Variant report

Variant	rs2382456
Chromosome Location	chr9:14197958-14197959
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr9:14197932..14199524-chr9:14315702..14317595,2	MCF-7	breast:
2	chr9:14185623..14188206-chr9:14197745..14200671,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000225472	Chromatin interaction

Extended variants
information (count: 48 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:39)

rs_ID	r²[population]
rs10738355	0.91[CEU][hapmap];1.00[CHB][hapmap];0.90[CHD][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.96[TSI][hapmap];0.85[YRI][hapmap];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10738356	0.91[EUR][1000 genomes]
rs10756532	0.82[CHB][hapmap]
rs10756535	0.82[AMR][1000 genomes]
rs10756536	0.86[CHB][hapmap];0.81[JPT][hapmap]
rs10810104	0.81[EUR][1000 genomes]
rs10810106	0.91[CEU][hapmap];0.90[CHB][hapmap];1.00[JPT][hapmap];0.90[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs10810110	0.83[MEX][hapmap];0.91[TSI][hapmap];0.88[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs10810113	0.80[CHB][hapmap]
rs10810114	0.80[CHB][hapmap]
rs10961400	0.95[CHB][hapmap]
rs10961402	0.90[CHB][hapmap];0.85[AMR][1000 genomes]
rs10961413	0.90[CEU][hapmap];0.88[CHB][hapmap];0.93[JPT][hapmap];0.91[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs10961414	0.83[CEU][hapmap];0.82[EUR][1000 genomes]
rs10961420	0.82[CHB][hapmap]
rs12235129	0.88[EUR][1000 genomes]
rs12376024	0.82[AMR][1000 genomes]
rs12377502	0.95[CHB][hapmap]
rs13287487	0.83[CEU][hapmap]
rs2382448	0.80[CHB][hapmap]
rs2382450	0.91[CEU][hapmap];0.80[CHB][hapmap]
rs2382451	0.83[CEU][hapmap]
rs2382454	0.91[CEU][hapmap];1.00[CHB][hapmap];0.84[CHD][hapmap];1.00[JPT][hapmap];0.94[MEX][hapmap];0.91[TSI][hapmap];0.85[AMR][1000 genomes];0.94[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2382457	0.91[CEU][hapmap];0.90[CHB][hapmap];0.81[JPT][hapmap];1.00[TSI][hapmap];0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2382458	0.83[CEU][hapmap];0.88[EUR][1000 genomes]
rs2382459	0.91[CEU][hapmap];0.88[GIH][hapmap];0.89[EUR][1000 genomes]
rs2890982	0.80[CHB][hapmap]
rs2890984	0.91[CEU][hapmap];0.90[CHB][hapmap];0.81[JPT][hapmap];0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2890985	0.91[CEU][hapmap];0.93[EUR][1000 genomes]
rs4532695	0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs4551459	0.83[CEU][hapmap];0.80[CHB][hapmap]
rs4628344	0.83[CEU][hapmap];0.87[EUR][1000 genomes]
rs6474822	0.86[CHB][hapmap]
rs6474823	0.91[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.85[YRI][hapmap];0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs6474824	0.82[ASW][hapmap];0.91[CEU][hapmap];1.00[CHB][hapmap];0.87[CHD][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];0.94[MEX][hapmap];0.85[MKK][hapmap];0.96[TSI][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];0.89[AMR][1000 genomes];0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6474825	0.91[CEU][hapmap];0.89[CHB][hapmap];1.00[JPT][hapmap];0.84[AMR][1000 genomes];0.93[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7034162	0.83[CEU][hapmap];0.80[CHB][hapmap];0.86[EUR][1000 genomes]
rs7035474	0.86[CHB][hapmap]
rs73413827	0.91[EUR][1000 genomes];0.86[ASN][1000 genomes]

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	nsv1033764	chr9:13764918-14226168	Enhancers Active TSS Weak transcription Flanking Active TSS Strong transcription Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	8 gene(s)	inside rSNPs	diseases
2	nsv892593	chr9:13948798-14233159	Enhancers Strong transcription Weak transcription Flanking Active TSS Genic enhancers Active TSS Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	7 gene(s)	inside rSNPs	diseases
3	nsv1023303	chr9:14025605-14286269	Enhancers Weak transcription Active TSS Flanking Active TSS Strong transcription Genic enhancers Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	6 gene(s)	inside rSNPs	diseases
4	nsv540069	chr9:14025605-14286269	Weak transcription Enhancers Active TSS Strong transcription Flanking Active TSS Genic enhancers Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	6 gene(s)	inside rSNPs	diseases
5	nsv1029491	chr9:14033607-14942373	Enhancers ZNF genes & repeats Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Flanking Active TSS Weak transcription Strong transcription Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	25 gene(s)	inside rSNPs	diseases
6	nsv429998	chr9:14043516-14214688	Weak transcription Flanking Active TSS Enhancers Strong transcription Genic enhancers Active TSS Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	5 gene(s)	inside rSNPs	diseases
7	nsv892596	chr9:14145487-14208724	Weak transcription Flanking Active TSS Enhancers Active TSS Genic enhancers Strong transcription Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region	3 gene(s)	inside rSNPs	diseases
8	nsv892597	chr9:14163383-14233159	Flanking Active TSS Enhancers Weak transcription Active TSS Strong transcription Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region Chromatin interactive region	3 gene(s)	inside rSNPs	diseases
9	nsv915804	chr9:14182608-14903050	Enhancers Strong transcription Weak transcription Flanking Active TSS Flanking Bivalent TSS/Enh Active TSS ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	23 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	chr9:14123800-14198600	Weak transcription	Gastric	stomach
2	chr9:14177200-14203400	Weak transcription	Fetal Muscle Trunk	muscle
3	chr9:14182000-14198600	Weak transcription	Ovary	ovary
4	chr9:14182800-14198200	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
5	chr9:14183800-14198400	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
6	chr9:14186000-14198600	Weak transcription	Lung	lung
7	chr9:14186800-14198600	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
8	chr9:14187800-14198400	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
9	chr9:14188200-14198600	Weak transcription	Fetal Stomach	stomach
10	chr9:14188200-14199000	Weak transcription	iPS-18 Cell Line	embryonic stem cell
11	chr9:14189000-14198600	Weak transcription	Aorta	Aorta
12	chr9:14189800-14198600	Weak transcription	Small Intestine	intestine
13	chr9:14190400-14198000	Weak transcription	Muscle Satellite Cultured Cells	--
14	chr9:14190600-14198800	Weak transcription	A549	lung
15	chr9:14191800-14202800	Enhancers	Fetal Heart	heart
16	chr9:14192800-14198600	Weak transcription	iPS-20b Cell Line	embryonic stem cell
17	chr9:14192800-14198600	Weak transcription	Brain Cingulate Gyrus	brain
18	chr9:14192800-14198600	Weak transcription	Left Ventricle	heart
19	chr9:14192800-14198600	Weak transcription	Pancreas	Pancrea
20	chr9:14192800-14198800	Weak transcription	H1 Cell Line	embryonic stem cell
21	chr9:14192800-14207400	Weak transcription	Spleen	Spleen
22	chr9:14192800-14213400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
23	chr9:14193800-14203000	Enhancers	Fetal Brain Female	brain
24	chr9:14194000-14198400	Weak transcription	Brain Hippocampus Middle	brain
25	chr9:14194400-14198200	Weak transcription	Rectal Smooth Muscle	rectum
26	chr9:14194600-14199000	Enhancers	HUVEC	blood vessel
27	chr9:14194800-14198000	Weak transcription	Brain Germinal Matrix	brain
28	chr9:14195200-14198400	Weak transcription	Brain Substantia Nigra	brain
29	chr9:14195200-14198600	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
30	chr9:14195200-14198600	Weak transcription	Psoas Muscle	Psoas
31	chr9:14195800-14198000	Weak transcription	Brain Anterior Caudate	brain
32	chr9:14196000-14198000	Weak transcription	Sigmoid Colon	Sigmoid Colon
33	chr9:14196000-14199000	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
34	chr9:14196000-14205400	Enhancers	Fetal Lung	lung
35	chr9:14196600-14198600	Weak transcription	ES-I3 Cell Line	embryonic stem cell
36	chr9:14196600-14198800	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
37	chr9:14197000-14198600	Enhancers	Stomach Smooth Muscle	stomach
38	chr9:14197000-14201400	Enhancers	Duodenum Smooth Muscle	Duodenum
39	chr9:14197000-14201400	Enhancers	HMEC	breast
40	chr9:14197200-14198000	Weak transcription	Cortex derived primary cultured neurospheres	brain
41	chr9:14197200-14198000	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
42	chr9:14197200-14198400	Weak transcription	Liver	Liver
43	chr9:14197200-14199800	Enhancers	Fetal Brain Male	brain
44	chr9:14197400-14198400	Weak transcription	HSMMtube	muscle
45	chr9:14197400-14198600	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
46	chr9:14197400-14198600	Enhancers	Adipose Nuclei	Adipose
47	chr9:14197400-14198600	Enhancers	Skeletal Muscle Male	skeletal muscle
48	chr9:14197600-14198600	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
49	chr9:14197600-14198600	Weak transcription	Breast Myoepithelial Primary Cells	Breast
50	chr9:14197600-14198600	Enhancers	Right Atrium	heart

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