Variant report

Variant	rs2890982
Chromosome Location	chr9:14181653-14181654
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	chr9:14180288..14182933-chr9:14314004..14316162,2	MCF-7	breast:
2	chr9:14180541..14184155-chr9:14313790..14316409,3	MCF-7	breast:

Variant related genes	Relation type
ENSG00000147862	Chromatin interaction

Extended variants
information (count: 46 )
Associated
traits (count: 1 )

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

rs_ID	r²[population]
rs10738355	0.81[CEU][hapmap];0.80[CHB][hapmap]
rs10756532	0.91[CHB][hapmap];0.87[ASN][1000 genomes]
rs10756535	0.81[ASN][1000 genomes]
rs10756536	0.95[CHB][hapmap];0.85[GIH][hapmap];0.85[MEX][hapmap];0.82[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs10810104	0.96[ASN][1000 genomes]
rs10810106	0.81[CEU][hapmap];0.95[CHB][hapmap]
rs10810110	0.82[CHB][hapmap]
rs10961399	0.89[CEU][hapmap];0.95[CHB][hapmap];0.82[JPT][hapmap];0.83[AMR][1000 genomes];0.89[ASN][1000 genomes]
rs10961400	0.90[CEU][hapmap]
rs10961402	0.89[CEU][hapmap];0.80[CHB][hapmap]
rs10961413	0.88[CHB][hapmap]
rs10961420	0.89[CEU][hapmap]
rs12375873	0.89[CEU][hapmap]
rs12377502	0.85[GIH][hapmap]
rs12552956	0.82[ASN][1000 genomes]
rs12685276	0.89[CEU][hapmap]
rs13299433	0.87[AMR][1000 genomes];0.88[ASN][1000 genomes]
rs1873896	0.89[ASN][1000 genomes]
rs2382448	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2382450	0.81[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.85[GIH][hapmap];1.00[JPT][hapmap];0.85[MEX][hapmap];0.85[AMR][1000 genomes];0.89[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2382451	0.91[YRI][hapmap]
rs2382454	0.81[CEU][hapmap];0.80[CHB][hapmap]
rs2382456	0.80[CHB][hapmap]
rs2382457	0.81[CEU][hapmap]
rs2382458	0.81[CHB][hapmap]
rs2382459	0.81[CEU][hapmap];0.81[CHB][hapmap];0.82[TSI][hapmap]
rs28546939	0.87[AMR][1000 genomes];0.89[ASN][1000 genomes]
rs2890984	0.81[CEU][hapmap]
rs2890985	0.81[CEU][hapmap]
rs4551459	1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[ASN][1000 genomes]
rs4740560	0.82[YRI][hapmap]
rs6474822	0.95[CHB][hapmap];0.90[CHD][hapmap];0.85[GIH][hapmap];0.94[JPT][hapmap];0.84[MEX][hapmap];0.81[AMR][1000 genomes];0.83[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs6474823	0.81[CEU][hapmap]
rs6474824	0.81[CEU][hapmap];0.80[CHB][hapmap];0.85[GIH][hapmap]
rs6474825	0.80[CEU][hapmap]
rs7034162	1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[ASN][1000 genomes]
rs7035474	0.95[CHB][hapmap];0.90[CHD][hapmap];0.94[JPT][hapmap];0.85[MEX][hapmap];0.91[YRI][hapmap];0.89[AMR][1000 genomes];0.83[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs9776572	0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:8 , 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

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs2890982	NFIB	cis	lymphoblastoid	seeQTL

Chromatin state (count:59 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr9:14123800-14198600	Weak transcription	Gastric	stomach
2	chr9:14165800-14181800	Weak transcription	Psoas Muscle	Psoas
3	chr9:14166200-14183200	Weak transcription	Esophagus	oesophagus
4	chr9:14170400-14186200	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
5	chr9:14172200-14181800	Weak transcription	Right Ventricle	heart
6	chr9:14177200-14203400	Weak transcription	Fetal Muscle Trunk	muscle
7	chr9:14179600-14183400	Enhancers	Fetal Heart	heart
8	chr9:14179600-14183400	Enhancers	NH-A	brain
9	chr9:14180000-14183400	Enhancers	Cortex derived primary cultured neurospheres	brain
10	chr9:14180200-14182000	Flanking Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
11	chr9:14180200-14182000	Enhancers	Fetal Stomach	stomach
12	chr9:14180200-14182000	Flanking Active TSS	HMEC	breast
13	chr9:14180600-14181800	Flanking Active TSS	Adipose Nuclei	Adipose
14	chr9:14180600-14181800	Weak transcription	Sigmoid Colon	Sigmoid Colon
15	chr9:14180600-14181800	Active TSS	Stomach Smooth Muscle	stomach
16	chr9:14180600-14182000	Flanking Active TSS	NHEK	skin
17	chr9:14180800-14182200	Enhancers	Fetal Adrenal Gland	Adrenal Gland
18	chr9:14180800-14183600	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
19	chr9:14181000-14181800	Flanking Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
20	chr9:14181000-14181800	Weak transcription	Left Ventricle	heart
21	chr9:14181000-14181800	Active TSS	Right Atrium	heart
22	chr9:14181000-14182400	Enhancers	Brain Dorsolateral Prefrontal Cortex	brain
23	chr9:14181000-14182400	Weak transcription	Fetal Brain Male	brain
24	chr9:14181000-14189200	Weak transcription	Fetal Muscle Leg	muscle
25	chr9:14181000-14189200	Weak transcription	Small Intestine	intestine
26	chr9:14181000-14192400	Weak transcription	Pancreas	Pancrea
27	chr9:14181200-14182000	Flanking Active TSS	HUVEC	blood vessel
28	chr9:14181200-14182400	Enhancers	Fetal Brain Female	brain
29	chr9:14181200-14182800	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
30	chr9:14181400-14181800	Flanking Active TSS	Foreskin Keratinocyte Primary Cells skin03	Skin
31	chr9:14181400-14181800	Weak transcription	Brain Germinal Matrix	brain
32	chr9:14181400-14181800	Enhancers	Brain Substantia Nigra	brain
33	chr9:14181400-14181800	Enhancers	Rectal Smooth Muscle	rectum
34	chr9:14181400-14182200	Enhancers	Liver	Liver
35	chr9:14181400-14182400	Enhancers	Brain Inferior Temporal Lobe	brain
36	chr9:14181400-14182400	Weak transcription	Duodenum Mucosa	Duodenum
37	chr9:14181400-14182600	Enhancers	Brain Angular Gyrus	brain
38	chr9:14181400-14182800	Enhancers	Fetal Lung	lung
39	chr9:14181400-14183400	Enhancers	HSMM	muscle
40	chr9:14181400-14185400	Weak transcription	Stomach Mucosa	stomach
41	chr9:14181600-14181800	Flanking Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
42	chr9:14181600-14181800	Flanking Active TSS	Breast Myoepithelial Primary Cells	Breast
43	chr9:14181600-14181800	Flanking Active TSS	Colon Smooth Muscle	Colon
44	chr9:14181600-14181800	Flanking Active TSS	NHLF	lung
45	chr9:14181600-14182000	Enhancers	Duodenum Smooth Muscle	Duodenum
46	chr9:14181600-14182000	Enhancers	Ovary	ovary
47	chr9:14181600-14182000	Enhancers	Rectal Mucosa Donor 29	rectum
48	chr9:14181600-14182000	Weak transcription	Skeletal Muscle Female	skeletal muscle
49	chr9:14181600-14182000	Enhancers	NHDF-Ad	bronchial
50	chr9:14181600-14182000	Flanking Active TSS	Osteobl	bone

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