Variant report

Variant	rs6484496
Chromosome Location	chr11:8823590-8823591
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr11:8715578..8718169-chr11:8819916..8823970,3	MCF-7	breast:
2	chr11:8709766..8713200-chr11:8820077..8823864,3	K562	blood:

Variant related genes	Relation type
ENSG00000166444	Chromatin interaction
ENSG00000166441	Chromatin interaction

Extended variants
information (count: 24 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:20)

rs_ID	r²[population]
rs10769955	0.85[EUR][1000 genomes]
rs10769957	0.88[EUR][1000 genomes]
rs10769958	0.87[AMR][1000 genomes];0.87[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs11042059	0.86[EUR][1000 genomes]
rs11042060	0.85[EUR][1000 genomes]
rs11042067	0.87[AMR][1000 genomes];0.87[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs11042069	0.90[EUR][1000 genomes]
rs12224436	0.89[EUR][1000 genomes]
rs12421789	0.88[AMR][1000 genomes];0.86[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs2316865	0.90[EUR][1000 genomes]
rs3763918	0.90[AMR][1000 genomes];0.92[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs4579928	0.87[AMR][1000 genomes];0.87[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs4929911	0.90[EUR][1000 genomes]
rs4929912	0.82[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs4929914	0.86[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs4929916	0.85[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs6484484	0.87[EUR][1000 genomes]
rs7107867	0.96[AMR][1000 genomes];0.91[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7129667	0.94[AMR][1000 genomes];0.91[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7944560	0.87[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv2758256	chr11:8784813-9009573	Enhancers Weak transcription Flanking Active TSS Genic enhancers Strong transcription Active TSS Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	34 gene(s)	inside rSNPs	diseases
2	esv2759803	chr11:8784813-9009573	Flanking Active TSS Weak transcription Enhancers Strong transcription Active TSS Bivalent/Poised TSS Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	34 gene(s)	inside rSNPs	diseases
3	nsv553447	chr11:8792622-8825966	Genic enhancers Strong transcription Weak transcription Enhancers Flanking Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Active TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
4	nsv527920	chr11:8816695-8856822	Weak transcription Active TSS Enhancers Flanking Active TSS Transcr. at gene 5' and 3' Genic enhancers ZNF genes & repeats Strong transcription Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs6484496	TMEM9B-AS1	cis	lung	GTEx
rs6484496	TMEM9B-AS1	cis	Muscle Skeletal	GTEx

Chromatin state (count:85 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr11:8797800-8827200	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
2	chr11:8800800-8825800	Weak transcription	Brain Angular Gyrus	brain
3	chr11:8800800-8827400	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
4	chr11:8801600-8827400	Weak transcription	Esophagus	oesophagus
5	chr11:8809000-8830200	Weak transcription	Fetal Brain Male	brain
6	chr11:8809200-8826600	Weak transcription	Muscle Satellite Cultured Cells	--
7	chr11:8809200-8829200	Weak transcription	Fetal Kidney	kidney
8	chr11:8811800-8827000	Weak transcription	HMEC	breast
9	chr11:8811800-8828600	Weak transcription	Hela-S3	cervix
10	chr11:8811800-8828800	Weak transcription	Aorta	Aorta
11	chr11:8811800-8830400	Weak transcription	Placenta Amnion	Placenta Amnion
12	chr11:8811800-8830600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
13	chr11:8814200-8828400	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
14	chr11:8814800-8825400	Weak transcription	Brain Inferior Temporal Lobe	brain
15	chr11:8815000-8827800	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
16	chr11:8815200-8826800	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
17	chr11:8815600-8825200	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
18	chr11:8815800-8827800	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
19	chr11:8816400-8825400	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
20	chr11:8816400-8831800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
21	chr11:8816600-8826600	Weak transcription	Brain Anterior Caudate	brain
22	chr11:8816600-8827400	Strong transcription	Fetal Muscle Trunk	muscle
23	chr11:8816600-8828400	Weak transcription	NHDF-Ad	bronchial
24	chr11:8816600-8828800	Weak transcription	Brain Substantia Nigra	brain
25	chr11:8816600-8830000	Weak transcription	iPS-20b Cell Line	embryonic stem cell
26	chr11:8816600-8830600	Weak transcription	iPS-18 Cell Line	embryonic stem cell
27	chr11:8816800-8825200	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
28	chr11:8816800-8828600	Weak transcription	Small Intestine	intestine
29	chr11:8817000-8828600	Weak transcription	Fetal Intestine Large	intestine
30	chr11:8817200-8825600	Weak transcription	Spleen	Spleen
31	chr11:8817200-8828600	Weak transcription	Fetal Intestine Small	intestine
32	chr11:8817400-8828200	Weak transcription	Cortex derived primary cultured neurospheres	brain
33	chr11:8817600-8825000	Weak transcription	NHLF	lung
34	chr11:8819000-8825600	Weak transcription	Adipose Nuclei	Adipose
35	chr11:8819200-8826600	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
36	chr11:8819400-8825200	Strong transcription	Fetal Muscle Leg	muscle
37	chr11:8819800-8828600	Weak transcription	Osteobl	bone
38	chr11:8819800-8829800	Weak transcription	iPS-15b Cell Line	embryonic stem cell
39	chr11:8820000-8826200	Strong transcription	HSMMtube	muscle
40	chr11:8820000-8828200	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
41	chr11:8820200-8823800	Weak transcription	NH-A	brain
42	chr11:8820400-8824200	Enhancers	Left Ventricle	heart
43	chr11:8820600-8826400	Genic enhancers	Breast Myoepithelial Primary Cells	Breast
44	chr11:8821200-8826600	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
45	chr11:8821400-8824000	Weak transcription	Skeletal Muscle Female	skeletal muscle
46	chr11:8821400-8827600	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
47	chr11:8821600-8830200	Enhancers	Primary neutrophils fromperipheralblood	blood
48	chr11:8822200-8826600	Weak transcription	Skeletal Muscle Male	skeletal muscle
49	chr11:8822200-8827200	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
50	chr11:8822200-8827400	Weak transcription	Psoas Muscle	Psoas

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links