Variant report

Variant	rs7039938
Chromosome Location	chr9:3436704-3436705
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 15 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:5)

rs_ID	r²[population]
rs12005509	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs17728710	1.00[EUR][1000 genomes]
rs7850206	1.00[EUR][1000 genomes]
rs913284	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs913285	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:10 , 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	nsv613147	chr9:3368111-3440355	Weak transcription Enhancers Flanking Active TSS ZNF genes & repeats Strong transcription Genic enhancers Active TSS	TF binding region Chromatin interactive region	2 gene(s)	inside rSNPs	diseases
10	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

No data

Chromatin state (count:30 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr9:3398800-3437200	Weak transcription	Primary B cells from cord blood	blood
2	chr9:3419000-3437000	Weak transcription	Brain Substantia Nigra	brain
3	chr9:3422600-3436800	Weak transcription	Psoas Muscle	Psoas
4	chr9:3425600-3453200	Weak transcription	Primary hematopoietic stem cells	blood
5	chr9:3426600-3444600	Weak transcription	Sigmoid Colon	Sigmoid Colon
6	chr9:3426800-3437000	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
7	chr9:3426800-3446200	Weak transcription	Left Ventricle	heart
8	chr9:3428200-3438200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
9	chr9:3428200-3443200	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
10	chr9:3429800-3443800	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
11	chr9:3431800-3441400	Weak transcription	Primary B cells from peripheral blood	blood
12	chr9:3432400-3467800	Weak transcription	GM12878-XiMat	blood
13	chr9:3432600-3437200	Weak transcription	Brain Hippocampus Middle	brain
14	chr9:3432600-3460600	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
15	chr9:3433600-3437800	Enhancers	Pancreatic Islets	Pancreatic Islet
16	chr9:3434400-3437200	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
17	chr9:3435000-3437600	Weak transcription	Brain Angular Gyrus	brain
18	chr9:3435000-3437800	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
19	chr9:3435000-3473200	Weak transcription	Primary T cells from cord blood	blood
20	chr9:3435400-3438200	Enhancers	Brain Germinal Matrix	brain
21	chr9:3435600-3437000	Weak transcription	Primary T helper cells fromperipheralblood	blood
22	chr9:3435800-3444000	Weak transcription	Breast Myoepithelial Primary Cells	Breast
23	chr9:3436200-3437400	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
24	chr9:3436200-3437400	Enhancers	Skeletal Muscle Male	skeletal muscle
25	chr9:3436600-3436800	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
26	chr9:3436600-3437000	Enhancers	Colon Smooth Muscle	Colon
27	chr9:3436600-3437600	Enhancers	Fetal Heart	heart
28	chr9:3436600-3437800	Enhancers	Cortex derived primary cultured neurospheres	brain
29	chr9:3436600-3437800	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
30	chr9:3436600-3439000	Weak transcription	HUVEC	blood vessel

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