rs16894191
Chromosome Location	chr6:28641689-28641690
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr6:28615726..28617849-chr6:28641065..28643260,2	MCF-7	breast:
2	chr6:27801448..27804005-chr6:28640638..28642144,2	K562	blood:
3	chr6:28640241..28643540-chr6:28644556..28647910,4	K562	blood:
4	chr6:28458124..28459784-chr6:28640264..28642062,2	K562	blood:
5	chr6:28507775..28510636-chr6:28641558..28643450,2	K562	blood:
6	chr6:28623399..28625951-chr6:28639865..28642751,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000272278	Chromatin interaction
ENSG00000235570	Chromatin interaction

Extended variants
information (count: 40 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:37)

rs_ID	r²[population]
rs10738069	0.88[EUR][1000 genomes]
rs10807034	0.80[EUR][1000 genomes]
rs10807035	0.82[EUR][1000 genomes]
rs10807039	0.88[EUR][1000 genomes]
rs12662929	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs16894166	0.95[ASN][1000 genomes]
rs16894169	0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs16894171	1.00[AFR][1000 genomes];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2057296	0.84[AFR][1000 genomes];0.84[EUR][1000 genomes]
rs4711173	0.81[ASN][1000 genomes]
rs4711178	0.87[AFR][1000 genomes]
rs4713173	0.93[AFR][1000 genomes];0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4713175	0.89[AFR][1000 genomes]
rs4947335	1.00[AFR][1000 genomes];0.93[AMR][1000 genomes];0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs55776584	0.89[AFR][1000 genomes]
rs55963280	0.96[AFR][1000 genomes];0.93[AMR][1000 genomes];0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs56227726	0.80[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs58490223	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs62402376	0.81[ASN][1000 genomes]
rs62402378	0.86[ASN][1000 genomes]
rs62402390	0.84[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs62402392	1.00[AFR][1000 genomes];0.93[AMR][1000 genomes];0.94[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs62402394	0.98[AFR][1000 genomes];0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs62402400	0.94[AFR][1000 genomes];0.82[EUR][1000 genomes]
rs62406542	0.96[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs62406553	0.81[AMR][1000 genomes];0.89[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6456824	0.83[ASN][1000 genomes]
rs6942252	0.87[ASN][1000 genomes]
rs72850099	0.96[ASN][1000 genomes]
rs732395	0.89[EUR][1000 genomes]
rs7743296	0.96[AFR][1000 genomes];0.85[EUR][1000 genomes]
rs7746909	0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7748225	0.87[EUR][1000 genomes]
rs7748643	0.81[ASN][1000 genomes]
rs7760867	0.89[EUR][1000 genomes]
rs7767144	0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs9295775	0.82[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv830621	chr6:28473951-28675709	Bivalent/Poised TSS Weak transcription Enhancers Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Flanking Active TSS Transcr. at gene 5' and 3' Strong transcription Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	30 gene(s)	inside rSNPs	diseases
2	nsv1031671	chr6:28575172-28678126	Active TSS Enhancers Flanking Bivalent TSS/Enh Flanking Active TSS Bivalent/Poised TSS Bivalent Enhancer Weak transcription ZNF genes & repeats Transcr. at gene 5' and 3' Strong transcription Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	16 gene(s)	inside rSNPs	diseases
3	nsv534089	chr6:28636972-28841640	Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Active TSS Flanking Active TSS Enhancers Weak transcription ZNF genes & repeats Transcr. at gene 5' and 3' Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	43 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:77 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:28634800-28643000	Weak transcription	K562	blood
2	chr6:28641400-28641800	Active TSS	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
3	chr6:28641400-28641800	Active TSS	iPS-20b Cell Line	embryonic stem cell
4	chr6:28641400-28641800	Active TSS	NHEK	skin
5	chr6:28641400-28642000	Active TSS	HMEC	breast
6	chr6:28641400-28642400	Active TSS	HUES6 Cell Line	embryonic stem cell
7	chr6:28641400-28642400	Bivalent/Poised TSS	Fetal Kidney	kidney
8	chr6:28641400-28642600	Active TSS	HUES48 Cell Line	embryonic stem cell
9	chr6:28641400-28642600	Bivalent Enhancer	Placenta Amnion	Placenta Amnion
10	chr6:28641400-28642800	Active TSS	Fetal Brain Female	brain
11	chr6:28641400-28643000	Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
12	chr6:28641600-28641800	Active TSS	H9 Derived Neuron Cultured Cells	ES cell derived
13	chr6:28641600-28641800	Active TSS	HUES64 Cell Line	embryonic stem cell
14	chr6:28641600-28641800	Active TSS	iPS-15b Cell Line	embryonic stem cell
15	chr6:28641600-28641800	Active TSS	iPS-18 Cell Line	embryonic stem cell
16	chr6:28641600-28641800	Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
17	chr6:28641600-28641800	Bivalent/Poised TSS	Breast Myoepithelial Primary Cells	Breast
18	chr6:28641600-28641800	Bivalent Enhancer	Primary hematopoietic stem cells short term culture	blood
19	chr6:28641600-28641800	Bivalent/Poised TSS	Primary T helper naive cells fromperipheralblood	blood
20	chr6:28641600-28641800	Bivalent Enhancer	Primary T regulatory cells fromperipheralblood	blood
21	chr6:28641600-28641800	Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
22	chr6:28641600-28641800	Active TSS	Muscle Satellite Cultured Cells	--
23	chr6:28641600-28641800	Bivalent/Poised TSS	Foreskin Melanocyte Primary Cells skin03	Skin
24	chr6:28641600-28641800	Bivalent/Poised TSS	Brain Cingulate Gyrus	brain
25	chr6:28641600-28641800	Flanking Active TSS	Brain Inferior Temporal Lobe	brain
26	chr6:28641600-28641800	Bivalent/Poised TSS	Fetal Heart	heart
27	chr6:28641600-28641800	Bivalent Enhancer	Fetal Intestine Small	intestine
28	chr6:28641600-28641800	Active TSS	Fetal Lung	lung
29	chr6:28641600-28641800	Bivalent Enhancer	Fetal Muscle Trunk	muscle
30	chr6:28641600-28641800	Enhancers	Placenta	Placenta
31	chr6:28641600-28641800	Bivalent Enhancer	Fetal Thymus	thymus
32	chr6:28641600-28641800	Active TSS	GM12878-XiMat	blood
33	chr6:28641600-28641800	Active TSS	Hela-S3	cervix
34	chr6:28641600-28641800	Active TSS	HepG2	liver
35	chr6:28641600-28641800	Active TSS	NH-A	brain
36	chr6:28641600-28641800	Active TSS	NHLF	lung
37	chr6:28641600-28641800	Active TSS	Osteobl	bone
38	chr6:28641600-28642000	Active TSS	ES-I3 Cell Line	embryonic stem cell
39	chr6:28641600-28642000	Active TSS	H1 Cell Line	embryonic stem cell
40	chr6:28641600-28642000	Flanking Active TSS	Ganglion Eminence derived primary cultured neurospheres	brain
41	chr6:28641600-28642000	Active TSS	Foreskin Keratinocyte Primary Cells skin02	Skin
42	chr6:28641600-28642000	Active TSS	Brain Anterior Caudate	brain
43	chr6:28641600-28642000	Bivalent/Poised TSS	Brain Germinal Matrix	brain
44	chr6:28641600-28642000	Active TSS	Fetal Adrenal Gland	Adrenal Gland
45	chr6:28641600-28642000	Bivalent Enhancer	Psoas Muscle	Psoas
46	chr6:28641600-28642200	Active TSS	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
47	chr6:28641600-28642200	Bivalent Enhancer	Primary T killer memory cells from peripheral blood	blood
48	chr6:28641600-28642200	Bivalent/Poised TSS	Fetal Stomach	stomach
49	chr6:28641600-28642400	Active TSS	ES-WA7 Cell Line	embryonic stem cell
50	chr6:28641600-28642400	Active TSS	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived

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