Variant report

Variant	rs2236407
Chromosome Location	chr9:98237796-98237797
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr9:98219926..98222684-chr9:98235733..98238442,2	K562	blood:
2	chr9:98236732..98239700-chr9:98240483..98242788,2	MCF-7	breast:
3	chr9:98233432..98236653-chr9:98236835..98241063,4	MCF-7	breast:

Variant related genes	Relation type
ENSG00000185920	Chromatin interaction

Extended variants
information (count: 27 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:22)

rs_ID	r²[population]
rs10512248	0.83[CEU][hapmap];0.84[CHB][hapmap];0.90[JPT][hapmap];0.85[MEX][hapmap];0.83[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs1355619	0.83[ASN][1000 genomes]
rs1355620	0.83[ASN][1000 genomes]
rs16909919	0.83[CEU][hapmap];0.84[CHB][hapmap];0.90[JPT][hapmap];0.85[MEX][hapmap];0.82[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs2066829	0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2236406	0.92[AMR][1000 genomes];0.93[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2274692	0.94[AMR][1000 genomes];0.94[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2282042	0.83[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2297086	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.95[TSI][hapmap];0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2297088	0.91[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs28457763	0.83[CEU][hapmap];0.84[CHB][hapmap];0.90[JPT][hapmap];0.85[MEX][hapmap];0.82[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs28495472	0.90[AMR][1000 genomes];0.92[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs28496034	0.81[ASN][1000 genomes]
rs28504650	0.92[CEU][hapmap];0.90[CHB][hapmap];0.84[CHD][hapmap];0.90[JPT][hapmap];1.00[MEX][hapmap];0.91[TSI][hapmap];0.80[AMR][1000 genomes];0.95[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs28536201	0.83[ASN][1000 genomes]
rs28557305	0.82[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs28620532	0.94[AMR][1000 genomes];0.93[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs28620668	0.80[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs28629854	0.83[CEU][hapmap];0.84[CHB][hapmap];0.90[JPT][hapmap];0.85[MEX][hapmap];0.82[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs28701981	0.96[CEU][hapmap];0.95[CHB][hapmap];0.90[CHD][hapmap];0.91[GIH][hapmap];0.95[JPT][hapmap];1.00[MEX][hapmap];0.93[TSI][hapmap];0.92[AMR][1000 genomes];0.92[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs3758302	0.83[ASN][1000 genomes]
rs4448343	0.84[CHB][hapmap];0.90[JPT][hapmap];0.85[MEX][hapmap];0.81[EUR][1000 genomes];0.83[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:5 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv531633	chr9:98078300-98431120	Flanking Active TSS Active TSS Strong transcription Enhancers Weak transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	44 gene(s)	inside rSNPs	diseases
2	nsv831658	chr9:98152971-98342178	Transcr. at gene 5' and 3' Weak transcription Flanking Active TSS Bivalent Enhancer Active TSS Strong transcription Enhancers Bivalent/Poised TSS ZNF genes & repeats Genic enhancers Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	23 gene(s)	inside rSNPs	diseases
3	nsv949520	chr9:98204199-98238358	Weak transcription Strong transcription Genic enhancers Active TSS ZNF genes & repeats Flanking Active TSS Enhancers Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	6 gene(s)	inside rSNPs	diseases
4	nsv430083	chr9:98204245-98445645	Weak transcription Active TSS Enhancers Strong transcription Flanking Active TSS Bivalent/Poised TSS Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	22 gene(s)	inside rSNPs	diseases
5	nsv1051665	chr9:98234404-98264577	Weak transcription Bivalent Enhancer Enhancers Genic enhancers Active TSS Strong transcription Flanking Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs2236407	FBP1	cis	parietal	SCAN

Chromatin state (count:113 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr9:98223400-98266400	Weak transcription	Hela-S3	cervix
2	chr9:98225800-98239600	Weak transcription	HMEC	breast
3	chr9:98225800-98239800	Strong transcription	HUES48 Cell Line	embryonic stem cell
4	chr9:98225800-98244000	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
5	chr9:98226000-98248400	Weak transcription	HUVEC	blood vessel
6	chr9:98226000-98251000	Weak transcription	Osteobl	bone
7	chr9:98226200-98238400	Weak transcription	NH-A	brain
8	chr9:98226200-98239000	Strong transcription	Breast Myoepithelial Primary Cells	Breast
9	chr9:98226200-98239400	Weak transcription	NHEK	skin
10	chr9:98226200-98240800	Strong transcription	Fetal Intestine Large	intestine
11	chr9:98226200-98243400	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
12	chr9:98226200-98254000	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
13	chr9:98226400-98239200	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
14	chr9:98226400-98239400	Strong transcription	iPS-20b Cell Line	embryonic stem cell
15	chr9:98226400-98243000	Weak transcription	ES-I3 Cell Line	embryonic stem cell
16	chr9:98226400-98247800	Weak transcription	Stomach Mucosa	stomach
17	chr9:98226600-98239000	Strong transcription	iPS-18 Cell Line	embryonic stem cell
18	chr9:98226600-98239200	Strong transcription	HUES6 Cell Line	embryonic stem cell
19	chr9:98226600-98239400	Strong transcription	HUES64 Cell Line	embryonic stem cell
20	chr9:98226600-98239600	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
21	chr9:98226600-98239600	Strong transcription	Cortex derived primary cultured neurospheres	brain
22	chr9:98226600-98240000	Weak transcription	Primary T killer memory cells from peripheral blood	blood
23	chr9:98226600-98240200	Strong transcription	Rectal Mucosa Donor 31	rectum
24	chr9:98226600-98253800	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
25	chr9:98226800-98239400	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
26	chr9:98227000-98242600	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
27	chr9:98227000-98242800	Strong transcription	Fetal Muscle Leg	muscle
28	chr9:98227000-98243600	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
29	chr9:98227000-98243600	Strong transcription	Fetal Intestine Small	intestine
30	chr9:98227200-98239200	Strong transcription	H1 Cell Line	embryonic stem cell
31	chr9:98227200-98243000	Strong transcription	Fetal Muscle Trunk	muscle
32	chr9:98227200-98243000	Strong transcription	Skeletal Muscle Female	skeletal muscle
33	chr9:98227200-98244800	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
34	chr9:98227400-98239600	Strong transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
35	chr9:98227400-98242000	Strong transcription	Ganglion Eminence derived primary cultured neurospheres	brain
36	chr9:98227400-98242800	Strong transcription	Adipose Nuclei	Adipose
37	chr9:98227600-98248800	Weak transcription	Small Intestine	intestine
38	chr9:98227800-98243200	Strong transcription	Primary T cells fromperipheralblood	blood
39	chr9:98228000-98240400	Strong transcription	Left Ventricle	heart
40	chr9:98228000-98243400	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
41	chr9:98228200-98238600	Strong transcription	Brain Substantia Nigra	brain
42	chr9:98228600-98239200	Strong transcription	Brain Hippocampus Middle	brain
43	chr9:98229000-98238800	Strong transcription	Brain Inferior Temporal Lobe	brain
44	chr9:98229600-98238200	Strong transcription	Brain Germinal Matrix	brain
45	chr9:98229800-98246800	Weak transcription	Colon Smooth Muscle	Colon
46	chr9:98231000-98239800	Weak transcription	HSMM	muscle
47	chr9:98231200-98237800	Weak transcription	Placenta Amnion	Placenta Amnion
48	chr9:98231400-98239400	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
49	chr9:98231400-98239400	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
50	chr9:98231600-98239400	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived

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