Variant report

Variant	rs55987123
Chromosome Location	chr6:31010658-31010659
allele	A/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:10)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

(count:10 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr6:30910257..30910994-chr6:31010511..31011179,2	MCF-7	breast:
2	chr6:30796298..30796948-chr6:31010213..31011129,3	MCF-7	breast:
3	chr6:30976019..30976653-chr6:31010220..31010809,2	MCF-7	breast:
4	chr6:30880584..30886230-chr6:31009556..31012955,9	MCF-7	breast:
5	chr6:31010612..31011425-chr6:31055068..31055590,2	K562	blood:
6	chr6:30883250..30883934-chr6:31010475..31011616,5	MCF-7	breast:
7	chr6:30949349..30950069-chr6:31010283..31011164,2	MCF-7	breast:
8	chr6:30910196..30910957-chr6:31010233..31011130,2	MCF-7	breast:
9	chr6:30851860..30853560-chr6:31009534..31012397,2	MCF-7	breast:
10	chr6:30882943..30883998-chr6:31010336..31011408,3	MCF-7	breast:

No data

Variant related genes	Relation type
ENSG00000137411	Chromatin interaction
ENSG00000204580	Chromatin interaction

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

rSNPs within LD-proxies of this variant (count:39)

rs_ID	r²[population]
rs10456389	0.91[AMR][1000 genomes]
rs10947122	0.86[ASN][1000 genomes]
rs11759188	0.86[ASN][1000 genomes]
rs12528584	0.92[AMR][1000 genomes]
rs12528596	0.92[AMR][1000 genomes]
rs12661923	0.86[ASN][1000 genomes]
rs12661935	0.86[ASN][1000 genomes]
rs17190071	0.86[ASN][1000 genomes]
rs2394425	0.96[AFR][1000 genomes];0.91[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs2394426	0.96[AFR][1000 genomes];0.91[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs2394427	0.96[AFR][1000 genomes];0.92[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs2894048	0.96[AFR][1000 genomes];0.91[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs3888579	0.96[AFR][1000 genomes];0.92[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs3891154	0.96[AFR][1000 genomes];0.92[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs4713427	0.90[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs4713428	0.90[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs62399429	0.86[ASN][1000 genomes]
rs62399430	0.82[ASN][1000 genomes]
rs62399431	0.86[ASN][1000 genomes]
rs62399443	0.86[ASN][1000 genomes]
rs62401664	0.86[ASN][1000 genomes]
rs62401665	0.86[ASN][1000 genomes]
rs62401667	0.86[ASN][1000 genomes]
rs62401670	0.86[ASN][1000 genomes]
rs62401671	0.86[ASN][1000 genomes]
rs62401672	0.86[ASN][1000 genomes]
rs62401673	0.86[ASN][1000 genomes]
rs62401674	0.86[ASN][1000 genomes]
rs62401697	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs62401698	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs72847031	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs72847032	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs72847034	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs9295945	0.88[AFR][1000 genomes];0.92[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs9295946	0.96[AFR][1000 genomes];0.92[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs9295947	0.96[AFR][1000 genomes];0.91[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs9357106	0.88[AFR][1000 genomes];0.90[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs9380211	0.96[AFR][1000 genomes];0.92[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs9394032	0.96[AFR][1000 genomes];0.92[AMR][1000 genomes];0.97[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:6 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv3519970	chr6:30382942-31378788	Genic enhancers Weak transcription Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh Enhancers Transcr. at gene 5' and 3' Strong transcription Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	1030 gene(s)	inside rSNPs	diseases
2	esv3519971	chr6:30382942-31378788	Bivalent Enhancer Flanking Active TSS Active TSS Weak transcription Enhancers Transcr. at gene 5' and 3' Strong transcription Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	1030 gene(s)	inside rSNPs	diseases
3	nsv601481	chr6:30422632-31284253	Weak transcription Genic enhancers Transcr. at gene 5' and 3' Flanking Active TSS Strong transcription Enhancers Active TSS Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	1012 gene(s)	inside rSNPs	diseases
4	nsv1015372	chr6:30704734-31582152	Active TSS Flanking Active TSS Enhancers Weak transcription Genic enhancers Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Strong transcription ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	334 gene(s)	inside rSNPs	diseases
5	nsv538173	chr6:30704734-31582152	Flanking Active TSS Enhancers Weak transcription Active TSS Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Strong transcription Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	334 gene(s)	inside rSNPs	diseases
6	nsv1029442	chr6:31006647-31449207	Flanking Active TSS Bivalent Enhancer Weak transcription Enhancers Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Genic enhancers Strong transcription ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA	82 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:27 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:31004400-31010800	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
2	chr6:31005800-31010800	Weak transcription	Cortex derived primary cultured neurospheres	brain
3	chr6:31005800-31010800	Weak transcription	Hela-S3	cervix
4	chr6:31005800-31011000	Weak transcription	Skeletal Muscle Female	skeletal muscle
5	chr6:31006000-31010800	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
6	chr6:31006000-31011000	Weak transcription	Brain Anterior Caudate	brain
7	chr6:31006000-31014800	Weak transcription	Right Atrium	heart
8	chr6:31006200-31010800	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
9	chr6:31006200-31010800	Weak transcription	Skeletal Muscle Male	skeletal muscle
10	chr6:31006200-31010800	Weak transcription	NHDF-Ad	bronchial
11	chr6:31009000-31011000	Weak transcription	Breast Myoepithelial Primary Cells	Breast
12	chr6:31009400-31011200	Enhancers	Stomach Mucosa	stomach
13	chr6:31009600-31011000	Enhancers	A549	lung
14	chr6:31009600-31027400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
15	chr6:31010200-31015800	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
16	chr6:31010600-31010800	Active TSS	Primary Natural Killer cells fromperipheralblood	blood
17	chr6:31010600-31010800	Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
18	chr6:31010600-31010800	Active TSS	Duodenum Smooth Muscle	Duodenum
19	chr6:31010600-31010800	Flanking Active TSS	Fetal Muscle Leg	muscle
20	chr6:31010600-31010800	Active TSS	GM12878-XiMat	blood
21	chr6:31010600-31011000	Flanking Active TSS	Primary monocytes fromperipheralblood	blood
22	chr6:31010600-31011000	Active TSS	Primary B cells from cord blood	blood
23	chr6:31010600-31011000	Flanking Active TSS	Primary B cells from peripheral blood	blood
24	chr6:31010600-31011000	Active TSS	Brain Substantia Nigra	brain
25	chr6:31010600-31011200	Enhancers	Primary mononuclear cells fromperipheralblood	Blood
26	chr6:31010600-31011200	Flanking Active TSS	Monocytes-CD14+_RO01746	blood
27	chr6:31010600-31021600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links