Variant report

Variant	rs72888531
Chromosome Location	chr2:47198113-47198114
allele	C/T
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:21)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

(count:21 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr2:47167293..47170062-chr2:47196955..47199343,2	K562	blood:
2	chr2:47166510..47168193-chr2:47197498..47199709,2	MCF-7	breast:
3	chr2:47197939..47198482-chr2:47256135..47256820,3	MCF-7	breast:
4	chr2:47168224..47170419-chr2:47197148..47199025,2	MCF-7	breast:
5	chr2:47168921..47169535-chr2:47198042..47198630,2	MCF-7	breast:
6	chr2:47192520..47194152-chr2:47197519..47201107,3	K562	blood:
7	chr2:47184160..47184888-chr2:47197610..47198458,4	MCF-7	breast:
8	chr2:47197750..47199615-chr2:47402613..47404212,2	MCF-7	breast:
9	chr2:47197603..47198444-chr2:47263258..47263910,2	MCF-7	breast:
10	chr2:47196068..47199021-chr2:47522197..47525047,2	K562	blood:
11	chr2:47197718..47199744-chr2:47426207..47428375,2	MCF-7	breast:
12	chr2:47196076..47198728-chr2:47417712..47420454,3	MCF-7	breast:
13	chr2:47184299..47184895-chr2:47197606..47198181,3	MCF-7	breast:
14	chr2:47197025..47200212-chr2:47401779..47404367,3	K562	blood:
15	chr2:47195860..47200774-chr2:47207735..47210386,4	K562	blood:
16	chr2:47195345..47199186-chr2:47202255..47204268,3	MCF-7	breast:
17	chr2:47166867..47170590-chr2:47194468..47200247,20	MCF-7	breast:
18	chr2:47196446..47198984-chr2:47567520..47569154,2	MCF-7	breast:
19	chr2:47197790..47198513-chr2:47256135..47256820,5	MCF-7	breast:
20	chr2:47197833..47198523-chr2:47206891..47207596,2	MCF-7	breast:
21	chr2:47182193..47183883-chr2:47197911..47200319,2	K562	blood:

No data

Variant related genes	Relation type
ENSG00000068724	Chromatin interaction
ENSG00000143933	Chromatin interaction
ENSG00000180398	Chromatin interaction

Extended variants
information (count: 16 )
Associated
traits (count: 0)

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

rs_ID	r²[population]
rs13387604	0.81[EUR][1000 genomes]
rs13426875	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs2304286	0.84[AMR][1000 genomes];0.98[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs28704094	0.92[AFR][1000 genomes];0.89[AMR][1000 genomes];0.94[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs4542901	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs58580247	0.84[AMR][1000 genomes];0.98[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs6544945	0.85[ASN][1000 genomes]
rs72888530	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73926318	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7564680	0.93[AFR][1000 genomes];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][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	nsv817517	chr2:46819371-47715140	Enhancers Weak transcription Genic enhancers Bivalent Enhancer Flanking Active TSS Strong transcription Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	152 gene(s)	inside rSNPs	diseases
2	nsv457352	chr2:47004788-47325973	Active TSS Enhancers Genic enhancers Strong transcription Weak transcription Flanking Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	37 gene(s)	inside rSNPs	diseases
3	nsv581749	chr2:47004788-47325973	Flanking Active TSS Enhancers Genic enhancers Strong transcription Weak transcription Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	37 gene(s)	inside rSNPs	diseases
4	nsv1004828	chr2:47056849-47814482	Weak transcription Enhancers Strong transcription Genic enhancers Flanking Active TSS Transcr. at gene 5' and 3' Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	144 gene(s)	inside rSNPs	diseases
5	nsv524970	chr2:47162739-47302095	Enhancers Genic enhancers Flanking Active TSS Weak transcription Strong transcription Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	20 gene(s)	inside rSNPs	diseases
6	nsv1000377	chr2:47189386-47344029	Weak transcription Flanking Active TSS Genic enhancers Enhancers Strong transcription Transcr. at gene 5' and 3' Bivalent Enhancer Active TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	10 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:115 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:47169800-47214600	Weak transcription	Fetal Kidney	kidney
2	chr2:47174400-47212400	Weak transcription	iPS-15b Cell Line	embryonic stem cell
3	chr2:47177200-47210400	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
4	chr2:47181600-47210800	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
5	chr2:47184600-47205000	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
6	chr2:47185000-47206000	Weak transcription	Primary T killer memory cells from peripheral blood	blood
7	chr2:47185200-47210200	Weak transcription	HUES64 Cell Line	embryonic stem cell
8	chr2:47185400-47205800	Weak transcription	HUES48 Cell Line	embryonic stem cell
9	chr2:47185400-47210400	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
10	chr2:47186200-47200800	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
11	chr2:47186400-47205600	Weak transcription	H9 Cell Line	embryonic stem cell
12	chr2:47186800-47205200	Weak transcription	Gastric	stomach
13	chr2:47186800-47205800	Weak transcription	Primary T helper naive cells from peripheral blood	blood
14	chr2:47187400-47206000	Weak transcription	Fetal Brain Female	brain
15	chr2:47187800-47203200	Weak transcription	Brain Germinal Matrix	brain
16	chr2:47187800-47210200	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
17	chr2:47188000-47205200	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
18	chr2:47188000-47207000	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
19	chr2:47191200-47198800	Enhancers	Placenta	Placenta
20	chr2:47193800-47204000	Strong transcription	Primary T cells from cord blood	blood
21	chr2:47194800-47198800	Enhancers	Placenta Amnion	Placenta Amnion
22	chr2:47194800-47200200	Strong transcription	Thymus	Thymus
23	chr2:47195000-47198800	Genic enhancers	Primary Natural Killer cells fromperipheralblood	blood
24	chr2:47195000-47198800	Genic enhancers	Fetal Intestine Small	intestine
25	chr2:47195200-47202200	Genic enhancers	Primary hematopoietic stem cells short term culture	blood
26	chr2:47195400-47202000	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
27	chr2:47195600-47199000	Enhancers	Breast Myoepithelial Primary Cells	Breast
28	chr2:47195600-47200200	Enhancers	Stomach Mucosa	stomach
29	chr2:47195600-47205200	Weak transcription	Fetal Lung	lung
30	chr2:47195600-47210400	Weak transcription	HUES6 Cell Line	embryonic stem cell
31	chr2:47195600-47212800	Weak transcription	Cortex derived primary cultured neurospheres	brain
32	chr2:47195800-47198800	Enhancers	NHEK	skin
33	chr2:47195800-47199000	Enhancers	Liver	Liver
34	chr2:47195800-47199200	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
35	chr2:47195800-47199200	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
36	chr2:47195800-47199800	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
37	chr2:47195800-47199800	Enhancers	Rectal Mucosa Donor 31	rectum
38	chr2:47195800-47200000	Enhancers	HMEC	breast
39	chr2:47195800-47200200	Enhancers	Muscle Satellite Cultured Cells	--
40	chr2:47195800-47200600	Weak transcription	Fetal Muscle Leg	muscle
41	chr2:47195800-47202000	Enhancers	Primary monocytes fromperipheralblood	blood
42	chr2:47195800-47202000	Weak transcription	Primary T helper cells PMA-I stimulated	--
43	chr2:47196000-47200600	Weak transcription	HSMMtube	muscle
44	chr2:47196000-47205800	Weak transcription	Rectal Smooth Muscle	rectum
45	chr2:47196400-47211800	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
46	chr2:47196600-47198200	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
47	chr2:47196600-47198200	Enhancers	Brain Cingulate Gyrus	brain
48	chr2:47196600-47198200	Enhancers	Skeletal Muscle Female	skeletal muscle
49	chr2:47196600-47198400	Enhancers	Brain Hippocampus Middle	brain
50	chr2:47196600-47198800	Enhancers	Brain Substantia Nigra	brain

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