Variant report

Variant	rs516090
Chromosome Location	chr9:14099484-14099485
allele	A/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr9:14081509..14084690-chr9:14096320..14100204,3	MCF-7	breast:
2	chr9:14097652..14100494-chr9:14313670..14316038,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000147862	Chromatin interaction

Extended variants
information (count: 22 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:16)

rs_ID	r²[population]
rs10756530	0.84[EUR][1000 genomes]
rs10810093	0.81[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs1689280	0.82[EUR][1000 genomes]
rs35870361	0.89[EUR][1000 genomes]
rs480700	0.83[EUR][1000 genomes]
rs497789	0.92[AMR][1000 genomes];0.92[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs508940	0.90[AFR][1000 genomes];0.91[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs510777	0.96[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs516075	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs516325	0.81[EUR][1000 genomes]
rs574460	0.89[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs580501	0.82[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs580845	0.80[AMR][1000 genomes];0.84[ASN][1000 genomes]
rs7019649	0.80[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs7034211	0.80[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs7862890	0.80[AMR][1000 genomes];0.82[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:6 , 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

No data

Chromatin state (count:67 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr9:14075400-14116000	Weak transcription	Gastric	stomach
2	chr9:14078000-14112800	Weak transcription	Duodenum Mucosa	Duodenum
3	chr9:14081400-14115800	Weak transcription	Hela-S3	cervix
4	chr9:14086000-14115600	Weak transcription	Rectal Mucosa Donor 31	rectum
5	chr9:14090600-14115200	Weak transcription	Brain Cingulate Gyrus	brain
6	chr9:14096600-14099600	Weak transcription	Right Ventricle	heart
7	chr9:14096800-14099600	Enhancers	Cortex derived primary cultured neurospheres	brain
8	chr9:14096800-14099800	Weak transcription	Fetal Muscle Trunk	muscle
9	chr9:14096800-14120000	Weak transcription	Brain Substantia Nigra	brain
10	chr9:14097400-14103200	Weak transcription	Brain Angular Gyrus	brain
11	chr9:14097400-14111800	Weak transcription	Left Ventricle	heart
12	chr9:14097400-14135400	Weak transcription	HSMMtube	muscle
13	chr9:14097600-14102400	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
14	chr9:14097600-14102400	Weak transcription	Brain Germinal Matrix	brain
15	chr9:14097600-14112400	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
16	chr9:14097800-14107600	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
17	chr9:14097800-14111800	Weak transcription	HMEC	breast
18	chr9:14098200-14100000	Enhancers	Skeletal Muscle Male	skeletal muscle
19	chr9:14098200-14106600	Weak transcription	iPS-20b Cell Line	embryonic stem cell
20	chr9:14098400-14100200	Genic enhancers	Fetal Muscle Leg	muscle
21	chr9:14098400-14102400	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
22	chr9:14098400-14103000	Weak transcription	NHEK	skin
23	chr9:14098400-14115800	Weak transcription	Rectal Mucosa Donor 29	rectum
24	chr9:14098800-14099800	Enhancers	HUVEC	blood vessel
25	chr9:14098800-14100000	Enhancers	Fetal Lung	lung
26	chr9:14098800-14100200	Weak transcription	H1 Cell Line	embryonic stem cell
27	chr9:14098800-14100200	Enhancers	Fetal Heart	heart
28	chr9:14098800-14102000	Weak transcription	Breast Myoepithelial Primary Cells	Breast
29	chr9:14098800-14102400	Weak transcription	Brain Anterior Caudate	brain
30	chr9:14098800-14102400	Weak transcription	Rectal Smooth Muscle	rectum
31	chr9:14098800-14102800	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
32	chr9:14098800-14103000	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
33	chr9:14098800-14107600	Weak transcription	Fetal Intestine Small	intestine
34	chr9:14098800-14115600	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
35	chr9:14098800-14116000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
36	chr9:14099000-14099600	Weak transcription	Duodenum Smooth Muscle	Duodenum
37	chr9:14099000-14102200	Weak transcription	HSMM	muscle
38	chr9:14099000-14102800	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
39	chr9:14099000-14107600	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
40	chr9:14099000-14111800	Weak transcription	Pancreas	Pancrea
41	chr9:14099000-14112200	Weak transcription	Stomach Smooth Muscle	stomach
42	chr9:14099000-14112600	Weak transcription	Skeletal Muscle Female	skeletal muscle
43	chr9:14099000-14113600	Weak transcription	Fetal Brain Male	brain
44	chr9:14099000-14115600	Weak transcription	Sigmoid Colon	Sigmoid Colon
45	chr9:14099000-14116000	Weak transcription	Psoas Muscle	Psoas
46	chr9:14099200-14100200	Enhancers	A549	lung
47	chr9:14099200-14101600	Weak transcription	HUES48 Cell Line	embryonic stem cell
48	chr9:14099200-14101800	Weak transcription	ES-I3 Cell Line	embryonic stem cell
49	chr9:14099200-14101800	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
50	chr9:14099200-14102000	Weak transcription	iPS-18 Cell Line	embryonic stem cell

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links