Variant report

Variant	rs540412
Chromosome Location	chr9:97896615-97896616
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr9:97892364..97896798-chr9:97897558..97901820,5	K562	blood:

Variant related genes	Relation type
ENSG00000158169	Chromatin interaction

Extended variants
information (count: 45 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:41)

rs_ID	r²[population]
rs1045276	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.84[YRI][hapmap];0.84[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs10491560	1.00[CEU][hapmap];0.94[CHB][hapmap];1.00[JPT][hapmap];0.89[YRI][hapmap];0.84[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs10761376	0.80[AMR][1000 genomes];0.87[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs10821446	0.83[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs10821450	0.89[AFR][1000 genomes];0.91[AMR][1000 genomes];0.88[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs171417	0.91[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.94[CHD][hapmap];1.00[GIH][hapmap];0.90[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];0.92[TSI][hapmap];0.95[YRI][hapmap];0.85[AFR][1000 genomes];0.96[AMR][1000 genomes];0.92[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs184818	0.91[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.94[CHD][hapmap];0.97[GIH][hapmap];0.90[JPT][hapmap];0.93[LWK][hapmap];1.00[MEX][hapmap];0.92[TSI][hapmap];0.95[YRI][hapmap];0.85[AMR][1000 genomes]
rs187172	1.00[MEX][hapmap];0.87[TSI][hapmap];0.85[AMR][1000 genomes]
rs2282216	0.85[JPT][hapmap]
rs2404692	0.83[TSI][hapmap]
rs356666	0.91[ASW][hapmap];1.00[CEU][hapmap];0.94[CHB][hapmap];0.94[CHD][hapmap];0.95[GIH][hapmap];0.90[JPT][hapmap];0.96[LWK][hapmap];0.98[MKK][hapmap];0.85[TSI][hapmap];0.90[YRI][hapmap];0.87[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs356669	1.00[MEX][hapmap];0.92[TSI][hapmap];0.89[AMR][1000 genomes]
rs356673	0.91[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.94[CHD][hapmap];1.00[GIH][hapmap];0.90[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];0.92[TSI][hapmap];0.95[YRI][hapmap];0.83[AFR][1000 genomes];0.91[AMR][1000 genomes];0.91[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs356675	1.00[CEU][hapmap];1.00[CHB][hapmap];0.90[JPT][hapmap];0.83[AFR][1000 genomes];0.98[AMR][1000 genomes];0.93[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs356677	0.91[ASW][hapmap];1.00[CEU][hapmap];0.94[CHB][hapmap];0.94[CHD][hapmap];1.00[GIH][hapmap];0.90[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.95[MKK][hapmap];0.92[TSI][hapmap];0.95[YRI][hapmap];0.87[AMR][1000 genomes];0.90[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs356678	0.91[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.94[CHD][hapmap];1.00[GIH][hapmap];0.90[JPT][hapmap];0.96[LWK][hapmap];1.00[MEX][hapmap];0.85[MKK][hapmap];0.92[TSI][hapmap];0.95[YRI][hapmap];0.86[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs356679	0.89[AMR][1000 genomes]
rs356680	0.91[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.94[CHD][hapmap];0.97[GIH][hapmap];0.90[JPT][hapmap];0.96[LWK][hapmap];1.00[MEX][hapmap];0.87[MKK][hapmap];0.92[TSI][hapmap];0.95[YRI][hapmap];0.91[AMR][1000 genomes];0.90[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs356682	1.00[CEU][hapmap];0.89[AMR][1000 genomes];0.90[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs356683	0.91[AMR][1000 genomes];0.90[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs356684	1.00[CEU][hapmap];1.00[CHB][hapmap];0.90[JPT][hapmap];0.91[AMR][1000 genomes];0.90[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs356687	0.87[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs356688	0.91[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs356689	0.91[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.94[CHD][hapmap];1.00[GIH][hapmap];0.90[JPT][hapmap];0.96[LWK][hapmap];1.00[MEX][hapmap];0.95[MKK][hapmap];0.92[TSI][hapmap];0.95[YRI][hapmap];0.89[AMR][1000 genomes];0.90[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs3780567	0.81[JPT][hapmap]
rs3824486	0.85[JPT][hapmap]
rs416792	1.00[CEU][hapmap];1.00[CHB][hapmap];0.90[JPT][hapmap];0.86[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs437511	0.89[AFR][1000 genomes];0.98[AMR][1000 genomes];0.95[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs4647376	0.85[JPT][hapmap]
rs4647534	0.81[JPT][hapmap]
rs4744451	0.81[JPT][hapmap]
rs526189	0.85[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs565293	1.00[CEU][hapmap];1.00[CHB][hapmap];0.94[CHD][hapmap];1.00[GIH][hapmap];0.90[JPT][hapmap];1.00[MEX][hapmap];0.85[MKK][hapmap];1.00[TSI][hapmap];0.96[AMR][1000 genomes];0.94[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs609324	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs657637	1.00[CEU][hapmap];1.00[GIH][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.96[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs7023722	0.82[ASN][1000 genomes]
rs7033633	0.81[ASW][hapmap];1.00[CEU][hapmap];0.94[CHB][hapmap];0.86[CHD][hapmap];0.92[GIH][hapmap];1.00[JPT][hapmap];0.83[MEX][hapmap];0.83[MKK][hapmap];0.88[TSI][hapmap];0.84[YRI][hapmap];0.83[ASN][1000 genomes]
rs7034586	0.82[ASN][1000 genomes]
rs7863582	0.84[EUR][1000 genomes]
rs7865753	0.80[AMR][1000 genomes];0.87[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs944934	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]

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	nsv933919	chr9:97619512-97919344	Weak transcription Transcr. at gene 5' and 3' Genic enhancers Enhancers Flanking Active TSS Strong transcription Flanking Bivalent TSS/Enh Active TSS Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	293 gene(s)	inside rSNPs	diseases
2	nsv1038523	chr9:97797032-97923774	Strong transcription Enhancers Weak transcription Flanking Active TSS Bivalent Enhancer Active TSS Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	274 gene(s)	inside rSNPs	diseases
3	nsv540175	chr9:97797032-97923774	Weak transcription Flanking Bivalent TSS/Enh Enhancers Strong transcription Bivalent/Poised TSS Genic enhancers Flanking Active TSS Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	274 gene(s)	inside rSNPs	diseases
4	nsv831656	chr9:97831551-97989980	Weak transcription Strong transcription Active TSS Genic enhancers Enhancers Bivalent Enhancer Flanking 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	274 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs540412	FAM120A	cis	cerebellum	SCAN
rs540412	PHF2	cis	cerebellum	SCAN
rs540412	NINJ1	cis	cerebellum	SCAN

Chromatin state (count:69 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr9:97844000-97898400	Weak transcription	Primary T helper cells fromperipheralblood	blood
2	chr9:97875400-97900400	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
3	chr9:97875600-97900000	Weak transcription	Spleen	Spleen
4	chr9:97875600-97906000	Weak transcription	Primary hematopoietic stem cells short term culture	blood
5	chr9:97887400-97916400	Weak transcription	Thymus	Thymus
6	chr9:97888000-97900000	Weak transcription	Primary T cells from cord blood	blood
7	chr9:97890000-97898600	Weak transcription	Left Ventricle	heart
8	chr9:97890000-97898600	Weak transcription	Right Atrium	heart
9	chr9:97890000-97900000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
10	chr9:97890000-97906600	Weak transcription	Right Ventricle	heart
11	chr9:97890000-97919600	Weak transcription	Hela-S3	cervix
12	chr9:97890000-97928000	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
13	chr9:97890200-97898400	Weak transcription	Primary monocytes fromperipheralblood	blood
14	chr9:97890200-97900400	Weak transcription	Esophagus	oesophagus
15	chr9:97890400-97897000	Weak transcription	Colonic Mucosa	Colon
16	chr9:97890400-97902800	Weak transcription	Muscle Satellite Cultured Cells	--
17	chr9:97890600-97900000	Weak transcription	Breast Myoepithelial Primary Cells	Breast
18	chr9:97890600-97900000	Weak transcription	Rectal Smooth Muscle	rectum
19	chr9:97891800-97898200	Enhancers	Liver	Liver
20	chr9:97892200-97896800	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
21	chr9:97892600-97900400	Weak transcription	Brain Germinal Matrix	brain
22	chr9:97893200-97901600	Weak transcription	Pancreatic Islets	Pancreatic Islet
23	chr9:97893400-97898200	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
24	chr9:97893800-97896800	Enhancers	HUES6 Cell Line	embryonic stem cell
25	chr9:97893800-97896800	Weak transcription	Fetal Brain Male	brain
26	chr9:97893800-97896800	Weak transcription	Fetal Brain Female	brain
27	chr9:97893800-97897000	Weak transcription	Placenta	Placenta
28	chr9:97893800-97897000	Weak transcription	Lung	lung
29	chr9:97893800-97904800	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
30	chr9:97893800-97905400	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
31	chr9:97893800-97905800	Weak transcription	Osteobl	bone
32	chr9:97893800-97906400	Weak transcription	Ovary	ovary
33	chr9:97893800-97912600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
34	chr9:97893800-97918800	Weak transcription	Gastric	stomach
35	chr9:97893800-97940400	Weak transcription	Pancreas	Pancrea
36	chr9:97894200-97906200	Weak transcription	Colon Smooth Muscle	Colon
37	chr9:97894200-97909800	Weak transcription	A549	lung
38	chr9:97894200-97925600	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
39	chr9:97894600-97897200	Strong transcription	Fetal Muscle Leg	muscle
40	chr9:97894600-97897200	Genic enhancers	Fetal Stomach	stomach
41	chr9:97894600-97899400	Weak transcription	Stomach Smooth Muscle	stomach
42	chr9:97894600-97905000	Weak transcription	Fetal Lung	lung
43	chr9:97894800-97905400	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
44	chr9:97895000-97900200	Weak transcription	HUES48 Cell Line	embryonic stem cell
45	chr9:97895400-97897000	Strong transcription	Cortex derived primary cultured neurospheres	brain
46	chr9:97895400-97897200	Enhancers	Stomach Mucosa	stomach
47	chr9:97895600-97899600	Weak transcription	Skeletal Muscle Male	skeletal muscle
48	chr9:97895600-97901000	Weak transcription	H1 Cell Line	embryonic stem cell
49	chr9:97895800-97897200	Enhancers	Fetal Intestine Large	intestine
50	chr9:97895800-97899400	Weak transcription	Skeletal Muscle Female	skeletal muscle

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