Variant report

Variant	rs4946725
Chromosome Location	chr6:106540276-106540277
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 23 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:16)

rs_ID	r²[population]
rs1010273	1.00[JPT][hapmap];0.91[AMR][1000 genomes];0.86[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12175062	0.90[CEU][hapmap];0.81[CHD][hapmap];0.92[GIH][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];0.94[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs1934593	0.90[CEU][hapmap];0.80[EUR][1000 genomes]
rs1985899	1.00[AFR][1000 genomes];0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs3804333	1.00[LWK][hapmap]
rs3827644	1.00[LWK][hapmap]
rs4946722	0.81[CEU][hapmap];1.00[LWK][hapmap];0.89[MEX][hapmap];0.93[MKK][hapmap];0.86[TSI][hapmap];0.89[AFR][1000 genomes];0.97[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs4946724	1.00[ASW][hapmap];1.00[CEU][hapmap];0.81[CHD][hapmap];0.92[GIH][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs6910095	1.00[ASW][hapmap]
rs9373832	0.89[EUR][1000 genomes]
rs9373839	1.00[LWK][hapmap]
rs9386507	0.88[JPT][hapmap]
rs9386508	0.88[JPT][hapmap]
rs9386509	0.88[JPT][hapmap]
rs9398060	0.88[JPT][hapmap]
rs9398062	0.85[JPT][hapmap]

Variant overlapped rSNPs/rCNVs (count:7 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv932155	chr6:106281728-107030467	Enhancers Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh Weak transcription Bivalent Enhancer Bivalent/Poised TSS Strong transcription Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	41 gene(s)	inside rSNPs	diseases
2	nsv1025231	chr6:106451012-106634389	Enhancers Active TSS Strong transcription Flanking Active TSS Weak transcription Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	9 gene(s)	inside rSNPs	diseases
3	nsv830755	chr6:106461705-106624202	Weak transcription Active TSS Bivalent Enhancer Enhancers Flanking Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Genic enhancers Strong transcription Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	8 gene(s)	inside rSNPs	diseases
4	nsv1025900	chr6:106529777-106898421	Strong transcription Enhancers Weak transcription Active TSS Flanking Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3' Genic enhancers Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	34 gene(s)	inside rSNPs	diseases
5	nsv1018270	chr6:106531658-106908606	Weak transcription Enhancers Strong transcription Flanking Active TSS Bivalent Enhancer Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	34 gene(s)	inside rSNPs	diseases
6	nsv538399	chr6:106531658-106908606	Flanking Active TSS Active TSS Enhancers Strong transcription Genic enhancers Weak transcription Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	34 gene(s)	inside rSNPs	diseases
7	esv1832544	chr6:106539914-106642993	Enhancers Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Active TSS ZNF genes & repeats Weak transcription Active TSS Strong transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	8 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs4946725	PRDM1	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:59 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:106533600-106541200	Active TSS	Rectal Mucosa Donor 29	rectum
2	chr6:106536200-106545800	Weak transcription	Spleen	Spleen
3	chr6:106536400-106545200	Weak transcription	HSMMtube	muscle
4	chr6:106536400-106545600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
5	chr6:106537000-106543400	Weak transcription	NHEK	skin
6	chr6:106537000-106545000	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
7	chr6:106537200-106545200	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
8	chr6:106537400-106544200	Weak transcription	Dnd41	blood
9	chr6:106537400-106544400	Weak transcription	HUES64 Cell Line	embryonic stem cell
10	chr6:106537400-106545000	Weak transcription	Rectal Smooth Muscle	rectum
11	chr6:106537400-106545200	Weak transcription	Psoas Muscle	Psoas
12	chr6:106537400-106545200	Weak transcription	HSMM	muscle
13	chr6:106537800-106545600	Weak transcription	Lung	lung
14	chr6:106538000-106545200	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
15	chr6:106538200-106545400	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
16	chr6:106538400-106542000	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
17	chr6:106538400-106543200	Weak transcription	Muscle Satellite Cultured Cells	--
18	chr6:106538600-106540400	Weak transcription	Monocytes-CD14+_RO01746	blood
19	chr6:106538600-106541000	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
20	chr6:106538600-106543000	Weak transcription	NH-A	brain
21	chr6:106538600-106543600	Strong transcription	Fetal Intestine Large	intestine
22	chr6:106538600-106544400	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
23	chr6:106538600-106544800	Weak transcription	NHLF	lung
24	chr6:106538600-106545000	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
25	chr6:106538600-106545000	Weak transcription	Rectal Mucosa Donor 31	rectum
26	chr6:106538800-106542000	Weak transcription	Osteobl	bone
27	chr6:106538800-106543200	Weak transcription	A549	lung
28	chr6:106538800-106544200	Weak transcription	Primary neutrophils fromperipheralblood	blood
29	chr6:106538800-106544400	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
30	chr6:106539000-106540400	Weak transcription	Primary T helper naive cells from peripheral blood	blood
31	chr6:106539000-106540400	Strong transcription	Fetal Intestine Small	intestine
32	chr6:106539000-106540600	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
33	chr6:106539200-106540400	Weak transcription	Primary T helper cells PMA-I stimulated	--
34	chr6:106539200-106540600	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
35	chr6:106539200-106540600	Weak transcription	Primary T killer memory cells from peripheral blood	blood
36	chr6:106539200-106540800	Weak transcription	NHDF-Ad	bronchial
37	chr6:106539200-106541000	Genic enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
38	chr6:106539200-106541800	Weak transcription	Primary B cells from peripheral blood	blood
39	chr6:106539200-106541800	Weak transcription	Primary hematopoietic stem cells short term culture	blood
40	chr6:106539200-106541800	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
41	chr6:106539200-106541800	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
42	chr6:106539200-106542400	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
43	chr6:106539200-106543600	Weak transcription	Breast Myoepithelial Primary Cells	Breast
44	chr6:106539200-106545000	Weak transcription	HMEC	breast
45	chr6:106539200-106545200	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
46	chr6:106539200-106545400	Strong transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
47	chr6:106539200-106545400	Weak transcription	Sigmoid Colon	Sigmoid Colon
48	chr6:106539400-106540400	Enhancers	Primary T cells fromperipheralblood	blood
49	chr6:106539400-106542000	Enhancers	Primary T helper 17 cells PMA-I stimulated	--
50	chr6:106540000-106540400	Flanking Active TSS	Primary T regulatory cells fromperipheralblood	blood

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