Variant report

Variant	rs16883561
Chromosome Location	chr6:74009153-74009154
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:0)
CpG islands
(count:0)
Chromatin interactive
region (count:9)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

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

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr6:74004356..74006447-chr6:74007681..74009584,2	K562	blood:
2	chr6:74008749..74010443-chr6:74018010..74020997,3	MCF-7	breast:
3	6:73927031-73938730..6:74000304-74012200	K562	blood:
4	6:74000304-74012200..6:74062967-74076046	GM12878	blood:
5	chr6:74008984..74013407-chr6:74017731..74021238,5	K562	blood:
6	chr6:74008167..74010358-chr6:74012095..74014040,2	K562	blood:
7	6:74000304-74012200..6:74160392-74184826	K562	blood:
8	6:74000304-74012200..6:74078047-74099067	H1-hESC	embryonic stem cell:	embryo
9	6:74000304-74012200..6:74099986-74112890	H1-hESC	embryonic stem cell:	embryo

No data

Variant related genes	Relation type
ENSG00000203909	Chromatin interaction
ENSG00000231332	Chromatin interaction
ENSG00000256980	Chromatin interaction
ENSG00000207023	Chromatin interaction
ENSG00000238464	Chromatin interaction
ENSG00000203908	Chromatin interaction
ENSG00000224221	Chromatin interaction
ENSG00000135297	Chromatin interaction
ENSG00000164430	Chromatin interaction
ENSG00000235174	Chromatin interaction
ENSG00000135314	Chromatin interaction
ENSG00000080007	Chromatin interaction
ENSG00000203907	Chromatin interaction

Extended variants
information (count: 45 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:44)

rs_ID	r²[population]
rs13197259	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs13197436	0.86[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs13209676	0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13211102	0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs13217787	0.86[EUR][1000 genomes]
rs16883538	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs16883544	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs16883547	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs16883555	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs16883559	0.84[CEU][hapmap];0.84[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs2054042	0.86[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2054043	0.86[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2124003	0.84[CEU][hapmap]
rs2603472	0.93[CHB][hapmap];0.86[ASN][1000 genomes]
rs2603474	0.86[ASN][1000 genomes]
rs2984126	0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2984128	0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2984130	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34602913	0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs34826679	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs34926279	0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs34977156	0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs35227086	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35705185	0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs35806061	0.96[AMR][1000 genomes];0.95[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs35830226	0.86[EUR][1000 genomes]
rs35879937	0.95[EUR][1000 genomes]
rs35892768	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs36044937	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs36049164	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs36114303	0.81[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs3734511	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs6915288	0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs71573587	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs71573588	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs71573589	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs71573590	0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs71573591	0.96[AMR][1000 genomes];0.91[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7752970	0.96[AMR][1000 genomes];0.91[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7753960	0.83[CEU][hapmap]
rs7754533	0.84[CEU][hapmap]
rs7758669	0.89[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs7769905	0.84[CEU][hapmap]
rs947753	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[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	esv3410973	chr6:73716033-74419545	Active TSS Bivalent Enhancer Flanking Active TSS Weak transcription Enhancers Strong transcription Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats Genic enhancers Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	191 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:93 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:73973600-74018600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
2	chr6:73973600-74018600	Weak transcription	A549	lung
3	chr6:73973600-74018800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
4	chr6:73974000-74018400	Weak transcription	iPS-15b Cell Line	embryonic stem cell
5	chr6:73974400-74009400	Weak transcription	ES-I3 Cell Line	embryonic stem cell
6	chr6:73983800-74018600	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
7	chr6:73984400-74018600	Weak transcription	iPS-18 Cell Line	embryonic stem cell
8	chr6:73989000-74017200	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
9	chr6:73992400-74013200	Weak transcription	GM12878-XiMat	blood
10	chr6:73994200-74018600	Weak transcription	Stomach Mucosa	stomach
11	chr6:73996000-74009800	Weak transcription	K562	blood
12	chr6:73996000-74015800	Weak transcription	Hela-S3	cervix
13	chr6:74001000-74017200	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
14	chr6:74002000-74013000	Weak transcription	HUES48 Cell Line	embryonic stem cell
15	chr6:74005200-74018600	Weak transcription	HUES6 Cell Line	embryonic stem cell
16	chr6:74006000-74011200	Strong transcription	Dnd41	blood
17	chr6:74007400-74010600	Strong transcription	Primary hematopoietic stem cells short term culture	blood
18	chr6:74007800-74010000	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
19	chr6:74007800-74017400	Weak transcription	iPS-20b Cell Line	embryonic stem cell
20	chr6:74008400-74012600	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
21	chr6:74008400-74013200	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
22	chr6:74008600-74009200	Bivalent/Poised TSS	Foreskin Melanocyte Primary Cells skin01	Skin
23	chr6:74008600-74009200	Bivalent/Poised TSS	Rectal Smooth Muscle	rectum
24	chr6:74008600-74009400	Active TSS	Brain Cingulate Gyrus	brain
25	chr6:74008600-74009600	Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
26	chr6:74008600-74009600	Active TSS	Brain Dorsolateral Prefrontal Cortex	brain
27	chr6:74008600-74009600	Active TSS	Duodenum Smooth Muscle	Duodenum
28	chr6:74008600-74009600	Flanking Active TSS	Fetal Muscle Leg	muscle
29	chr6:74008600-74009800	Flanking Active TSS	Breast Myoepithelial Primary Cells	Breast
30	chr6:74008600-74009800	Active TSS	Fetal Kidney	kidney
31	chr6:74008600-74010000	Enhancers	Fetal Heart	heart
32	chr6:74008800-74009200	Transcr. at gene 5' and 3'	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
33	chr6:74008800-74009200	Transcr. at gene 5' and 3'	Primary hematopoietic stem cells G-CSF-mobilized Male	--
34	chr6:74008800-74009200	Active TSS	Colon Smooth Muscle	Colon
35	chr6:74008800-74009200	Flanking Active TSS	Placenta Amnion	Placenta Amnion
36	chr6:74008800-74009200	Active TSS	Rectal Mucosa Donor 29	rectum
37	chr6:74008800-74009200	Flanking Active TSS	NHEK	skin
38	chr6:74008800-74009400	Strong transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
39	chr6:74008800-74009400	Enhancers	iPS DF 19.11 Cell Line	embryonic stem cell
40	chr6:74008800-74009400	Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
41	chr6:74008800-74009400	Active TSS	Primary hematopoietic stem cells	blood
42	chr6:74008800-74009400	Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Female	--
43	chr6:74008800-74009400	Flanking Active TSS	Ganglion Eminence derived primary cultured neurospheres	brain
44	chr6:74008800-74009400	Transcr. at gene 5' and 3'	Foreskin Keratinocyte Primary Cells skin02	Skin
45	chr6:74008800-74009400	Bivalent/Poised TSS	Brain Inferior Temporal Lobe	brain
46	chr6:74008800-74009400	Flanking Bivalent TSS/Enh	Fetal Adrenal Gland	Adrenal Gland
47	chr6:74008800-74009400	Active TSS	Fetal Intestine Large	intestine
48	chr6:74008800-74009400	Active TSS	Fetal Lung	lung
49	chr6:74008800-74009400	Active TSS	NH-A	brain
50	chr6:74008800-74009600	Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links