Variant report

Variant	rs12343445
Chromosome Location	chr9:116937355-116937356
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr9:116927944..116931145-chr9:116936589..116939261,3	MCF-7	breast:
2	chr9:116918121..116920168-chr9:116937255..116940070,3	K562	blood:
3	chr9:116936810..116939518-chr9:116945636..116948871,3	K562	blood:

Variant related genes	Relation type
ENSG00000196739	Chromatin interaction

Extended variants
information (count: 28 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:15)

rs_ID	r²[population]
rs10739404	0.90[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs10739405	0.93[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs10759683	0.82[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs10759684	1.00[CEU][hapmap];1.00[CHB][hapmap];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs10817576	0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs10982092	0.87[AFR][1000 genomes];0.85[AMR][1000 genomes];0.93[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs1431819	0.83[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs4406486	1.00[CEU][hapmap];1.00[CHB][hapmap];0.94[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs4978568	1.00[CEU][hapmap];1.00[CHB][hapmap];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs4979345	0.94[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs4979346	1.00[CEU][hapmap];1.00[CHB][hapmap];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs4979347	0.85[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs4979349	0.83[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs7855790	1.00[CEU][hapmap];1.00[CHB][hapmap];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs7870521	0.82[AMR][1000 genomes];0.89[EUR][1000 genomes];0.82[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:13 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv430093	chr9:116330446-117325446	Weak transcription Enhancers Strong transcription Flanking Active TSS Bivalent/Poised TSS Active TSS Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	165 gene(s)	inside rSNPs	diseases
2	esv2422396	chr9:116792944-117354862	Weak transcription Enhancers Strong transcription Bivalent Enhancer Flanking Active TSS Genic enhancers Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	155 gene(s)	inside rSNPs	diseases
3	esv2422492	chr9:116811294-117366643	Genic enhancers ZNF genes & repeats Flanking Active TSS Weak transcription Strong transcription Enhancers Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	155 gene(s)	inside rSNPs	diseases
4	esv2761285	chr9:116811897-117103268	Genic enhancers Weak transcription Flanking Active TSS Strong transcription Enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh Active TSS Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	128 gene(s)	inside rSNPs	diseases
5	nsv870215	chr9:116842614-117070344	Enhancers Weak transcription Genic enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Strong transcription Bivalent Enhancer Bivalent/Poised TSS Flanking Active TSS Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	124 gene(s)	inside rSNPs	diseases
6	nsv893752	chr9:116899258-116944333	Flanking Bivalent TSS/Enh Enhancers Weak transcription Flanking Active TSS Genic enhancers Bivalent/Poised TSS Active TSS Bivalent Enhancer Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
7	nsv466531	chr9:116916931-116940418	Active TSS Flanking Bivalent TSS/Enh Weak transcription Enhancers Genic enhancers Strong transcription Flanking Active TSS Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
8	nsv615231	chr9:116916931-116940418	Enhancers Flanking Bivalent TSS/Enh Flanking Active TSS Bivalent Enhancer Strong transcription Active TSS Weak transcription Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
9	nsv466532	chr9:116930100-116957958	Weak transcription Enhancers Strong transcription Active TSS Genic enhancers Flanking Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
10	nsv615232	chr9:116930100-116957958	Weak transcription Enhancers Strong transcription Genic enhancers Flanking Active TSS Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3' Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
11	nsv466533	chr9:116930100-117248479	Enhancers Strong transcription Weak transcription Genic enhancers Flanking Active TSS Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA	128 gene(s)	inside rSNPs	diseases
12	nsv615233	chr9:116930100-117248479	Genic enhancers Weak transcription Enhancers Flanking Active TSS Strong transcription ZNF genes & repeats Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA	128 gene(s)	inside rSNPs	diseases
13	esv2761551	chr9:116935526-116940489	Weak transcription Enhancers Genic enhancers Transcr. at gene 5' and 3' Flanking Active TSS Active TSS Strong transcription	Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:90 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr9:116919000-116937600	Weak transcription	Placenta Amnion	Placenta Amnion
2	chr9:116919200-116972000	Weak transcription	H9 Cell Line	embryonic stem cell
3	chr9:116919600-116939600	Weak transcription	Hela-S3	cervix
4	chr9:116926200-116937400	Weak transcription	Right Ventricle	heart
5	chr9:116926200-116943800	Weak transcription	iPS-20b Cell Line	embryonic stem cell
6	chr9:116926400-116950200	Weak transcription	HUES64 Cell Line	embryonic stem cell
7	chr9:116926400-116950400	Weak transcription	H1 Cell Line	embryonic stem cell
8	chr9:116926600-116939400	Weak transcription	Fetal Kidney	kidney
9	chr9:116929200-116937800	Weak transcription	HUVEC	blood vessel
10	chr9:116930000-116938800	Genic enhancers	Fetal Muscle Leg	muscle
11	chr9:116930600-116954400	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
12	chr9:116931000-116946400	Genic enhancers	Fetal Stomach	stomach
13	chr9:116931000-116971800	Weak transcription	HUES48 Cell Line	embryonic stem cell
14	chr9:116932200-116938600	Genic enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
15	chr9:116932600-116938000	Enhancers	Fetal Thymus	thymus
16	chr9:116932800-116939200	Weak transcription	Osteobl	bone
17	chr9:116932800-116943800	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
18	chr9:116932800-116971800	Weak transcription	iPS-15b Cell Line	embryonic stem cell
19	chr9:116933000-116939400	Weak transcription	Fetal Lung	lung
20	chr9:116933200-116938200	Genic enhancers	Fetal Intestine Small	intestine
21	chr9:116933200-116939000	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
22	chr9:116933200-116939200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
23	chr9:116933200-116940400	Weak transcription	Spleen	Spleen
24	chr9:116934400-116940600	Enhancers	Fetal Adrenal Gland	Adrenal Gland
25	chr9:116934400-116942800	Enhancers	Colon Smooth Muscle	Colon
26	chr9:116934600-116940600	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
27	chr9:116934800-116937600	Weak transcription	Cortex derived primary cultured neurospheres	brain
28	chr9:116934800-116937600	Enhancers	Foreskin Melanocyte Primary Cells skin01	Skin
29	chr9:116934800-116940000	Enhancers	Stomach Smooth Muscle	stomach
30	chr9:116934800-116942000	Enhancers	Rectal Smooth Muscle	rectum
31	chr9:116935000-116937400	Enhancers	Foreskin Fibroblast Primary Cells skin02	Skin
32	chr9:116935000-116946600	Enhancers	Liver	Liver
33	chr9:116935200-116940800	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
34	chr9:116935200-116941600	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
35	chr9:116935200-116942000	Enhancers	Pancreas	Pancrea
36	chr9:116935200-116944800	Enhancers	Fetal Heart	heart
37	chr9:116935200-116944800	Enhancers	Left Ventricle	heart
38	chr9:116935200-116945400	Enhancers	Skeletal Muscle Female	skeletal muscle
39	chr9:116935400-116940000	Enhancers	Fetal Intestine Large	intestine
40	chr9:116935600-116937600	Enhancers	Colonic Mucosa	Colon
41	chr9:116935600-116939000	Weak transcription	Ovary	ovary
42	chr9:116935800-116939000	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
43	chr9:116935800-116939200	Weak transcription	Adipose Nuclei	Adipose
44	chr9:116935800-116939400	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
45	chr9:116936000-116937600	Weak transcription	Aorta	Aorta
46	chr9:116936000-116937800	Enhancers	Brain Substantia Nigra	brain
47	chr9:116936000-116939000	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
48	chr9:116936000-116939400	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
49	chr9:116936000-116939600	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
50	chr9:116936000-116940000	Enhancers	Fetal Muscle Trunk	muscle

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