Variant report

Variant	rs12471906
Chromosome Location	chr2:47535524-47535525
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr2:47395267..47408439-chr2:47533772..47553038,55	MCF-7	breast:
2	chr2:47398936..47406040-chr2:47522760..47537371,25	K562	blood:
3	chr2:47402139..47404719-chr2:47535417..47537672,3	K562	blood:

Variant related genes	Relation type
ENSG00000143933	Chromatin interaction

Extended variants
information (count: 18 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:12)

rs_ID	r²[population]
rs10168995	0.81[CHB][hapmap];1.00[YRI][hapmap]
rs10171003	0.80[AMR][1000 genomes]
rs10180711	0.98[AMR][1000 genomes];0.93[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs10192326	0.89[CHB][hapmap]
rs4558636	1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[AMR][1000 genomes];0.95[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs4560164	0.89[AFR][1000 genomes];0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs6544977	1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[AMR][1000 genomes];0.96[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs6544978	0.88[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs6720211	1.00[CEU][hapmap];0.90[CHB][hapmap];0.86[JPT][hapmap];0.88[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs6734711	0.81[CHB][hapmap]
rs9789479	0.91[CHB][hapmap];1.00[JPT][hapmap];0.84[AMR][1000 genomes];0.84[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs9789683	0.84[AMR][1000 genomes];0.85[EUR][1000 genomes];0.89[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	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
3	nsv531348	chr2:47433147-47827310	Flanking Bivalent TSS/Enh Weak transcription Strong transcription Enhancers Flanking Active TSS Genic enhancers Active TSS Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	50 gene(s)	inside rSNPs	diseases
4	nsv457385	chr2:47468331-47552277	Enhancers Weak transcription Flanking Active TSS Active TSS Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh Genic enhancers Strong transcription	Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
5	nsv581755	chr2:47468331-47552277	Weak transcription Enhancers Flanking Active TSS Active TSS Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats Genic enhancers Flanking Bivalent TSS/Enh Strong transcription	Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
6	nsv999576	chr2:47506116-47773960	Weak transcription Strong transcription Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh Enhancers Bivalent/Poised TSS Genic enhancers Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	43 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:60 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:47519800-47537200	Weak transcription	Fetal Stomach	stomach
2	chr2:47520800-47540000	Enhancers	Primary monocytes fromperipheralblood	blood
3	chr2:47523200-47537000	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
4	chr2:47523400-47536600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
5	chr2:47523600-47536800	Weak transcription	Fetal Kidney	kidney
6	chr2:47525400-47537400	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
7	chr2:47526400-47536800	Weak transcription	Fetal Lung	lung
8	chr2:47526400-47536800	Weak transcription	Spleen	Spleen
9	chr2:47526600-47537800	Weak transcription	Fetal Brain Male	brain
10	chr2:47527400-47536800	Weak transcription	Brain Germinal Matrix	brain
11	chr2:47528400-47536200	Weak transcription	Lung	lung
12	chr2:47528600-47536800	Weak transcription	Psoas Muscle	Psoas
13	chr2:47529200-47536800	Enhancers	Brain Substantia Nigra	brain
14	chr2:47529400-47538000	Weak transcription	Small Intestine	intestine
15	chr2:47530000-47536200	Weak transcription	Primary B cells from peripheral blood	blood
16	chr2:47530200-47536400	Enhancers	HepG2	liver
17	chr2:47530400-47536800	Enhancers	Brain Inferior Temporal Lobe	brain
18	chr2:47530400-47541200	Enhancers	Fetal Intestine Small	intestine
19	chr2:47530400-47541600	Enhancers	Fetal Intestine Large	intestine
20	chr2:47531000-47536800	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
21	chr2:47531000-47537000	Weak transcription	Osteobl	bone
22	chr2:47531200-47536000	Enhancers	Brain Hippocampus Middle	brain
23	chr2:47531200-47536200	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
24	chr2:47531200-47536200	Weak transcription	Primary B cells from cord blood	blood
25	chr2:47531200-47536400	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
26	chr2:47531200-47536600	Weak transcription	Primary hematopoietic stem cells	blood
27	chr2:47531200-47536800	Weak transcription	HUES6 Cell Line	embryonic stem cell
28	chr2:47531200-47536800	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
29	chr2:47532000-47537200	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
30	chr2:47532200-47537400	Weak transcription	HSMM	muscle
31	chr2:47532400-47536800	Enhancers	Brain Anterior Caudate	brain
32	chr2:47532600-47536200	Weak transcription	Rectal Mucosa Donor 31	rectum
33	chr2:47532600-47536800	Enhancers	Monocytes-CD14+_RO01746	blood
34	chr2:47532800-47535800	Enhancers	Brain Cingulate Gyrus	brain
35	chr2:47533600-47535800	Enhancers	A549	lung
36	chr2:47533800-47536600	Enhancers	Duodenum Mucosa	Duodenum
37	chr2:47534200-47535800	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
38	chr2:47534200-47536800	Enhancers	Primary neutrophils fromperipheralblood	blood
39	chr2:47534400-47536800	Weak transcription	Adipose Nuclei	Adipose
40	chr2:47534400-47537400	Enhancers	Primary hematopoietic stem cells short term culture	blood
41	chr2:47534400-47550400	Weak transcription	Ovary	ovary
42	chr2:47534600-47535600	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
43	chr2:47534600-47536600	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
44	chr2:47534600-47537000	Weak transcription	NHLF	lung
45	chr2:47534600-47537800	Weak transcription	Fetal Brain Female	brain
46	chr2:47534800-47536600	Weak transcription	Cortex derived primary cultured neurospheres	brain
47	chr2:47534800-47536800	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
48	chr2:47534800-47536800	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
49	chr2:47534800-47536800	Weak transcription	Duodenum Smooth Muscle	Duodenum
50	chr2:47534800-47536800	Weak transcription	Fetal Heart	heart

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