Variant report

Variant	rs9808216
Chromosome Location	chr2:47423591-47423592
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr2:47412361..47428396-chr2:47486545..47501626,43	MCF-7	breast:
2	chr2:47423169..47425083-chr2:47433358..47436246,2	K562	blood:
3	chr2:47422552..47429870-chr2:47496148..47502457,12	MCF-7	breast:
4	chr2:47421460..47424746-chr2:47425269..47428028,4	K562	blood:

Extended variants
information (count: 24 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:20)

rs_ID	r²[population]
rs11842	1.00[ASN][1000 genomes]
rs13013543	1.00[CHD][hapmap]
rs13013607	1.00[CHD][hapmap]
rs13027231	1.00[CEU][hapmap]
rs13388457	1.00[JPT][hapmap]
rs13397696	1.00[CHB][hapmap];0.82[ASN][1000 genomes]
rs13413278	1.00[CHB][hapmap]
rs17036300	1.00[CHB][hapmap]
rs2016682	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs28615318	1.00[ASN][1000 genomes]
rs4953469	1.00[CHB][hapmap]
rs4953470	1.00[CHB][hapmap]
rs4953471	1.00[CHB][hapmap]
rs4953476	1.00[ASN][1000 genomes]
rs59527781	1.00[ASN][1000 genomes]
rs6544960	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs6749284	1.00[CHB][hapmap]
rs6750222	1.00[CHD][hapmap]
rs6757363	1.00[CHD][hapmap]
rs7566126	1.00[CEU][hapmap]

Variant overlapped rSNPs/rCNVs (count:4 , 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	nsv457374	chr2:47313624-47448865	Enhancers Flanking Active TSS Weak transcription Genic enhancers Strong transcription Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	87 gene(s)	inside rSNPs	diseases
4	nsv581754	chr2:47313624-47448865	Weak transcription Strong transcription Genic enhancers Enhancers Flanking Active TSS Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	87 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs9808216	ABCG8	cis	cerebellum	SCAN
rs9808216	CALM2	cis	cerebellum	SCAN
rs9808216	CXCL13	trans	lymphoblastoid	seeQTL

Chromatin state (count:64 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:47416200-47423800	Enhancers	HMEC	breast
2	chr2:47416800-47424000	Enhancers	Fetal Intestine Small	intestine
3	chr2:47418200-47423600	Enhancers	Fetal Brain Male	brain
4	chr2:47419400-47423600	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
5	chr2:47419800-47424800	Enhancers	NH-A	brain
6	chr2:47419800-47425200	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
7	chr2:47419800-47426000	Weak transcription	Pancreas	Pancrea
8	chr2:47420200-47423800	Enhancers	Cortex derived primary cultured neurospheres	brain
9	chr2:47420200-47426400	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
10	chr2:47420400-47423800	Enhancers	Brain Germinal Matrix	brain
11	chr2:47420600-47423800	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
12	chr2:47420600-47423800	Enhancers	iPS-18 Cell Line	embryonic stem cell
13	chr2:47420600-47423800	Enhancers	Brain Substantia Nigra	brain
14	chr2:47420600-47428000	Weak transcription	Ovary	ovary
15	chr2:47420800-47424200	Weak transcription	Primary hematopoietic stem cells	blood
16	chr2:47421000-47424000	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
17	chr2:47421000-47424000	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
18	chr2:47421000-47424000	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
19	chr2:47421200-47424400	Weak transcription	Primary monocytes fromperipheralblood	blood
20	chr2:47421400-47424600	Weak transcription	Fetal Thymus	thymus
21	chr2:47421400-47426200	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
22	chr2:47421400-47428200	Weak transcription	Stomach Smooth Muscle	stomach
23	chr2:47421400-47432200	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
24	chr2:47421400-47432800	Weak transcription	iPS-15b Cell Line	embryonic stem cell
25	chr2:47421600-47426200	Weak transcription	HUES48 Cell Line	embryonic stem cell
26	chr2:47421600-47432600	Weak transcription	Colon Smooth Muscle	Colon
27	chr2:47422000-47424000	Enhancers	HepG2	liver
28	chr2:47422200-47426000	Weak transcription	HUES6 Cell Line	embryonic stem cell
29	chr2:47422200-47426000	Weak transcription	Lung	lung
30	chr2:47422200-47426200	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
31	chr2:47422200-47432800	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
32	chr2:47422400-47425600	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
33	chr2:47422400-47425800	Weak transcription	K562	blood
34	chr2:47422400-47426000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
35	chr2:47422400-47426000	Weak transcription	Placenta	Placenta
36	chr2:47422400-47427200	Enhancers	A549	lung
37	chr2:47422400-47428000	Weak transcription	Brain Anterior Caudate	brain
38	chr2:47422400-47428000	Weak transcription	Brain Inferior Temporal Lobe	brain
39	chr2:47422400-47428200	Weak transcription	Brain Angular Gyrus	brain
40	chr2:47422600-47423600	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
41	chr2:47422600-47425400	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
42	chr2:47422600-47425800	Weak transcription	NHEK	skin
43	chr2:47422600-47426000	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
44	chr2:47422600-47426000	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
45	chr2:47422600-47426000	Weak transcription	Placenta Amnion	Placenta Amnion
46	chr2:47422600-47426000	Weak transcription	NHDF-Ad	bronchial
47	chr2:47422600-47426000	Weak transcription	NHLF	lung
48	chr2:47422600-47427200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
49	chr2:47422600-47427800	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
50	chr2:47422800-47423600	Weak transcription	Fetal Intestine Large	intestine

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