Variant report

Variant	rs10116536
Chromosome Location	chr9:100428977-100428978
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	FOS	chr9:100428759-100429084	MCF10A-Er-Src	breast:	n/a	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr9:100428922..100431712-chr9:100433916..100435618,2	MCF-7	breast:

Variant related genes	Relation type
NCBP1	TF binding region
ENSG00000136937	Chromatin interaction

Extended variants
information (count: 29 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:28)

rs_ID	r²[population]
rs10119687	0.96[CEU][hapmap];1.00[TSI][hapmap];0.95[EUR][1000 genomes]
rs10120102	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[YRI][hapmap];0.88[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10123969	0.88[AFR][1000 genomes];0.99[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10983405	0.88[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10983424	0.92[EUR][1000 genomes]
rs10983428	0.92[EUR][1000 genomes]
rs12344605	0.96[CEU][hapmap];1.00[CHB][hapmap];0.80[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs12346336	0.88[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12347253	0.91[EUR][1000 genomes]
rs12349178	0.83[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12350221	0.92[EUR][1000 genomes]
rs12350946	0.92[EUR][1000 genomes]
rs16923269	0.96[CEU][hapmap];0.99[EUR][1000 genomes]
rs16923677	0.92[CEU][hapmap];0.96[EUR][1000 genomes]
rs16923719	0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs16923815	0.90[EUR][1000 genomes]
rs17335265	1.00[ASW][hapmap];0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[GIH][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.94[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs28376250	0.87[EUR][1000 genomes]
rs3176639	0.86[ASW][hapmap];0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[GIH][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.88[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3176748	0.96[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]
rs4284139	0.96[CEU][hapmap];1.00[CHB][hapmap];0.94[MEX][hapmap];1.00[TSI][hapmap];0.83[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4480232	0.96[CEU][hapmap];0.96[EUR][1000 genomes]
rs4617277	0.83[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs61047578	0.91[EUR][1000 genomes]
rs7031623	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[YRI][hapmap];0.94[AFR][1000 genomes];0.84[AMR][1000 genomes];0.82[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72751548	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7849509	0.83[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs952765	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[YRI][hapmap];0.89[AFR][1000 genomes];1.00[ASN][1000 genomes]

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

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv893610	chr9:100324086-100496160	Active TSS Strong transcription Enhancers ZNF genes & repeats Weak transcription Genic enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	32 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs10116536	FBP1	cis	cerebellum	SCAN

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr9:100400800-100451600	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
2	chr9:100401200-100429000	Strong transcription	Primary hematopoietic stem cells short term culture	blood
3	chr9:100401200-100456000	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
4	chr9:100402400-100439600	Strong transcription	HUES64 Cell Line	embryonic stem cell
5	chr9:100402400-100451400	Strong transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
6	chr9:100402400-100455600	Strong transcription	Dnd41	blood
7	chr9:100402600-100456000	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
8	chr9:100402600-100456200	Strong transcription	Primary B cells from peripheral blood	blood
9	chr9:100402800-100429000	Strong transcription	Primary T helper cells fromperipheralblood	blood
10	chr9:100402800-100454200	Strong transcription	Fetal Thymus	thymus
11	chr9:100402800-100456000	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
12	chr9:100403000-100439400	Strong transcription	HUES48 Cell Line	embryonic stem cell
13	chr9:100403000-100439800	Strong transcription	HUES6 Cell Line	embryonic stem cell
14	chr9:100403000-100449400	Strong transcription	HSMM	muscle
15	chr9:100403000-100450400	Strong transcription	Duodenum Mucosa	Duodenum
16	chr9:100403000-100454400	Strong transcription	Placenta	Placenta
17	chr9:100403000-100454600	Strong transcription	Breast Myoepithelial Primary Cells	Breast
18	chr9:100403200-100454400	Strong transcription	Rectal Mucosa Donor 31	rectum
19	chr9:100403200-100455000	Strong transcription	Primary T cells fromperipheralblood	blood
20	chr9:100403400-100434400	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
21	chr9:100403400-100439600	Strong transcription	iPS-20b Cell Line	embryonic stem cell
22	chr9:100403400-100444200	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
23	chr9:100403600-100453800	Strong transcription	Rectal Mucosa Donor 29	rectum
24	chr9:100403800-100436200	Strong transcription	Adipose Nuclei	Adipose
25	chr9:100403800-100439000	Strong transcription	iPS-18 Cell Line	embryonic stem cell
26	chr9:100404000-100435800	Strong transcription	A549	lung
27	chr9:100404000-100449200	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
28	chr9:100404800-100455400	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
29	chr9:100405000-100437800	Strong transcription	GM12878-XiMat	blood
30	chr9:100405800-100438600	Strong transcription	Primary T helper naive cells fromperipheralblood	blood
31	chr9:100409400-100439800	Strong transcription	HMEC	breast
32	chr9:100409600-100433200	Strong transcription	Fetal Intestine Large	intestine
33	chr9:100409600-100440000	Strong transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
34	chr9:100410200-100437800	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
35	chr9:100410200-100454000	Strong transcription	Fetal Muscle Trunk	muscle
36	chr9:100411200-100451000	Strong transcription	Liver	Liver
37	chr9:100412400-100438200	Strong transcription	Fetal Muscle Leg	muscle
38	chr9:100412400-100438400	Strong transcription	Colon Smooth Muscle	Colon
39	chr9:100412400-100439000	Strong transcription	H1 Cell Line	embryonic stem cell
40	chr9:100412600-100439000	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
41	chr9:100412600-100454200	Strong transcription	Duodenum Smooth Muscle	Duodenum
42	chr9:100413000-100451800	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
43	chr9:100413400-100437800	Strong transcription	Stomach Smooth Muscle	stomach
44	chr9:100413400-100438600	Strong transcription	Primary T cells from cord blood	blood
45	chr9:100414000-100438400	Strong transcription	Sigmoid Colon	Sigmoid Colon
46	chr9:100414200-100438600	Strong transcription	Brain Hippocampus Middle	brain
47	chr9:100414400-100438400	Strong transcription	Thymus	Thymus
48	chr9:100414400-100448400	Strong transcription	HUVEC	blood vessel
49	chr9:100414600-100429200	Strong transcription	Primary T helper 17 cells PMA-I stimulated	--
50	chr9:100414600-100436000	Strong transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived

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