Variant report

Variant	rs4960016
Chromosome Location	chr6:4688861-4688862
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr6:4682974..4686881-chr6:4686986..4689567,5	K562	blood:
2	chr6:4687535..4690499-chr6:4691352..4693513,3	K562	blood:
3	chr6:4686682..4689633-chr6:4775001..4777998,2	MCF-7	breast:
4	chr6:4687463..4689972-chr6:4776640..4778169,2	MCF-7	breast:
5	chr6:4687332..4689780-chr6:4704649..4707466,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000236336	Chromatin interaction
ENSG00000153046	Chromatin interaction

Extended variants
information (count: 8 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:5)

rs_ID	r²[population]
rs4960020	1.00[CEU][hapmap];1.00[CHB][hapmap];0.85[JPT][hapmap];0.96[AMR][1000 genomes];0.95[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs4960022	0.96[AMR][1000 genomes];0.93[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs6926001	1.00[CHB][hapmap];1.00[CHD][hapmap];0.97[GIH][hapmap];0.95[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.98[AMR][1000 genomes];0.87[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs907835	0.93[CHB][hapmap];0.80[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs9405761	0.82[CHB][hapmap];0.83[AFR][1000 genomes];0.90[AMR][1000 genomes];0.87[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	esv3366530	chr6:4471528-4865322	ZNF genes & repeats Enhancers Flanking Active TSS Active TSS Weak transcription Strong transcription Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases
2	nsv528627	chr6:4614058-4731340	Flanking Bivalent TSS/Enh Enhancers Active TSS Weak transcription Flanking Active TSS Genic enhancers Bivalent/Poised TSS Strong transcription Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
3	nsv883416	chr6:4666878-4690760	Bivalent Enhancer Enhancers Weak transcription Flanking Active TSS Active TSS ZNF genes & repeats Bivalent/Poised TSS	Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs4960016	C6orf146	cis	cerebellum	SCAN

Chromatin state (count:26 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:4669000-4695600	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
2	chr6:4688000-4689000	Flanking Active TSS	K562	blood
3	chr6:4688200-4689000	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
4	chr6:4688200-4689000	Flanking Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
5	chr6:4688200-4689000	Enhancers	Primary hematopoietic stem cells short term culture	blood
6	chr6:4688200-4689000	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
7	chr6:4688200-4689000	Enhancers	Fetal Adrenal Gland	Adrenal Gland
8	chr6:4688200-4689200	Flanking Active TSS	Hela-S3	cervix
9	chr6:4688400-4689000	Flanking Active TSS	HUVEC	blood vessel
10	chr6:4688400-4689000	Flanking Active TSS	NH-A	brain
11	chr6:4688400-4689000	Flanking Active TSS	NHDF-Ad	bronchial
12	chr6:4688400-4689000	Flanking Active TSS	Osteobl	bone
13	chr6:4688600-4689200	Flanking Active TSS	A549	lung
14	chr6:4688800-4689000	Flanking Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
15	chr6:4688800-4689000	Flanking Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
16	chr6:4688800-4689000	Flanking Active TSS	Muscle Satellite Cultured Cells	--
17	chr6:4688800-4689000	Flanking Active TSS	Foreskin Keratinocyte Primary Cells skin02	Skin
18	chr6:4688800-4689000	Flanking Active TSS	Foreskin Keratinocyte Primary Cells skin03	Skin
19	chr6:4688800-4689000	Flanking Active TSS	Adipose Nuclei	Adipose
20	chr6:4688800-4689000	Flanking Active TSS	NHEK	skin
21	chr6:4688800-4689000	Enhancers	NHLF	lung
22	chr6:4688800-4689200	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
23	chr6:4688800-4689200	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
24	chr6:4688800-4689200	Enhancers	HMEC	breast
25	chr6:4688800-4689600	Enhancers	Primary monocytes fromperipheralblood	blood
26	chr6:4688800-4689600	Flanking Active TSS	Monocytes-CD14+_RO01746	blood

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links