Variant report

Variant	rs13090902
Chromosome Location	chr3:42630225-42630226
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr3:42629929..42632831-chr3:42695818..42698742,2	MCF-7	breast:
2	chr3:42620803..42625287-chr3:42629964..42635186,7	MCF-7	breast:
3	chr3:42622045..42625365-chr3:42627615..42632564,8	MCF-7	breast:
4	chr3:42629985..42631739-chr3:42857764..42859472,2	MCF-7	breast:
5	chr3:42629943..42634676-chr3:42635408..42643782,10	MCF-7	breast:
6	chr3:42617574..42619731-chr3:42628804..42631519,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000093183	Chromatin interaction
ENSG00000114857	Chromatin interaction
ENSG00000008324	Chromatin interaction
ENSG00000230084	Chromatin interaction

Extended variants
information (count: 84 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:83)

rs_ID	r²[population]
rs1062051	0.96[AMR][1000 genomes];0.91[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs13067987	0.81[EUR][1000 genomes]
rs13072295	0.83[AFR][1000 genomes];0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs13085695	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs13089845	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13093680	0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs13095447	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs17074602	0.83[ASN][1000 genomes]
rs17074662	0.84[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs17074664	0.89[ASN][1000 genomes]
rs17074669	0.89[ASN][1000 genomes]
rs17074673	0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs17074674	0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs17074680	0.89[ASN][1000 genomes]
rs17074693	0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2241542	0.83[ASN][1000 genomes]
rs2271182	0.84[ASN][1000 genomes]
rs2284303	0.83[AFR][1000 genomes];0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2284304	0.83[AFR][1000 genomes];0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs2300057	0.83[AFR][1000 genomes];0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs2300058	0.83[AFR][1000 genomes];0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs2302352	0.82[AFR][1000 genomes];0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs33969824	0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs33984028	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs34683820	0.88[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs34687113	0.86[AFR][1000 genomes];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs34762478	0.88[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs34801786	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34852409	0.89[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs34977988	0.89[AFR][1000 genomes];0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs35216140	0.82[EUR][1000 genomes]
rs35506005	0.81[ASN][1000 genomes]
rs35676838	0.89[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35770315	0.89[ASN][1000 genomes]
rs35871059	0.82[EUR][1000 genomes]
rs35890296	0.89[AMR][1000 genomes];1.00[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs36033201	0.84[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs36043081	0.82[EUR][1000 genomes]
rs3774401	0.86[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs3774402	0.86[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs3774404	0.86[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs3774406	0.81[ASN][1000 genomes]
rs3774407	0.84[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs3821836	0.92[ASN][1000 genomes]
rs3846058	0.86[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs3846059	0.87[AMR][1000 genomes];1.00[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs3856737	0.87[AMR][1000 genomes];1.00[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs3886782	0.97[ASN][1000 genomes]
rs3900780	0.81[EUR][1000 genomes]
rs56047094	0.82[EUR][1000 genomes]
rs56797870	0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs57259216	0.88[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs58868911	0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs59914338	0.85[AMR][1000 genomes];1.00[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs60232916	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs60348477	0.88[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs60535002	0.82[EUR][1000 genomes]
rs61149998	0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs6441928	0.86[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs66786953	0.89[AFR][1000 genomes];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs67059259	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs67165547	0.85[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs67533173	0.81[AFR][1000 genomes];0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs67583158	0.82[EUR][1000 genomes]
rs6771105	0.82[EUR][1000 genomes]
rs6772312	0.95[ASN][1000 genomes]
rs6778982	0.88[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs6782164	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs67832425	0.82[EUR][1000 genomes]
rs6788548	0.88[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs6790204	0.81[EUR][1000 genomes]
rs6793186	0.88[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs6795296	0.81[AFR][1000 genomes];0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs6797491	0.82[EUR][1000 genomes]
rs68004576	0.82[EUR][1000 genomes]
rs68028490	0.80[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs68071013	0.80[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs72864072	0.87[AMR][1000 genomes];1.00[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs73829255	0.82[EUR][1000 genomes]
rs7617403	0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs7617736	0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs7623867	0.81[EUR][1000 genomes]
rs7624628	0.86[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.85[ASN][1000 genomes]

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

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1002944	chr3:42559762-42728909	Strong transcription Flanking Active TSS Weak transcription Enhancers Genic enhancers Transcr. at gene 5' and 3' Active TSS ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	41 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:47 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:42624200-42631400	Weak transcription	Placenta Amnion	Placenta Amnion
2	chr3:42624200-42631600	Weak transcription	HSMMtube	muscle
3	chr3:42624400-42631200	Weak transcription	Brain Anterior Caudate	brain
4	chr3:42624400-42631200	Weak transcription	Duodenum Smooth Muscle	Duodenum
5	chr3:42624400-42631200	Weak transcription	Skeletal Muscle Male	skeletal muscle
6	chr3:42624400-42631400	Weak transcription	Liver	Liver
7	chr3:42624400-42631400	Weak transcription	Brain Angular Gyrus	brain
8	chr3:42624400-42631400	Weak transcription	Fetal Muscle Leg	muscle
9	chr3:42624400-42632400	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
10	chr3:42624600-42631200	Weak transcription	Adipose Nuclei	Adipose
11	chr3:42624600-42631400	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
12	chr3:42624600-42631400	Weak transcription	Brain Cingulate Gyrus	brain
13	chr3:42624600-42631400	Weak transcription	Fetal Brain Male	brain
14	chr3:42624600-42631400	Weak transcription	A549	lung
15	chr3:42624800-42631400	Weak transcription	Primary B cells from cord blood	blood
16	chr3:42624800-42631400	Weak transcription	Primary T helper naive cells from peripheral blood	blood
17	chr3:42624800-42631400	Weak transcription	Brain Hippocampus Middle	brain
18	chr3:42624800-42631400	Weak transcription	Duodenum Mucosa	Duodenum
19	chr3:42624800-42631400	Weak transcription	Rectal Mucosa Donor 29	rectum
20	chr3:42624800-42631600	Weak transcription	Cortex derived primary cultured neurospheres	brain
21	chr3:42624800-42631600	Weak transcription	Gastric	stomach
22	chr3:42625000-42631000	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
23	chr3:42625000-42631000	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
24	chr3:42625000-42631200	Weak transcription	Breast Myoepithelial Primary Cells	Breast
25	chr3:42625000-42631200	Weak transcription	GM12878-XiMat	blood
26	chr3:42625000-42631400	Weak transcription	HUES6 Cell Line	embryonic stem cell
27	chr3:42625000-42631400	Weak transcription	Brain Germinal Matrix	brain
28	chr3:42625000-42631400	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
29	chr3:42625000-42631400	Weak transcription	Fetal Intestine Small	intestine
30	chr3:42625000-42631600	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
31	chr3:42625200-42631400	Weak transcription	HUES64 Cell Line	embryonic stem cell
32	chr3:42625200-42631600	Weak transcription	H9 Cell Line	embryonic stem cell
33	chr3:42625400-42631400	Weak transcription	HUES48 Cell Line	embryonic stem cell
34	chr3:42625400-42631400	Weak transcription	iPS-18 Cell Line	embryonic stem cell
35	chr3:42625600-42631200	Weak transcription	Dnd41	blood
36	chr3:42625600-42631400	Weak transcription	iPS-20b Cell Line	embryonic stem cell
37	chr3:42625600-42631400	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
38	chr3:42628000-42631200	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
39	chr3:42628800-42631600	Weak transcription	NHLF	lung
40	chr3:42629000-42631200	Weak transcription	Rectal Smooth Muscle	rectum
41	chr3:42629800-42630400	Enhancers	NHEK	skin
42	chr3:42629800-42631000	Weak transcription	ES-I3 Cell Line	embryonic stem cell
43	chr3:42629800-42631600	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
44	chr3:42630000-42630400	Enhancers	HMEC	breast
45	chr3:42630200-42631000	Weak transcription	K562	blood
46	chr3:42630200-42631600	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
47	chr3:42630200-42631800	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links