Variant report

Variant	rs2382459
Chromosome Location	chr9:14201649-14201650
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	chr9:14200461..14204358-chr9:14312033..14315867,4	MCF-7	breast:

Variant related genes	Relation type
ENSG00000147862	Chromatin interaction

Extended variants
information (count: 47 )
Associated
traits (count: 1 )

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

rs_ID	r²[population]
rs10738355	1.00[CEU][hapmap];0.90[EUR][1000 genomes]
rs10738356	0.85[AMR][1000 genomes];0.93[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs10738357	0.86[AFR][1000 genomes]
rs10756532	0.81[CHB][hapmap]
rs10756536	0.85[CHB][hapmap]
rs10756539	0.81[EUR][1000 genomes]
rs10810106	1.00[CEU][hapmap];0.85[CHB][hapmap];0.88[EUR][1000 genomes]
rs10810110	0.91[CHB][hapmap];0.88[CHD][hapmap];0.89[JPT][hapmap];0.90[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs10810113	1.00[ASW][hapmap];0.81[CHD][hapmap];0.88[LWK][hapmap];1.00[YRI][hapmap];0.89[AFR][1000 genomes];0.86[AMR][1000 genomes]
rs10810114	0.89[AFR][1000 genomes];0.86[AMR][1000 genomes]
rs10961413	1.00[CEU][hapmap];0.89[EUR][1000 genomes]
rs10961414	0.91[CEU][hapmap]
rs10961419	0.82[AFR][1000 genomes]
rs10961420	0.83[JPT][hapmap];0.83[ASN][1000 genomes]
rs12235129	0.88[EUR][1000 genomes]
rs12551619	0.85[YRI][hapmap]
rs13287487	0.91[CEU][hapmap]
rs2382448	0.81[CEU][hapmap];0.81[CHB][hapmap]
rs2382450	1.00[CEU][hapmap];0.81[CHB][hapmap]
rs2382451	0.91[CEU][hapmap]
rs2382454	1.00[CEU][hapmap];0.89[EUR][1000 genomes]
rs2382456	0.91[CEU][hapmap];0.88[GIH][hapmap];0.89[EUR][1000 genomes]
rs2382457	1.00[CEU][hapmap];0.81[CHB][hapmap];0.91[EUR][1000 genomes]
rs2382458	0.91[CEU][hapmap];1.00[CHB][hapmap];0.82[JPT][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];0.97[AMR][1000 genomes];0.95[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs2890982	0.81[CEU][hapmap];0.81[CHB][hapmap];0.82[TSI][hapmap]
rs2890984	1.00[CEU][hapmap];0.81[CHB][hapmap];0.91[EUR][1000 genomes]
rs2890985	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4532695	0.91[EUR][1000 genomes]
rs4551459	0.91[CEU][hapmap];0.81[CHB][hapmap]
rs4628344	0.91[CEU][hapmap];1.00[YRI][hapmap];0.88[AFR][1000 genomes];0.81[EUR][1000 genomes]
rs61754862	0.83[AMR][1000 genomes]
rs6474822	0.85[CHB][hapmap]
rs6474823	1.00[CEU][hapmap];0.89[EUR][1000 genomes]
rs6474824	1.00[CEU][hapmap];0.88[EUR][1000 genomes]
rs6474825	1.00[CEU][hapmap];0.88[EUR][1000 genomes]
rs7034162	0.91[CEU][hapmap];0.81[CHB][hapmap];0.82[EUR][1000 genomes]
rs7035474	0.85[CHB][hapmap]
rs73413827	0.89[EUR][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

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs2382459	NFIB	cis	lymphoblastoid	seeQTL

Chromatin state (count:65 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr9:14177200-14203400	Weak transcription	Fetal Muscle Trunk	muscle
2	chr9:14191800-14202800	Enhancers	Fetal Heart	heart
3	chr9:14192800-14207400	Weak transcription	Spleen	Spleen
4	chr9:14192800-14213400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
5	chr9:14193800-14203000	Enhancers	Fetal Brain Female	brain
6	chr9:14196000-14205400	Enhancers	Fetal Lung	lung
7	chr9:14197600-14202800	Weak transcription	Rectal Mucosa Donor 31	rectum
8	chr9:14198200-14204000	Enhancers	Colon Smooth Muscle	Colon
9	chr9:14198600-14203200	Enhancers	Breast Myoepithelial Primary Cells	Breast
10	chr9:14199000-14209200	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
11	chr9:14199200-14202200	Weak transcription	HSMMtube	muscle
12	chr9:14199200-14203200	Weak transcription	NHLF	lung
13	chr9:14199200-14209600	Weak transcription	ES-I3 Cell Line	embryonic stem cell
14	chr9:14199400-14202800	Weak transcription	Brain Cingulate Gyrus	brain
15	chr9:14199400-14203000	Weak transcription	Duodenum Mucosa	Duodenum
16	chr9:14199400-14203200	Weak transcription	HSMM	muscle
17	chr9:14199400-14205600	Weak transcription	Small Intestine	intestine
18	chr9:14199400-14207400	Weak transcription	Esophagus	oesophagus
19	chr9:14199400-14207400	Weak transcription	Gastric	stomach
20	chr9:14199400-14209400	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
21	chr9:14199400-14215800	Weak transcription	H1 Cell Line	embryonic stem cell
22	chr9:14199600-14202200	Weak transcription	NH-A	brain
23	chr9:14199600-14202400	Weak transcription	Brain Hippocampus Middle	brain
24	chr9:14199600-14202400	Enhancers	Stomach Smooth Muscle	stomach
25	chr9:14199600-14203000	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
26	chr9:14199600-14203000	Weak transcription	Ovary	ovary
27	chr9:14199800-14202200	Weak transcription	Brain Germinal Matrix	brain
28	chr9:14199800-14202800	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
29	chr9:14199800-14203000	Weak transcription	Brain Anterior Caudate	brain
30	chr9:14200000-14202200	Weak transcription	Brain Inferior Temporal Lobe	brain
31	chr9:14200000-14202800	Weak transcription	Brain Substantia Nigra	brain
32	chr9:14200000-14203000	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
33	chr9:14200000-14203000	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
34	chr9:14200000-14203000	Weak transcription	Muscle Satellite Cultured Cells	--
35	chr9:14200000-14203600	Weak transcription	A549	lung
36	chr9:14200200-14202400	Weak transcription	Liver	Liver
37	chr9:14200200-14202400	Weak transcription	Fetal Stomach	stomach
38	chr9:14200200-14202400	Weak transcription	Rectal Smooth Muscle	rectum
39	chr9:14200200-14202800	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
40	chr9:14200200-14202800	Weak transcription	Osteobl	bone
41	chr9:14200200-14203000	Weak transcription	Stomach Mucosa	stomach
42	chr9:14200200-14203200	Weak transcription	Brain Angular Gyrus	brain
43	chr9:14200200-14203600	Weak transcription	Pancreas	Pancrea
44	chr9:14200200-14205400	Weak transcription	NHDF-Ad	bronchial
45	chr9:14200200-14207200	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
46	chr9:14200200-14207400	Weak transcription	Lung	lung
47	chr9:14201200-14202600	Weak transcription	Skeletal Muscle Male	skeletal muscle
48	chr9:14201200-14203000	Weak transcription	NHEK	skin
49	chr9:14201200-14220000	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
50	chr9:14201400-14202200	Weak transcription	Duodenum Smooth Muscle	Duodenum

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