Variant report

Variant	rs9646473
Chromosome Location	chr18:12710623-12710624
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr18:12701192..12707641-chr18:12709846..12713056,10	K562	blood:
2	chr18:12700615..12704798-chr18:12705051..12713643,12	MCF-7	breast:
3	chr18:12710368..12712792-chr18:12946299..12947830,2	K562	blood:
4	chr18:12700926..12704807-chr18:12708679..12712222,6	K562	blood:

Variant related genes	Relation type
ENSG00000085415	Chromatin interaction
ENSG00000128789	Chromatin interaction
ENSG00000101624	Chromatin interaction

Extended variants
information (count: 40 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:29)

rs_ID	r²[population]
rs11874912	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[GIH][hapmap];0.96[LWK][hapmap];1.00[TSI][hapmap];0.93[YRI][hapmap];0.96[AFR][1000 genomes];0.87[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11875046	0.94[AMR][1000 genomes];0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11875203	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11875489	0.84[AFR][1000 genomes];0.94[AMR][1000 genomes];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11875516	0.84[AFR][1000 genomes];0.94[AMR][1000 genomes];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11876168	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11877349	0.81[AFR][1000 genomes];0.94[AMR][1000 genomes];0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12185471	1.00[CEU][hapmap];1.00[CHB][hapmap];0.85[AMR][1000 genomes];0.85[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12964902	1.00[ASN][1000 genomes]
rs2155734	0.92[CEU][hapmap];1.00[GIH][hapmap];1.00[TSI][hapmap];0.84[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34619612	1.00[ASN][1000 genomes]
rs35533206	1.00[ASN][1000 genomes]
rs45460897	0.82[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs55914043	0.91[AMR][1000 genomes];0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs56089701	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs56132337	0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs56152190	1.00[ASN][1000 genomes]
rs56271712	0.88[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs56359953	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs56382499	0.94[AMR][1000 genomes];0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs56392324	0.83[AFR][1000 genomes];0.94[AMR][1000 genomes];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs56792052	1.00[ASN][1000 genomes]
rs56909423	0.84[AFR][1000 genomes];0.94[AMR][1000 genomes];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs58011896	0.84[AFR][1000 genomes];0.94[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs61470666	0.85[AMR][1000 genomes];0.83[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7226376	0.86[EUR][1000 genomes]
rs7243917	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[GIH][hapmap];0.87[LWK][hapmap];1.00[MEX][hapmap];0.89[MKK][hapmap];1.00[TSI][hapmap];0.93[YRI][hapmap];0.82[AFR][1000 genomes];0.94[AMR][1000 genomes];0.85[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7244345	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72870545	1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:11 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1063125	chr18:12046892-12918251	Weak transcription Strong transcription Flanking Bivalent TSS/Enh Active TSS Enhancers Flanking Active TSS Genic enhancers Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	130 gene(s)	inside rSNPs	diseases
2	nsv491873	chr18:12159445-12739784	Weak transcription Flanking Active TSS Strong transcription Enhancers Active TSS Genic enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	79 gene(s)	inside rSNPs	diseases
3	esv3528039	chr18:12396582-12851293	Flanking Active TSS Weak transcription Enhancers Strong transcription Genic enhancers ZNF genes & repeats Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	36 gene(s)	inside rSNPs	diseases
4	esv3528041	chr18:12396641-12851245	Weak transcription Strong transcription Enhancers ZNF genes & repeats Active TSS Flanking Bivalent TSS/Enh Flanking Active TSS Bivalent Enhancer Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	36 gene(s)	inside rSNPs	diseases
5	nsv523743	chr18:12474505-12742809	Active TSS Weak transcription Enhancers Strong transcription Bivalent/Poised TSS ZNF genes & repeats Flanking Active TSS Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	23 gene(s)	inside rSNPs	diseases
6	esv1820040	chr18:12635601-12725236	Weak transcription Enhancers Active TSS Strong transcription Flanking Active TSS Flanking Bivalent TSS/Enh Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	20 gene(s)	inside rSNPs	diseases
7	esv1817845	chr18:12635601-12733705	Flanking Active TSS Weak transcription Active TSS Strong transcription Genic enhancers Enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	20 gene(s)	inside rSNPs	diseases
8	esv1821625	chr18:12635601-12733705	Active TSS Weak transcription Strong transcription Genic enhancers Enhancers Flanking Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	20 gene(s)	inside rSNPs	diseases
9	nsv1062014	chr18:12687210-13183383	Enhancers Active TSS Weak transcription Genic enhancers Flanking Active TSS Strong transcription Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	101 gene(s)	inside rSNPs	diseases
10	nsv543655	chr18:12687210-13183383	Flanking Bivalent TSS/Enh Strong transcription Active TSS Enhancers Weak transcription Flanking Active TSS Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	101 gene(s)	inside rSNPs	diseases
11	nsv1064273	chr18:12697601-12828251	Weak transcription Enhancers ZNF genes & repeats Strong transcription Flanking Active TSS Genic enhancers Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	23 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs9646473	PTPN2	cis	cerebellum	SCAN

Chromatin state (count:125 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr18:12703800-12713200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
2	chr18:12704200-12713000	Weak transcription	Aorta	Aorta
3	chr18:12704200-12713200	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
4	chr18:12704200-12713200	Weak transcription	Psoas Muscle	Psoas
5	chr18:12704200-12726800	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
6	chr18:12704600-12713000	Weak transcription	Pancreas	Pancrea
7	chr18:12704800-12727200	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
8	chr18:12704800-12727800	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
9	chr18:12705000-12722400	Weak transcription	ES-I3 Cell Line	embryonic stem cell
10	chr18:12705000-12725200	Weak transcription	Pancreatic Islets	Pancreatic Islet
11	chr18:12705000-12728600	Weak transcription	Stomach Mucosa	stomach
12	chr18:12705400-12714600	Strong transcription	Ganglion Eminence derived primary cultured neurospheres	brain
13	chr18:12705400-12726000	Strong transcription	Primary hematopoietic stem cells short term culture	blood
14	chr18:12705400-12727200	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
15	chr18:12705600-12711000	Strong transcription	Primary hematopoietic stem cells	blood
16	chr18:12705600-12711400	Strong transcription	Cortex derived primary cultured neurospheres	brain
17	chr18:12705600-12711800	Strong transcription	Rectal Mucosa Donor 29	rectum
18	chr18:12705600-12726000	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
19	chr18:12705600-12727000	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
20	chr18:12705600-12727200	Strong transcription	Primary monocytes fromperipheralblood	blood
21	chr18:12705600-12727200	Strong transcription	Duodenum Mucosa	Duodenum
22	chr18:12705600-12727200	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
23	chr18:12705800-12711000	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
24	chr18:12705800-12712600	Strong transcription	iPS-20b Cell Line	embryonic stem cell
25	chr18:12705800-12713200	Weak transcription	Fetal Brain Male	brain
26	chr18:12705800-12714800	Strong transcription	Duodenum Smooth Muscle	Duodenum
27	chr18:12705800-12726600	Strong transcription	Fetal Thymus	thymus
28	chr18:12705800-12727000	Strong transcription	Placenta	Placenta
29	chr18:12705800-12727200	Strong transcription	Primary T cells fromperipheralblood	blood
30	chr18:12705800-12727200	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
31	chr18:12705800-12727200	Strong transcription	Fetal Muscle Leg	muscle
32	chr18:12706000-12714200	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
33	chr18:12706000-12727000	Strong transcription	HUES6 Cell Line	embryonic stem cell
34	chr18:12706000-12727200	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
35	chr18:12706200-12716000	Strong transcription	Fetal Lung	lung
36	chr18:12706200-12726000	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
37	chr18:12706200-12726800	Strong transcription	Fetal Intestine Large	intestine
38	chr18:12706200-12727200	Strong transcription	Primary T helper cells PMA-I stimulated	--
39	chr18:12706200-12727200	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
40	chr18:12706400-12712600	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
41	chr18:12706400-12726600	Strong transcription	Liver	Liver
42	chr18:12706400-12727000	Strong transcription	Primary T helper naive cells fromperipheralblood	blood
43	chr18:12706400-12727000	Strong transcription	Monocytes-CD14+_RO01746	blood
44	chr18:12706400-12727200	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
45	chr18:12706600-12712000	Strong transcription	Breast Myoepithelial Primary Cells	Breast
46	chr18:12706600-12719200	Strong transcription	Primary neutrophils fromperipheralblood	blood
47	chr18:12706600-12727200	Strong transcription	Primary T helper cells fromperipheralblood	blood
48	chr18:12706600-12727200	Strong transcription	Adipose Nuclei	Adipose
49	chr18:12706800-12711200	Strong transcription	Foreskin Fibroblast Primary Cells skin01	Skin
50	chr18:12706800-12723600	Strong transcription	Fetal Intestine Small	intestine

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