Variant report

Variant	rs10515521
Chromosome Location	chr5:142740166-142740167
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr5:142712062..142716024-chr5:142739998..142742842,3	MCF-7	breast:
2	chr5:142738940..142740563-chr5:142783444..142785593,2	K562	blood:

Variant related genes	Relation type
ENSG00000113580	Chromatin interaction
ENSG00000231579	Chromatin interaction

Extended variants
information (count: 33 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:32)

rs_ID	r²[population]
rs10052957	0.85[GIH][hapmap]
rs10076665	0.81[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs10482605	0.87[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs10482633	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[GIH][hapmap];0.95[LWK][hapmap];1.00[MEX][hapmap];0.97[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs10482642	1.00[ASW][hapmap];1.00[CEU][hapmap];0.96[GIH][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.97[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs10482682	1.00[ASW][hapmap];0.82[LWK][hapmap];0.92[YRI][hapmap]
rs10482689	1.00[ASW][hapmap];0.81[CEU][hapmap];0.96[GIH][hapmap];1.00[MEX][hapmap];0.97[TSI][hapmap];0.92[YRI][hapmap];0.91[AFR][1000 genomes];0.95[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs10482700	0.81[AFR][1000 genomes];0.95[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs11740747	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs11740792	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[GIH][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.89[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs1438731	0.95[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs17287758	0.83[AFR][1000 genomes];0.95[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs17339831	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[GIH][hapmap];1.00[LWK][hapmap];0.89[MEX][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs1837262	0.84[GIH][hapmap]
rs1866388	0.85[GIH][hapmap]
rs258750	0.85[GIH][hapmap]
rs2918416	0.85[GIH][hapmap]
rs2918417	0.85[GIH][hapmap]
rs2963149	0.85[GIH][hapmap]
rs4128428	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[GIH][hapmap];1.00[LWK][hapmap];0.88[MEX][hapmap];0.89[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.87[AFR][1000 genomes];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs6188	0.85[GIH][hapmap]
rs6198	1.00[CEU][hapmap];1.00[GIH][hapmap];1.00[MEX][hapmap];0.89[MKK][hapmap];0.97[TSI][hapmap];0.91[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs72801052	0.91[AFR][1000 genomes];0.95[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs72801070	0.87[AFR][1000 genomes];0.95[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs72801079	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs72801081	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs72801083	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs72801086	0.94[AFR][1000 genomes];0.93[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs72801088	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs852977	0.82[GIH][hapmap]
rs852982	0.82[GIH][hapmap]
rs860457	0.82[GIH][hapmap]

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	nsv1023976	chr5:142692062-142813664	Enhancers Flanking Active TSS Genic enhancers Weak transcription Active TSS Strong transcription Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs10515521	NR3C1	Cis_1M	lymphoblastoid	RTeQTL
rs10515521	TAF7	cis	cerebellum	SCAN

Chromatin state (count:83 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:142693800-142747400	Weak transcription	Fetal Muscle Trunk	muscle
2	chr5:142725000-142764200	Weak transcription	Lung	lung
3	chr5:142727600-142740200	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
4	chr5:142733800-142742000	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
5	chr5:142734000-142743000	Enhancers	Primary T helper naive cells from peripheral blood	blood
6	chr5:142734000-142756400	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
7	chr5:142734200-142740400	Weak transcription	Stomach Smooth Muscle	stomach
8	chr5:142734200-142742200	Weak transcription	Sigmoid Colon	Sigmoid Colon
9	chr5:142734200-142743600	Enhancers	Primary T helper cells PMA-I stimulated	--
10	chr5:142734200-142743600	Enhancers	Primary T helper cells fromperipheralblood	blood
11	chr5:142734200-142754200	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
12	chr5:142734400-142740200	Weak transcription	Primary B cells from peripheral blood	blood
13	chr5:142734400-142741000	Weak transcription	Psoas Muscle	Psoas
14	chr5:142734800-142740200	Weak transcription	Right Ventricle	heart
15	chr5:142735600-142740200	Weak transcription	Rectal Smooth Muscle	rectum
16	chr5:142735600-142742400	Weak transcription	Left Ventricle	heart
17	chr5:142735600-142743000	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
18	chr5:142735600-142743600	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
19	chr5:142735600-142743600	Weak transcription	HSMM	muscle
20	chr5:142735600-142743800	Weak transcription	Primary hematopoietic stem cells	blood
21	chr5:142735600-142756000	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
22	chr5:142735800-142748200	Weak transcription	Muscle Satellite Cultured Cells	--
23	chr5:142735800-142751200	Weak transcription	HMEC	breast
24	chr5:142735800-142751800	Weak transcription	NHEK	skin
25	chr5:142736000-142740400	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
26	chr5:142736200-142740600	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
27	chr5:142736200-142741600	Weak transcription	Fetal Muscle Leg	muscle
28	chr5:142736200-142741800	Weak transcription	Right Atrium	heart
29	chr5:142736200-142742200	Weak transcription	Ovary	ovary
30	chr5:142736200-142746200	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
31	chr5:142736200-142748200	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
32	chr5:142736200-142755800	Weak transcription	Small Intestine	intestine
33	chr5:142736200-142756000	Weak transcription	Placenta Amnion	Placenta Amnion
34	chr5:142736800-142740400	Weak transcription	Hela-S3	cervix
35	chr5:142736800-142740600	Weak transcription	Cortex derived primary cultured neurospheres	brain
36	chr5:142736800-142746800	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
37	chr5:142737000-142745200	Weak transcription	Primary neutrophils fromperipheralblood	blood
38	chr5:142737200-142740200	Weak transcription	Skeletal Muscle Male	skeletal muscle
39	chr5:142737200-142740600	Weak transcription	Brain Cingulate Gyrus	brain
40	chr5:142737200-142742600	Weak transcription	Breast Myoepithelial Primary Cells	Breast
41	chr5:142737400-142740200	Weak transcription	Skeletal Muscle Female	skeletal muscle
42	chr5:142737400-142741000	Weak transcription	Osteobl	bone
43	chr5:142737600-142740400	Weak transcription	Brain Inferior Temporal Lobe	brain
44	chr5:142737800-142740200	Weak transcription	Brain Angular Gyrus	brain
45	chr5:142737800-142740200	Weak transcription	Brain Anterior Caudate	brain
46	chr5:142737800-142740200	Weak transcription	Brain Substantia Nigra	brain
47	chr5:142738000-142740200	Weak transcription	Liver	Liver
48	chr5:142738000-142742200	Weak transcription	Monocytes-CD14+_RO01746	blood
49	chr5:142738200-142742000	Enhancers	A549	lung
50	chr5:142738400-142742800	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links