Variant report

Variant	rs9468341
Chromosome Location	chr6:28296658-28296659
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	POLR2A	chr6:28296430-28296932	K562	blood:	n/a	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr6:28235190..28237115-chr6:28295999..28298391,2	K562	blood:
2	chr6:28277054..28279277-chr6:28294657..28297286,2	K562	blood:

Variant related genes	Relation type
ZSCAN31	TF binding region

Extended variants
information (count: 50 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:49)

rs_ID	r²[population]
rs10080420	0.80[ASN][1000 genomes]
rs1150715	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1150722	0.90[AFR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1150723	0.92[AFR][1000 genomes];0.93[ASN][1000 genomes]
rs1150725	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1225600	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12332986	0.80[ASN][1000 genomes]
rs1600621	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1679723	1.00[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs1736892	1.00[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs1778510	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2191036	0.80[ASN][1000 genomes]
rs2799076	1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs28475822	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3757180	0.93[ASN][1000 genomes]
rs3757183	0.96[ASN][1000 genomes]
rs6456812	0.89[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs6456817	1.00[ASN][1000 genomes]
rs6456820	0.80[ASN][1000 genomes]
rs6899512	0.80[ASN][1000 genomes]
rs6901001	1.00[ASN][1000 genomes]
rs6902583	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6908459	1.00[ASN][1000 genomes]
rs6910120	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs6912921	0.93[ASN][1000 genomes]
rs6918043	1.00[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs6918631	1.00[ASN][1000 genomes]
rs6922161	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6922302	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6927023	0.80[ASN][1000 genomes]
rs6929449	1.00[ASN][1000 genomes]
rs6938371	0.93[ASN][1000 genomes]
rs6941222	0.80[ASN][1000 genomes]
rs7747772	0.84[ASN][1000 genomes]
rs7752721	0.96[ASN][1000 genomes]
rs7759855	0.83[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7767897	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9295769	1.00[ASN][1000 genomes]
rs9295770	0.93[ASN][1000 genomes]
rs9461450	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9461452	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9461453	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9461457	0.93[ASN][1000 genomes]
rs9468328	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9468335	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9468337	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9468375	0.86[ASN][1000 genomes]
rs9468384	0.80[ASN][1000 genomes]
rs9654587	0.93[ASN][1000 genomes]

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

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv830620	chr6:28173997-28348033	Flanking Active TSS Strong transcription Active TSS Bivalent/Poised TSS Weak transcription ZNF genes & repeats Enhancers Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	51 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:58 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:28288200-28299200	ZNF genes & repeats	Primary hematopoietic stem cells G-CSF-mobilized Male	--
2	chr6:28290800-28298200	ZNF genes & repeats	Breast Myoepithelial Primary Cells	Breast
3	chr6:28291400-28298000	ZNF genes & repeats	Liver	Liver
4	chr6:28292600-28297200	ZNF genes & repeats	Stomach Smooth Muscle	stomach
5	chr6:28294800-28302000	Weak transcription	HepG2	liver
6	chr6:28294800-28302800	Weak transcription	Placenta Amnion	Placenta Amnion
7	chr6:28295400-28296800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
8	chr6:28295400-28296800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
9	chr6:28295400-28296800	Weak transcription	Esophagus	oesophagus
10	chr6:28295400-28296800	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
11	chr6:28295400-28296800	Weak transcription	Gastric	stomach
12	chr6:28295400-28297000	Strong transcription	Fetal Muscle Trunk	muscle
13	chr6:28295400-28301400	Weak transcription	Rectal Smooth Muscle	rectum
14	chr6:28295400-28302400	Weak transcription	Brain Angular Gyrus	brain
15	chr6:28295400-28302800	Weak transcription	Primary T killer memory cells from peripheral blood	blood
16	chr6:28295400-28303000	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
17	chr6:28295400-28303000	Weak transcription	Thymus	Thymus
18	chr6:28295600-28296800	Weak transcription	HUES6 Cell Line	embryonic stem cell
19	chr6:28295600-28296800	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
20	chr6:28295600-28296800	Weak transcription	Cortex derived primary cultured neurospheres	brain
21	chr6:28295600-28296800	Weak transcription	Brain Hippocampus Middle	brain
22	chr6:28295600-28296800	Weak transcription	Brain Inferior Temporal Lobe	brain
23	chr6:28295600-28296800	Weak transcription	Psoas Muscle	Psoas
24	chr6:28295600-28296800	Weak transcription	Rectal Mucosa Donor 31	rectum
25	chr6:28295600-28296800	Weak transcription	Right Ventricle	heart
26	chr6:28295600-28296800	Weak transcription	Skeletal Muscle Female	skeletal muscle
27	chr6:28295600-28297000	Weak transcription	Brain Anterior Caudate	brain
28	chr6:28295600-28297000	Weak transcription	Duodenum Mucosa	Duodenum
29	chr6:28295600-28297200	Weak transcription	Fetal Brain Female	brain
30	chr6:28295600-28297800	Weak transcription	K562	blood
31	chr6:28295600-28302000	Weak transcription	Fetal Heart	heart
32	chr6:28295600-28302200	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
33	chr6:28295600-28302200	Weak transcription	Hela-S3	cervix
34	chr6:28295600-28302400	Weak transcription	Brain Substantia Nigra	brain
35	chr6:28295600-28302600	Weak transcription	Stomach Mucosa	stomach
36	chr6:28295600-28302800	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
37	chr6:28295600-28302800	Weak transcription	Fetal Brain Male	brain
38	chr6:28295800-28296800	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
39	chr6:28295800-28296800	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
40	chr6:28295800-28296800	Weak transcription	Adipose Nuclei	Adipose
41	chr6:28295800-28296800	Weak transcription	Duodenum Smooth Muscle	Duodenum
42	chr6:28295800-28296800	Weak transcription	Rectal Mucosa Donor 29	rectum
43	chr6:28295800-28302800	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
44	chr6:28296000-28296800	Weak transcription	Brain Cingulate Gyrus	brain
45	chr6:28296400-28297400	ZNF genes & repeats	Primary hematopoietic stem cells G-CSF-mobilized Female	--
46	chr6:28296400-28297400	Strong transcription	Left Ventricle	heart
47	chr6:28296600-28297000	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
48	chr6:28296600-28297000	ZNF genes & repeats	Colonic Mucosa	Colon
49	chr6:28296600-28297200	ZNF genes & repeats	Pancreas	Pancrea
50	chr6:28296600-28297400	ZNF genes & repeats	H1 Cell Line	embryonic stem cell

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links