Variant report

Variant	rs28539031
Chromosome Location	chr6:25139805-25139806
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	chr6:25139792-25140126	SK-N-MC	brain:	n/a	n/a
2	POLR2A	chr6:25139792-25140211	GM12878	blood:	n/a	n/a
3	YY1	chr6:25139745-25140151	K562	blood:	n/a	chr6:25139928-25139936 chr6:25139917-25139939 chr6:25139927-25139939 chr6:25139929-25139939 chr6:25139924-25139940
4	YY1	chr6:25139770-25140069	GM12878	blood:	n/a	chr6:25139928-25139936 chr6:25139917-25139939 chr6:25139927-25139939 chr6:25139929-25139939 chr6:25139924-25139940
5	YY1	chr6:25139770-25140130	GM12892	blood:	n/a	chr6:25139928-25139936 chr6:25139917-25139939 chr6:25139927-25139939 chr6:25139929-25139939 chr6:25139924-25139940
6	POLR2A	chr6:25139757-25140171	GM12892	blood:	n/a	n/a
7	HEY1	chr6:25139800-25140117	K562	blood:	n/a	chr6:25139984-25139999
8	YY1	chr6:25139797-25140085	K562	blood:	n/a	chr6:25139928-25139936 chr6:25139917-25139939 chr6:25139927-25139939 chr6:25139929-25139939 chr6:25139924-25139940
9	YY1	chr6:25139787-25140065	H1-hESC	embryonic stem cell:	n/a	chr6:25139928-25139936 chr6:25139917-25139939 chr6:25139927-25139939 chr6:25139929-25139939 chr6:25139924-25139940
10	YY1	chr6:25139770-25140091	GM12892	blood:	n/a	chr6:25139928-25139936 chr6:25139917-25139939 chr6:25139927-25139939 chr6:25139929-25139939 chr6:25139924-25139940
11	POLR2A	chr6:25139801-25140106	GM12891	blood:	n/a	n/a
12	POLR2A	chr6:25139746-25140211	ProgFib	skin:	n/a	n/a
13	POLR2A	chr6:25139786-25140286	GM12892	blood:	n/a	n/a
14	MAX	chr6:25139782-25140131	K562	blood:	n/a	n/a

Variant related genes	Relation type
ENSG00000219682	TF binding region
CMAHP	TF binding region

Extended variants
information (count: 19 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:10)

rs_ID	r²[population]
rs182499	0.86[ASN][1000 genomes]
rs188567	1.00[ASN][1000 genomes]
rs302981	1.00[ASN][1000 genomes]
rs303003	0.86[ASN][1000 genomes]
rs303012	0.86[ASN][1000 genomes]
rs416030	0.86[ASN][1000 genomes]
rs55851821	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6908916	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73386265	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9654578	0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:9 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1022966	chr6:24763776-25154212	Flanking Active TSS Weak transcription Active TSS Enhancers Flanking Bivalent TSS/Enh Strong transcription Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	39 gene(s)	inside rSNPs	diseases
2	nsv538160	chr6:24763776-25154212	Active TSS Strong transcription Flanking Active TSS Enhancers Bivalent Enhancer Weak transcription Transcr. at gene 5' and 3' Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	39 gene(s)	inside rSNPs	diseases
3	nsv1023989	chr6:24930362-25285679	Weak transcription Active TSS Enhancers Strong transcription Genic enhancers Flanking Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	43 gene(s)	inside rSNPs	diseases
4	nsv830611	chr6:25039374-25199112	Flanking Active TSS Enhancers Strong transcription Weak transcription Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	27 gene(s)	inside rSNPs	diseases
5	nsv470806	chr6:25082262-25156197	Weak transcription Flanking Active TSS Enhancers ZNF genes & repeats Strong transcription Genic enhancers Transcr. at gene 5' and 3' Active TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
6	nsv462662	chr6:25084718-25165486	Enhancers Transcr. at gene 5' and 3' Weak transcription Flanking Active TSS Genic enhancers Active TSS Strong transcription ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
7	nsv601166	chr6:25084718-25165486	Strong transcription Weak transcription Active TSS Enhancers Flanking Active TSS ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
8	esv1798120	chr6:25136860-25149538	Flanking Active TSS Transcr. at gene 5' and 3' Enhancers Active TSS Weak transcription Strong transcription Genic enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region	3 gene(s)	inside rSNPs	diseases
9	nsv1025694	chr6:25136860-25309450	Weak transcription Enhancers Strong transcription Flanking Active TSS Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats Genic enhancers Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	19 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs28539031	CMAH	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:41 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:25135200-25140200	Active TSS	Right Atrium	heart
2	chr6:25136200-25140000	Active TSS	Aorta	Aorta
3	chr6:25136600-25140000	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
4	chr6:25136800-25140000	Active TSS	Ovary	ovary
5	chr6:25137000-25140200	Active TSS	Psoas Muscle	Psoas
6	chr6:25138000-25140200	Active TSS	Breast Myoepithelial Primary Cells	Breast
7	chr6:25138400-25140200	Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
8	chr6:25138400-25140400	Active TSS	Fetal Intestine Large	intestine
9	chr6:25138600-25140000	Active TSS	Fetal Intestine Small	intestine
10	chr6:25138800-25140000	Active TSS	Fetal Adrenal Gland	Adrenal Gland
11	chr6:25138800-25140200	Active TSS	Foreskin Keratinocyte Primary Cells skin03	Skin
12	chr6:25138800-25152800	Weak transcription	Lung	lung
13	chr6:25139200-25154800	Weak transcription	Placenta Amnion	Placenta Amnion
14	chr6:25139400-25140000	Weak transcription	Right Ventricle	heart
15	chr6:25139400-25140000	Flanking Active TSS	Dnd41	blood
16	chr6:25139400-25140200	Enhancers	Fetal Brain Male	brain
17	chr6:25139600-25140000	Flanking Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
18	chr6:25139600-25140000	Flanking Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
19	chr6:25139600-25140000	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
20	chr6:25139600-25140000	Enhancers	Colon Smooth Muscle	Colon
21	chr6:25139600-25140000	Enhancers	NHLF	lung
22	chr6:25139600-25140200	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
23	chr6:25139600-25140200	Enhancers	Stomach Smooth Muscle	stomach
24	chr6:25139600-25140600	Enhancers	Primary monocytes fromperipheralblood	blood
25	chr6:25139600-25141800	Weak transcription	Fetal Thymus	thymus
26	chr6:25139600-25152800	Weak transcription	Thymus	Thymus
27	chr6:25139800-25140000	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
28	chr6:25139800-25140000	Enhancers	Primary hematopoietic stem cells	blood
29	chr6:25139800-25140000	Active TSS	Primary hematopoietic stem cells short term culture	blood
30	chr6:25139800-25140000	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
31	chr6:25139800-25140000	Enhancers	Muscle Satellite Cultured Cells	--
32	chr6:25139800-25140000	Enhancers	Fetal Muscle Trunk	muscle
33	chr6:25139800-25140000	Active TSS	HUVEC	blood vessel
34	chr6:25139800-25140000	Active TSS	NHEK	skin
35	chr6:25139800-25140200	Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
36	chr6:25139800-25140200	Enhancers	Liver	Liver
37	chr6:25139800-25140200	Enhancers	GM12878-XiMat	blood
38	chr6:25139800-25140200	Active TSS	Monocytes-CD14+_RO01746	blood
39	chr6:25139800-25140400	Active TSS	Fetal Lung	lung
40	chr6:25139800-25140400	Active TSS	Pancreas	Pancrea
41	chr6:25139800-25140800	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast

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