Variant report

Variant	rs9860290
Chromosome Location	chr3:99839106-99839107
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	chr3:99838255..99841576-chr3:99853652..99855888,3	K562	blood:

Extended variants
information (count: 71 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:61)

rs_ID	r²[population]
rs10049383	0.87[CEU][hapmap]
rs10212525	0.87[CEU][hapmap]
rs1021341	0.81[CEU][hapmap]
rs10511177	0.81[CEU][hapmap]
rs11537816	0.82[ASW][hapmap];0.91[AMR][1000 genomes]
rs13064704	0.87[CEU][hapmap]
rs13069311	0.84[ASW][hapmap];0.87[CEU][hapmap];0.84[MEX][hapmap];0.83[MKK][hapmap]
rs13093838	0.86[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs13323143	0.84[ASW][hapmap];0.87[CEU][hapmap];0.84[MEX][hapmap];0.83[MKK][hapmap]
rs1489816	0.87[CEU][hapmap];0.84[MEX][hapmap]
rs1688766	0.84[ASW][hapmap];0.87[CEU][hapmap];0.83[MKK][hapmap]
rs17392948	0.84[ASW][hapmap];0.93[CEU][hapmap];0.85[GIH][hapmap];1.00[MEX][hapmap];0.94[MKK][hapmap];0.82[TSI][hapmap];0.86[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs277636	0.85[JPT][hapmap]
rs28394036	0.82[AMR][1000 genomes]
rs28870092	0.91[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs34996634	0.86[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs35154249	0.86[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs35885423	0.84[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs4075038	0.84[ASW][hapmap];0.87[CEU][hapmap]
rs4361315	0.87[CEU][hapmap]
rs4571265	0.87[CEU][hapmap]
rs4928149	0.84[ASW][hapmap];0.93[CEU][hapmap];1.00[MEX][hapmap];0.94[MKK][hapmap];0.82[TSI][hapmap]
rs62285471	0.80[EUR][1000 genomes]
rs62285473	0.80[EUR][1000 genomes]
rs62285478	0.87[AMR][1000 genomes]
rs6790535	0.81[CEU][hapmap]
rs6790877	0.91[CEU][hapmap]
rs6799379	0.81[CEU][hapmap]
rs6802422	0.87[CEU][hapmap];0.84[MEX][hapmap]
rs6806178	0.81[CEU][hapmap]
rs7610486	0.84[ASW][hapmap];0.87[CEU][hapmap];0.84[MEX][hapmap];0.88[MKK][hapmap]
rs7616988	0.81[CEU][hapmap]
rs7618677	0.85[JPT][hapmap]
rs7620228	0.84[ASW][hapmap];0.87[CEU][hapmap];0.84[MEX][hapmap];0.83[MKK][hapmap]
rs7627991	0.84[ASW][hapmap];0.87[CEU][hapmap];0.84[MEX][hapmap];0.83[MKK][hapmap];0.80[EUR][1000 genomes]
rs7637157	0.85[JPT][hapmap]
rs923470	0.87[CEU][hapmap]
rs923471	0.87[CEU][hapmap]
rs9289985	0.82[ASW][hapmap];1.00[JPT][hapmap];0.82[MEX][hapmap];0.88[MKK][hapmap];0.91[AMR][1000 genomes]
rs9814359	0.81[CEU][hapmap]
rs9815439	0.81[CEU][hapmap]
rs9816538	0.85[AMR][1000 genomes]
rs9823908	0.84[ASW][hapmap];0.87[CEU][hapmap];0.84[MEX][hapmap];0.88[MKK][hapmap]
rs9825882	0.88[AMR][1000 genomes]
rs9828079	0.84[ASW][hapmap];0.87[CEU][hapmap];0.84[MEX][hapmap];0.83[MKK][hapmap]
rs9833888	0.87[CEU][hapmap];0.84[MEX][hapmap]
rs9833980	0.87[CEU][hapmap];0.84[MEX][hapmap]
rs9837602	0.87[CEU][hapmap];0.87[AMR][1000 genomes]
rs9839910	0.82[AMR][1000 genomes]
rs9841186	0.84[ASW][hapmap];0.86[CEU][hapmap];0.84[MEX][hapmap];0.83[MKK][hapmap]
rs9851645	0.87[CEU][hapmap]
rs9853522	0.86[AMR][1000 genomes]
rs9854260	0.82[ASW][hapmap];0.86[CEU][hapmap];0.80[GIH][hapmap];1.00[JPT][hapmap];0.95[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs9863738	0.85[JPT][hapmap]
rs9864437	0.87[CEU][hapmap];0.84[MEX][hapmap]
rs9873709	0.81[CEU][hapmap]
rs9873878	0.87[CEU][hapmap]
rs9875640	0.81[CEU][hapmap]
rs9875878	0.82[ASW][hapmap];0.82[GIH][hapmap];1.00[JPT][hapmap];0.82[MEX][hapmap];0.88[MKK][hapmap];0.91[AMR][1000 genomes]
rs9880795	0.85[JPT][hapmap]
rs9882337	1.00[JPT][hapmap]

Variant overlapped rSNPs/rCNVs (count:10 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv817478	chr3:99474086-99955548	Flanking Active TSS Weak transcription Enhancers Bivalent Enhancer Active TSS ZNF genes & repeats Genic enhancers Strong transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	21 gene(s)	inside rSNPs	diseases
2	nsv916476	chr3:99478229-100124625	Active TSS Weak transcription Flanking Active TSS Strong transcription Enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3' Genic enhancers Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	46 gene(s)	inside rSNPs	diseases
3	nsv869848	chr3:99652246-99904276	Weak transcription Enhancers ZNF genes & repeats Strong transcription Active TSS Flanking Active TSS Genic enhancers Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA	7 gene(s)	inside rSNPs	diseases
4	nsv932634	chr3:99660690-99888854	Enhancers Weak transcription Active TSS Bivalent Enhancer Flanking Active TSS ZNF genes & repeats Strong transcription Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA	5 gene(s)	inside rSNPs	diseases
5	nsv1010579	chr3:99660754-99901817	Enhancers Weak transcription Strong transcription Flanking Active TSS ZNF genes & repeats Genic enhancers Active TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA	7 gene(s)	inside rSNPs	diseases
6	nsv1008483	chr3:99660754-99903769	Enhancers Weak transcription Strong transcription Flanking Active TSS ZNF genes & repeats Active TSS Genic enhancers Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA	7 gene(s)	inside rSNPs	diseases
7	nsv1010897	chr3:99660754-99904783	Enhancers Weak transcription Strong transcription Flanking Active TSS Genic enhancers Active TSS ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA	7 gene(s)	inside rSNPs	diseases
8	nsv1001529	chr3:99661758-99892654	Enhancers Weak transcription Flanking Active TSS ZNF genes & repeats Active TSS Strong transcription Genic enhancers Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA	6 gene(s)	inside rSNPs	diseases
9	nsv536665	chr3:99661758-99892654	Enhancers Weak transcription Strong transcription Flanking Active TSS Genic enhancers Active TSS ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA	6 gene(s)	inside rSNPs	diseases
10	nsv591148	chr3:99774720-99905803	Weak transcription Enhancers Active TSS Strong transcription Flanking Active TSS ZNF genes & repeats Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs9860290	FILIP1L	cis	cerebellum	SCAN

Chromatin state (count:27 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:99795800-99866600	Weak transcription	Primary T cells from cord blood	blood
2	chr3:99825200-99840600	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
3	chr3:99825200-99844000	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
4	chr3:99825200-99844200	Weak transcription	Primary hematopoietic stem cells short term culture	blood
5	chr3:99825600-99841000	Weak transcription	H9 Cell Line	embryonic stem cell
6	chr3:99826600-99862600	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
7	chr3:99829200-99841000	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
8	chr3:99830000-99841200	Weak transcription	HUES64 Cell Line	embryonic stem cell
9	chr3:99831400-99841400	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
10	chr3:99833200-99839600	Weak transcription	Gastric	stomach
11	chr3:99833800-99840800	Weak transcription	Aorta	Aorta
12	chr3:99837400-99839800	Enhancers	Ovary	ovary
13	chr3:99837600-99839600	Enhancers	HSMMtube	muscle
14	chr3:99838000-99839200	Enhancers	Skeletal Muscle Male	skeletal muscle
15	chr3:99838000-99839200	Enhancers	Skeletal Muscle Female	skeletal muscle
16	chr3:99838000-99842000	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
17	chr3:99838400-99839400	Weak transcription	Left Ventricle	heart
18	chr3:99838600-99839400	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
19	chr3:99838600-99841200	Weak transcription	Brain Cingulate Gyrus	brain
20	chr3:99838800-99839200	Weak transcription	Fetal Muscle Leg	muscle
21	chr3:99838800-99839200	Weak transcription	Psoas Muscle	Psoas
22	chr3:99838800-99839400	Enhancers	Adipose Nuclei	Adipose
23	chr3:99838800-99839400	Enhancers	Fetal Heart	heart
24	chr3:99839000-99839200	Enhancers	Pancreatic Islets	Pancreatic Islet
25	chr3:99839000-99839200	Enhancers	NHDF-Ad	bronchial
26	chr3:99839000-99839800	Enhancers	Right Ventricle	heart
27	chr3:99839000-99842800	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived

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