Variant report

Variant	rs10113926
Chromosome Location	chr9:3491372-3491373
allele	C/T
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	GATA3	chr9:3490887-3491522	MCF-7	breast:	n/a	chr9:3491007-3491014
2	GATA3	chr9:3490914-3491396	T-47D	breast:	n/a	chr9:3491007-3491014

No.	Distal block	Cell Line	Cell type
1	chr9:3489811..3492188-chr9:3524629..3527115,2	MCF-7	breast:
2	chr9:3488422..3492745-chr9:3526119..3529756,3	K562	blood:
3	chr9:3486226..3487734-chr9:3489487..3491455,2	K562	blood:
4	chr9:3489743..3491847-chr9:3522486..3524735,2	K562	blood:
5	chr9:3491268..3494910-chr9:3525417..3527620,3	MCF-7	breast:

Variant related genes	Relation type
RFX3	TF binding region
ENSG00000080298	Chromatin interaction
ENSG00000232104	Chromatin interaction

Extended variants
information (count: 39 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:25)

rs_ID	r²[population]
rs10114162	0.98[AMR][1000 genomes];0.94[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs10114838	0.83[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs10115578	0.96[AMR][1000 genomes];0.83[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs10117292	0.94[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs10119475	0.84[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs10119982	0.98[AMR][1000 genomes];0.94[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs10121096	0.94[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs10123122	0.96[AMR][1000 genomes];0.83[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs10123592	0.94[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs10124613	0.92[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs10758273	0.94[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs10758286	0.93[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs10814148	0.94[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs10972184	0.83[EUR][1000 genomes]
rs10972200	0.83[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12238307	0.93[AMR][1000 genomes];0.81[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12340274	0.86[AMR][1000 genomes];0.94[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12353393	0.94[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs1342542	1.00[AMR][1000 genomes];0.90[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7026025	0.91[AMR][1000 genomes];0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7027858	0.98[AMR][1000 genomes];0.98[ASN][1000 genomes]
rs7037463	0.89[AMR][1000 genomes];0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7857554	0.94[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7861625	0.94[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs881167	0.94[EUR][1000 genomes];0.97[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:14 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1032921	chr9:3139007-3502815	Enhancers Flanking Active TSS Weak transcription Strong transcription Genic enhancers Flanking Bivalent TSS/Enh Active TSS ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	9 gene(s)	inside rSNPs	diseases
2	nsv539940	chr9:3139007-3502815	Strong transcription Weak transcription ZNF genes & repeats Enhancers Bivalent Enhancer Bivalent/Poised TSS Genic enhancers Active TSS Flanking Active TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	9 gene(s)	inside rSNPs	diseases
3	nsv531566	chr9:3288211-3545454	Weak transcription Enhancers Strong transcription Flanking Active TSS Transcr. at gene 5' and 3' Active TSS Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	30 gene(s)	inside rSNPs	diseases
4	nsv892089	chr9:3290569-3578094	Enhancers Weak transcription Strong transcription Active TSS Flanking Active TSS ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	30 gene(s)	inside rSNPs	diseases
5	nsv916259	chr9:3308176-4296711	Enhancers ZNF genes & repeats Weak transcription Strong transcription Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Active TSS Active TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	37 gene(s)	inside rSNPs	diseases
6	nsv1034280	chr9:3319718-3491987	Enhancers Weak transcription Strong transcription ZNF genes & repeats Active TSS Flanking Active TSS Genic enhancers Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
7	nsv539942	chr9:3319718-3491987	Weak transcription Enhancers Strong transcription Flanking Active TSS ZNF genes & repeats Active TSS Genic enhancers Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
8	nsv1028815	chr9:3319718-3584455	Enhancers Flanking Active TSS Strong transcription Weak transcription Active TSS ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	30 gene(s)	inside rSNPs	diseases
9	nsv892090	chr9:3391364-3496660	Strong transcription Enhancers ZNF genes & repeats Weak transcription Genic enhancers Active TSS Flanking Active TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
10	nsv1019324	chr9:3436845-3502815	ZNF genes & repeats Active TSS Strong transcription Enhancers Weak transcription Genic enhancers Flanking Active TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
11	nsv1022795	chr9:3436845-3744623	Enhancers Flanking Active TSS Weak transcription Strong transcription Active TSS ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	32 gene(s)	inside rSNPs	diseases
12	nsv892091	chr9:3459635-3508284	Weak transcription Enhancers Flanking Active TSS Strong transcription Active TSS ZNF genes & repeats Genic enhancers	TF binding region Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
13	nsv539944	chr9:3476471-3535344	Strong transcription Active TSS Weak transcription Flanking Active TSS Enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	29 gene(s)	inside rSNPs	diseases
14	nsv522711	chr9:3480671-3500471	Weak transcription Enhancers Strong transcription Active TSS Flanking Active TSS ZNF genes & repeats Genic enhancers	TF binding region Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:48 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr9:3468800-3496600	Weak transcription	HSMMtube	muscle
2	chr9:3469400-3495600	Weak transcription	Fetal Kidney	kidney
3	chr9:3473600-3496600	Weak transcription	Skeletal Muscle Female	skeletal muscle
4	chr9:3474000-3493600	Weak transcription	Fetal Stomach	stomach
5	chr9:3474400-3524400	Weak transcription	Thymus	Thymus
6	chr9:3475000-3492600	Weak transcription	Lung	lung
7	chr9:3477600-3495600	Weak transcription	Rectal Mucosa Donor 31	rectum
8	chr9:3479000-3498800	Weak transcription	Breast Myoepithelial Primary Cells	Breast
9	chr9:3479200-3500200	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
10	chr9:3479200-3507200	Weak transcription	Primary hematopoietic stem cells short term culture	blood
11	chr9:3479400-3496400	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
12	chr9:3479400-3508000	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
13	chr9:3479800-3492200	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
14	chr9:3479800-3508800	Weak transcription	Primary T helper naive cells from peripheral blood	blood
15	chr9:3479800-3511600	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
16	chr9:3480000-3506400	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
17	chr9:3480200-3499800	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
18	chr9:3480400-3496400	Weak transcription	NH-A	brain
19	chr9:3480400-3508000	Weak transcription	Primary T helper cells PMA-I stimulated	--
20	chr9:3480600-3491800	Weak transcription	Fetal Intestine Small	intestine
21	chr9:3480600-3495600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
22	chr9:3480600-3500200	Weak transcription	H1 Cell Line	embryonic stem cell
23	chr9:3480600-3508800	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
24	chr9:3480600-3510000	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
25	chr9:3480600-3524600	Weak transcription	Left Ventricle	heart
26	chr9:3480800-3491400	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
27	chr9:3480800-3507400	Weak transcription	Primary hematopoietic stem cells	blood
28	chr9:3481200-3494400	Weak transcription	Cortex derived primary cultured neurospheres	brain
29	chr9:3481200-3497800	Weak transcription	HUES64 Cell Line	embryonic stem cell
30	chr9:3483000-3499800	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
31	chr9:3483200-3508400	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
32	chr9:3484800-3504200	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
33	chr9:3484800-3507200	Weak transcription	Brain Hippocampus Middle	brain
34	chr9:3485000-3495600	Weak transcription	Monocytes-CD14+_RO01746	blood
35	chr9:3485000-3497000	Weak transcription	Brain Anterior Caudate	brain
36	chr9:3485000-3500000	Weak transcription	Primary monocytes fromperipheralblood	blood
37	chr9:3485000-3507400	Weak transcription	Primary B cells from peripheral blood	blood
38	chr9:3485200-3499800	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
39	chr9:3485200-3507800	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
40	chr9:3485600-3496000	Weak transcription	Primary T cells fromperipheralblood	blood
41	chr9:3485600-3500200	Weak transcription	Primary T cells from cord blood	blood
42	chr9:3486000-3492400	Weak transcription	GM12878-XiMat	blood
43	chr9:3486600-3494400	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
44	chr9:3490000-3493800	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
45	chr9:3490000-3500000	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
46	chr9:3490000-3508000	Weak transcription	Primary B cells from cord blood	blood
47	chr9:3490400-3499800	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
48	chr9:3491200-3494000	Weak transcription	Pancreatic Islets	Pancreatic Islet

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