Variant report

Variant	rs3176639
Chromosome Location	chr9:100458109-100458110
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:3)
CpG islands
(count:0)
Chromatin interactive
region (count:9)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:3 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	IRF1	chr9:100457877-100458160	K562	blood:	n/a	chr9:100458008-100458024
2	POLR2A	chr9:100458028-100458125	HepG2	liver:	n/a	n/a
3	MXI1	chr9:100457686-100460675	SK-N-SH	brain:	n/a	n/a

No data

(count:9 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr9:100457791..100462084-chr9:100462112..100466505,5	K562	blood:
2	chr9:100457693..100459222-chr9:100744821..100747461,2	K562	blood:
3	chr9:100393846..100397319-chr9:100457855..100461087,4	MCF-7	breast:
4	chr9:100455758..100458745-chr9:100534997..100536831,2	K562	blood:
5	chr9:100393858..100397326-chr9:100457081..100460285,5	MCF-7	breast:
6	chr9:100392082..100395139-chr9:100455935..100459131,3	K562	blood:
7	chr9:100456538..100459527-chr9:100606763..100609012,2	K562	blood:
8	chr9:100456373..100458750-chr9:100743910..100746135,2	K562	blood:
9	chr9:100411786..100413328-chr9:100457588..100459137,2	MCF-7	breast:

No data

Variant related genes	Relation type
KRT18P13	TF binding region
ENSG00000266608	TF binding region
ENSG00000136938	Chromatin interaction
ENSG00000136937	Chromatin interaction
ENSG00000136925	Chromatin interaction
ENSG00000266608	Chromatin interaction

Extended variants
information (count: 30 )
Associated
traits (count: 1 )

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

rs_ID	r²[population]
rs10116536	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]
rs10119687	1.00[CEU][hapmap];1.00[TSI][hapmap];0.98[EUR][1000 genomes]
rs10120102	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10123969	1.00[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10983405	0.88[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10983424	0.95[EUR][1000 genomes]
rs10983428	0.95[EUR][1000 genomes]
rs12344605	1.00[CEU][hapmap];1.00[CHB][hapmap];0.91[AFR][1000 genomes];0.81[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12346336	0.88[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12347253	0.94[EUR][1000 genomes]
rs12349178	0.83[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12350221	0.95[EUR][1000 genomes]
rs12350946	0.95[EUR][1000 genomes]
rs16923269	1.00[CEU][hapmap];0.98[EUR][1000 genomes]
rs16923677	0.96[CEU][hapmap];1.00[EUR][1000 genomes]
rs16923719	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs16923815	0.93[EUR][1000 genomes]
rs17335265	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];0.83[AFR][1000 genomes];0.80[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28376250	0.91[EUR][1000 genomes]
rs3176748	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[YRI][hapmap];0.88[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4284139	1.00[CEU][hapmap];1.00[CHB][hapmap];0.94[MEX][hapmap];1.00[TSI][hapmap];0.83[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4480232	1.00[CEU][hapmap];0.99[EUR][1000 genomes]
rs4617277	0.83[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs61047578	0.94[EUR][1000 genomes]
rs7031623	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[YRI][hapmap];0.83[AFR][1000 genomes];0.84[AMR][1000 genomes];0.83[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72751548	0.88[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7849509	0.83[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs952765	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[YRI][hapmap];1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:2 , 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
2	nsv1043753	chr9:100458109-100599265	Weak transcription Enhancers Flanking Active TSS Bivalent Enhancer Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	13 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs3176639	FBP1	cis	cerebellum	SCAN

Chromatin state (count:116 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr9:100437600-100458400	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
2	chr9:100438000-100458400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
3	chr9:100439000-100458800	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
4	chr9:100447200-100458400	Weak transcription	Colonic Mucosa	Colon
5	chr9:100451200-100458400	Weak transcription	Esophagus	oesophagus
6	chr9:100453800-100458400	Weak transcription	Left Ventricle	heart
7	chr9:100454000-100458200	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
8	chr9:100454000-100458200	Weak transcription	Fetal Muscle Trunk	muscle
9	chr9:100454000-100458400	Weak transcription	Primary neutrophils fromperipheralblood	blood
10	chr9:100454000-100458400	Weak transcription	Thymus	Thymus
11	chr9:100454400-100458200	Weak transcription	Placenta	Placenta
12	chr9:100454400-100458800	Weak transcription	Lung	lung
13	chr9:100454400-100459000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
14	chr9:100455400-100458200	Enhancers	Liver	Liver
15	chr9:100455600-100458400	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
16	chr9:100456000-100458200	Enhancers	Primary T helper 17 cells PMA-I stimulated	--
17	chr9:100456000-100458200	Enhancers	Primary T killer memory cells from peripheral blood	blood
18	chr9:100456400-100458400	Enhancers	Right Ventricle	heart
19	chr9:100456400-100458600	Enhancers	Primary T killer naive cells fromperipheralblood	blood
20	chr9:100456400-100458800	Flanking Active TSS	HUVEC	blood vessel
21	chr9:100456400-100459000	Flanking Active TSS	Dnd41	blood
22	chr9:100456600-100458200	Enhancers	Breast Myoepithelial Primary Cells	Breast
23	chr9:100456600-100458600	Flanking Active TSS	Duodenum Mucosa	Duodenum
24	chr9:100456800-100458200	Enhancers	Cortex derived primary cultured neurospheres	brain
25	chr9:100456800-100458200	Enhancers	Fetal Intestine Small	intestine
26	chr9:100456800-100458400	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
27	chr9:100456800-100458600	Flanking Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
28	chr9:100456800-100458600	Enhancers	Primary B cells from peripheral blood	blood
29	chr9:100456800-100458600	Flanking Active TSS	Primary T helper cells PMA-I stimulated	--
30	chr9:100456800-100458600	Enhancers	Small Intestine	intestine
31	chr9:100457000-100458200	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
32	chr9:100457000-100458200	Enhancers	Fetal Intestine Large	intestine
33	chr9:100457000-100458200	Enhancers	Monocytes-CD14+_RO01746	blood
34	chr9:100457000-100458400	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
35	chr9:100457000-100458600	Enhancers	Primary monocytes fromperipheralblood	blood
36	chr9:100457200-100458200	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
37	chr9:100457200-100458200	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
38	chr9:100457200-100458200	Enhancers	Psoas Muscle	Psoas
39	chr9:100457200-100458600	Enhancers	Primary B cells from cord blood	blood
40	chr9:100457200-100458600	Flanking Active TSS	Brain Inferior Temporal Lobe	brain
41	chr9:100457200-100458600	Flanking Active TSS	GM12878-XiMat	blood
42	chr9:100457200-100458800	Flanking Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
43	chr9:100457200-100458800	Enhancers	Primary mononuclear cells fromperipheralblood	Blood
44	chr9:100457200-100458800	Enhancers	Sigmoid Colon	Sigmoid Colon
45	chr9:100457400-100458400	Enhancers	Fetal Stomach	stomach
46	chr9:100457400-100458400	Enhancers	Gastric	stomach
47	chr9:100457400-100458600	Flanking Active TSS	HepG2	liver
48	chr9:100457400-100458800	Flanking Active TSS	Ganglion Eminence derived primary cultured neurospheres	brain
49	chr9:100457400-100458800	Flanking Active TSS	Brain Cingulate Gyrus	brain
50	chr9:100457400-100458800	Flanking Active TSS	Fetal Kidney	kidney

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