Variant report

Variant	rs12353393
Chromosome Location	chr9:3498606-3498607
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr9:3493140..3494788-chr9:3496837..3499206,2	K562	blood:
2	chr9:3498254..3500362-chr9:3527205..3528736,2	K562	blood:
3	chr9:3497780..3499700-chr9:3524560..3526876,2	K562	blood:

Variant related genes	Relation type
ENSG00000232104	Chromatin interaction
ENSG00000080298	Chromatin interaction

Extended variants
information (count: 49 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:38)

rs_ID	r²[population]
rs10113926	0.94[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs10114162	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs10114838	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.95[AMR][1000 genomes];0.89[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs10115088	0.85[CEU][hapmap];0.86[JPT][hapmap]
rs10115578	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.89[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs10117292	0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs10119475	0.94[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs10119982	1.00[CEU][hapmap];0.84[CHB][hapmap];0.95[JPT][hapmap];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs10121096	1.00[CEU][hapmap];1.00[CHB][hapmap];0.90[JPT][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs10123122	0.89[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs10123592	0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs10124613	0.98[AMR][1000 genomes];0.85[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs10758273	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs10758286	0.94[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs10814148	0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs10814189	0.82[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap]
rs10814190	0.95[CHB][hapmap];1.00[JPT][hapmap]
rs10814208	0.85[CEU][hapmap];0.95[JPT][hapmap]
rs10814233	0.85[CEU][hapmap];0.86[JPT][hapmap]
rs10972184	0.89[EUR][1000 genomes]
rs10972200	0.95[AMR][1000 genomes];0.89[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs10972435	0.85[CEU][hapmap];0.86[JPT][hapmap]
rs12004862	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap]
rs12238307	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.87[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12340274	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.87[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12553270	0.85[CEU][hapmap]
rs1342542	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.83[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2027089	0.85[CEU][hapmap];0.86[JPT][hapmap]
rs7022948	0.85[CEU][hapmap];0.82[JPT][hapmap]
rs7026025	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.82[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7027858	0.93[ASN][1000 genomes]
rs7027862	0.85[CEU][hapmap];0.82[JPT][hapmap]
rs7037463	0.82[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7041399	0.85[CEU][hapmap];0.86[JPT][hapmap]
rs7857554	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.94[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7861625	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7871777	0.85[CEU][hapmap];0.90[JPT][hapmap]
rs881167	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[YRI][hapmap];0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:11 , 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	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
7	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
8	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
9	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
10	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
11	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:58 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr9:3474400-3524400	Weak transcription	Thymus	Thymus
2	chr9:3479000-3498800	Weak transcription	Breast Myoepithelial Primary Cells	Breast
3	chr9:3479200-3500200	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
4	chr9:3479200-3507200	Weak transcription	Primary hematopoietic stem cells short term culture	blood
5	chr9:3479400-3508000	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
6	chr9:3479800-3508800	Weak transcription	Primary T helper naive cells from peripheral blood	blood
7	chr9:3479800-3511600	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
8	chr9:3480000-3506400	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
9	chr9:3480200-3499800	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
10	chr9:3480400-3508000	Weak transcription	Primary T helper cells PMA-I stimulated	--
11	chr9:3480600-3500200	Weak transcription	H1 Cell Line	embryonic stem cell
12	chr9:3480600-3508800	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
13	chr9:3480600-3510000	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
14	chr9:3480600-3524600	Weak transcription	Left Ventricle	heart
15	chr9:3480800-3507400	Weak transcription	Primary hematopoietic stem cells	blood
16	chr9:3483000-3499800	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
17	chr9:3483200-3508400	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
18	chr9:3484800-3504200	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
19	chr9:3484800-3507200	Weak transcription	Brain Hippocampus Middle	brain
20	chr9:3485000-3500000	Weak transcription	Primary monocytes fromperipheralblood	blood
21	chr9:3485000-3507400	Weak transcription	Primary B cells from peripheral blood	blood
22	chr9:3485200-3499800	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
23	chr9:3485200-3507800	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
24	chr9:3485600-3500200	Weak transcription	Primary T cells from cord blood	blood
25	chr9:3490000-3500000	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
26	chr9:3490000-3508000	Weak transcription	Primary B cells from cord blood	blood
27	chr9:3490400-3499800	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
28	chr9:3494000-3501000	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
29	chr9:3494400-3501200	Enhancers	Cortex derived primary cultured neurospheres	brain
30	chr9:3496000-3500400	Weak transcription	Fetal Kidney	kidney
31	chr9:3496400-3499000	Enhancers	HSMM	muscle
32	chr9:3496600-3499000	Enhancers	Duodenum Smooth Muscle	Duodenum
33	chr9:3496600-3499200	Enhancers	HSMMtube	muscle
34	chr9:3496800-3498800	Enhancers	Osteobl	bone
35	chr9:3496800-3499200	Enhancers	HUVEC	blood vessel
36	chr9:3496800-3499200	Enhancers	NHLF	lung
37	chr9:3497000-3499000	Enhancers	Brain Anterior Caudate	brain
38	chr9:3497000-3499200	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
39	chr9:3497000-3499200	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
40	chr9:3497000-3499200	Enhancers	Muscle Satellite Cultured Cells	--
41	chr9:3497200-3500000	Weak transcription	GM12878-XiMat	blood
42	chr9:3497400-3499000	Active TSS	Skeletal Muscle Female	skeletal muscle
43	chr9:3497600-3499200	Enhancers	Brain Germinal Matrix	brain
44	chr9:3497600-3500400	Enhancers	iPS-18 Cell Line	embryonic stem cell
45	chr9:3497800-3498800	Weak transcription	Rectal Mucosa Donor 31	rectum
46	chr9:3498000-3498800	Enhancers	Brain Dorsolateral Prefrontal Cortex	brain
47	chr9:3498000-3500400	Enhancers	HUES48 Cell Line	embryonic stem cell
48	chr9:3498200-3499000	Enhancers	Rectal Smooth Muscle	rectum
49	chr9:3498200-3499000	Active TSS	Skeletal Muscle Male	skeletal muscle
50	chr9:3498400-3498800	Weak transcription	HUES64 Cell Line	embryonic stem cell

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