Variant report

Variant	rs12336893
Chromosome Location	chr9:2632365-2632366
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr9:2619846..2622881-chr9:2631771..2635491,3	MCF-7	breast:

Variant related genes	Relation type
ENSG00000236404	Chromatin interaction
ENSG00000147852	Chromatin interaction

Extended variants
information (count: 16 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:7)

rs_ID	r²[population]
rs10812377	1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[ASN][1000 genomes]
rs10812378	1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[ASN][1000 genomes]
rs10812379	1.00[CHB][hapmap];1.00[JPT][hapmap];0.84[ASN][1000 genomes]
rs10967260	1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[ASN][1000 genomes]
rs6149	0.85[CHB][hapmap];1.00[JPT][hapmap];0.88[ASN][1000 genomes]
rs7024888	1.00[CEU][hapmap]
rs7035616	0.85[CHB][hapmap]

Variant overlapped rSNPs/rCNVs (count:9 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1020530	chr9:1870197-2658587	Weak transcription Flanking Active TSS Strong transcription Enhancers Active TSS Flanking Bivalent TSS/Enh 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 miRNA target site	27 gene(s)	inside rSNPs	diseases
2	nsv530929	chr9:1998911-2925112	Active TSS Weak transcription Strong transcription Flanking Active TSS Enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	39 gene(s)	inside rSNPs	diseases
3	nsv529508	chr9:2267812-2684272	Bivalent/Poised TSS Weak transcription Enhancers Flanking Bivalent TSS/Enh Flanking Active TSS Strong transcription Active TSS ZNF genes & repeats Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	12 gene(s)	inside rSNPs	diseases
4	nsv916750	chr9:2430846-2826706	Enhancers Flanking Active TSS ZNF genes & repeats Strong transcription Weak transcription Active TSS Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	14 gene(s)	inside rSNPs	diseases
5	nsv531564	chr9:2452325-2700375	Flanking Bivalent TSS/Enh Weak transcription Enhancers ZNF genes & repeats Strong transcription Bivalent/Poised TSS Flanking Active TSS Bivalent Enhancer Active TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	12 gene(s)	inside rSNPs	diseases
6	nsv1017581	chr9:2494815-3172020	Enhancers Weak transcription Genic enhancers Strong transcription ZNF genes & repeats Flanking Active TSS Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	27 gene(s)	inside rSNPs	diseases
7	nsv539934	chr9:2494815-3172020	Strong transcription Weak transcription Enhancers Genic enhancers Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer Flanking Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	27 gene(s)	inside rSNPs	diseases
8	nsv1029876	chr9:2526760-2633562	Enhancers Flanking Active TSS Bivalent Enhancer Weak transcription Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases
9	nsv892070	chr9:2610307-2633921	Flanking Active TSS Enhancers Active TSS Bivalent/Poised TSS Bivalent Enhancer Weak transcription Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Strong transcription ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:64 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr9:2623800-2641000	Weak transcription	Esophagus	oesophagus
2	chr9:2624000-2636000	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
3	chr9:2624200-2633800	Weak transcription	Fetal Stomach	stomach
4	chr9:2624200-2635200	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
5	chr9:2624200-2635200	Enhancers	Fetal Heart	heart
6	chr9:2624200-2635600	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
7	chr9:2624200-2636000	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
8	chr9:2624200-2641000	Weak transcription	Aorta	Aorta
9	chr9:2624400-2641200	Weak transcription	Fetal Kidney	kidney
10	chr9:2624400-2643000	Weak transcription	Rectal Smooth Muscle	rectum
11	chr9:2624400-2643200	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
12	chr9:2624600-2632400	Weak transcription	Fetal Lung	lung
13	chr9:2624800-2634000	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
14	chr9:2624800-2635000	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
15	chr9:2624800-2636000	Weak transcription	A549	lung
16	chr9:2625000-2632400	Weak transcription	iPS-20b Cell Line	embryonic stem cell
17	chr9:2625000-2634400	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
18	chr9:2625000-2641000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
19	chr9:2625400-2632600	Weak transcription	Brain Angular Gyrus	brain
20	chr9:2626600-2635000	Weak transcription	Dnd41	blood
21	chr9:2627200-2648400	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
22	chr9:2627400-2632600	Weak transcription	HUES48 Cell Line	embryonic stem cell
23	chr9:2629200-2632400	Weak transcription	Brain Cingulate Gyrus	brain
24	chr9:2629600-2632600	Weak transcription	Pancreatic Islets	Pancreatic Islet
25	chr9:2629600-2633600	Weak transcription	Stomach Mucosa	stomach
26	chr9:2629600-2633800	Weak transcription	H9 Cell Line	embryonic stem cell
27	chr9:2630600-2632600	Weak transcription	Fetal Muscle Leg	muscle
28	chr9:2630600-2632600	Weak transcription	Stomach Smooth Muscle	stomach
29	chr9:2630600-2632800	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
30	chr9:2630600-2633800	Weak transcription	Right Atrium	heart
31	chr9:2630600-2633800	Weak transcription	Right Ventricle	heart
32	chr9:2630600-2633800	Weak transcription	HSMMtube	muscle
33	chr9:2630600-2634200	Weak transcription	Pancreas	Pancrea
34	chr9:2630600-2638000	Weak transcription	Fetal Muscle Trunk	muscle
35	chr9:2630600-2639800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
36	chr9:2630600-2641000	Weak transcription	Gastric	stomach
37	chr9:2630600-2641200	Weak transcription	Lung	lung
38	chr9:2630800-2632600	Weak transcription	Psoas Muscle	Psoas
39	chr9:2630800-2632800	Weak transcription	Adipose Nuclei	Adipose
40	chr9:2631200-2634800	Enhancers	Skeletal Muscle Female	skeletal muscle
41	chr9:2631400-2633800	Enhancers	Skeletal Muscle Male	skeletal muscle
42	chr9:2631600-2633000	Enhancers	iPS-18 Cell Line	embryonic stem cell
43	chr9:2631600-2633200	Enhancers	H1 Cell Line	embryonic stem cell
44	chr9:2631800-2632400	Weak transcription	ES-I3 Cell Line	embryonic stem cell
45	chr9:2631800-2633400	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
46	chr9:2631800-2633400	Enhancers	HUES64 Cell Line	embryonic stem cell
47	chr9:2631800-2634200	Enhancers	Brain Anterior Caudate	brain
48	chr9:2632000-2632600	Enhancers	Brain Hippocampus Middle	brain
49	chr9:2632000-2635600	Enhancers	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
50	chr9:2632200-2632400	Enhancers	Fetal Brain Female	brain

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