Variant report

Variant	rs2513525
Chromosome Location	chr11:76266708-76266709
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr11:76265177..76267818-chr11:76279245..76281186,2	K562	blood:
2	chr11:76255778..76257554-chr11:76266242..76268584,2	MCF-7	breast:
3	chr11:76265376..76267987-chr11:76270130..76272636,2	K562	blood:

Variant related genes	Relation type
ENSG00000158636	Chromatin interaction

Extended variants
information (count: 48 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:47)

rs_ID	r²[population]
rs10160382	0.89[GIH][hapmap];0.88[MEX][hapmap];0.82[TSI][hapmap]
rs1044265	1.00[ASW][hapmap]
rs10793167	0.81[CEU][hapmap];0.91[YRI][hapmap]
rs10793169	1.00[ASW][hapmap];0.92[CEU][hapmap];0.80[GIH][hapmap];1.00[MEX][hapmap];0.90[MKK][hapmap];1.00[TSI][hapmap];0.96[YRI][hapmap]
rs10793171	0.93[ASW][hapmap];0.92[CEU][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.83[YRI][hapmap]
rs10899227	0.96[CEU][hapmap];0.86[AMR][1000 genomes]
rs11236739	0.83[JPT][hapmap]
rs11236752	0.80[EUR][1000 genomes]
rs11606394	1.00[ASW][hapmap];0.87[YRI][hapmap]
rs17134821	0.83[JPT][hapmap]
rs17134828	0.83[JPT][hapmap]
rs17749618	0.85[CEU][hapmap]
rs1939467	0.81[CEU][hapmap]
rs1939468	0.85[CEU][hapmap]
rs2155220	0.81[AFR][1000 genomes]
rs2251075	0.87[YRI][hapmap]
rs2508740	0.81[ASW][hapmap];0.96[CEU][hapmap];0.97[GIH][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.89[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs2508741	0.81[ASW][hapmap];0.96[CEU][hapmap];0.97[GIH][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.89[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs2508753	0.85[AFR][1000 genomes];0.93[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs2508756	1.00[ASW][hapmap];0.87[YRI][hapmap]
rs2508759	0.89[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs2508760	1.00[ASW][hapmap];0.96[CEU][hapmap];1.00[MEX][hapmap];0.90[MKK][hapmap];1.00[TSI][hapmap];0.96[YRI][hapmap];0.84[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs2508761	0.93[ASW][hapmap];0.96[CEU][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.83[YRI][hapmap];0.85[AMR][1000 genomes]
rs2508762	0.96[CEU][hapmap];0.89[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs2513504	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2513505	0.82[AFR][1000 genomes];0.91[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs2513508	0.93[ASW][hapmap];0.96[CEU][hapmap];0.80[GIH][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.87[YRI][hapmap];0.91[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs2513513	0.93[ASW][hapmap];1.00[CEU][hapmap];0.80[GIH][hapmap];1.00[MEX][hapmap];0.98[TSI][hapmap];0.83[YRI][hapmap];0.95[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs2513515	0.87[YRI][hapmap]
rs2513520	0.96[CEU][hapmap];0.84[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs2513523	0.93[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs3753051	0.85[CEU][hapmap]
rs3814711	0.92[CEU][hapmap]
rs4245443	0.93[ASW][hapmap];0.88[CEU][hapmap];0.80[GIH][hapmap];0.94[MEX][hapmap];1.00[TSI][hapmap];0.83[YRI][hapmap]
rs4272809	1.00[ASW][hapmap];0.96[CEU][hapmap];0.80[GIH][hapmap];1.00[MEX][hapmap];0.90[MKK][hapmap];1.00[TSI][hapmap];0.96[YRI][hapmap]
rs4300410	1.00[ASW][hapmap];0.96[CEU][hapmap];0.80[GIH][hapmap];1.00[MEX][hapmap];0.90[MKK][hapmap];1.00[TSI][hapmap];0.96[YRI][hapmap]
rs4625500	0.86[YRI][hapmap]
rs4945087	0.86[ASW][hapmap];0.87[YRI][hapmap]
rs4945090	0.96[CEU][hapmap];0.91[YRI][hapmap]
rs55977477	0.88[EUR][1000 genomes]
rs7107058	1.00[ASW][hapmap];0.92[CEU][hapmap];1.00[MEX][hapmap];0.90[MKK][hapmap];0.96[TSI][hapmap];0.96[YRI][hapmap]
rs7123361	0.85[CEU][hapmap];0.81[GIH][hapmap]
rs7125552	0.81[CEU][hapmap]
rs7926009	1.00[ASW][hapmap];0.96[CEU][hapmap];1.00[MEX][hapmap];0.90[MKK][hapmap];1.00[TSI][hapmap];0.96[YRI][hapmap]
rs7927515	0.89[CHB][hapmap];0.82[JPT][hapmap]
rs7949258	0.81[CEU][hapmap]
rs8848	0.93[ASW][hapmap];1.00[CEU][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.83[YRI][hapmap];0.91[AMR][1000 genomes];0.89[EUR][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	nsv1050713	chr11:76147085-76267117	Transcr. at gene 5' and 3' Weak transcription Flanking Active TSS Strong transcription ZNF genes & repeats Enhancers Active TSS Genic enhancers Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	45 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs2513525	ALG8	cis	cerebellum	SCAN
rs2513525	ARHGEF17	cis	cerebellum	SCAN

Chromatin state (count:45 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr11:76254800-76269800	Weak transcription	NHDF-Ad	bronchial
2	chr11:76256000-76273400	Weak transcription	Psoas Muscle	Psoas
3	chr11:76257200-76270200	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
4	chr11:76257200-76272200	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
5	chr11:76257400-76267800	Weak transcription	Esophagus	oesophagus
6	chr11:76257400-76269800	Weak transcription	Muscle Satellite Cultured Cells	--
7	chr11:76257400-76269800	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
8	chr11:76257400-76270600	Weak transcription	Skeletal Muscle Male	skeletal muscle
9	chr11:76257400-76270800	Weak transcription	Brain Cingulate Gyrus	brain
10	chr11:76257400-76271000	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
11	chr11:76257400-76271000	Weak transcription	HSMMtube	muscle
12	chr11:76257400-76271000	Weak transcription	NHEK	skin
13	chr11:76257400-76271800	Weak transcription	Lung	lung
14	chr11:76257400-76272200	Weak transcription	Spleen	Spleen
15	chr11:76257400-76272400	Weak transcription	Ovary	ovary
16	chr11:76257800-76271400	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
17	chr11:76258000-76270600	Weak transcription	Brain Substantia Nigra	brain
18	chr11:76258200-76270600	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
19	chr11:76258400-76270600	Weak transcription	Adipose Nuclei	Adipose
20	chr11:76258400-76270600	Weak transcription	NH-A	brain
21	chr11:76258600-76271600	Weak transcription	Primary T helper cells PMA-I stimulated	--
22	chr11:76259200-76271000	Weak transcription	Left Ventricle	heart
23	chr11:76259600-76271200	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
24	chr11:76259800-76271200	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
25	chr11:76260600-76271000	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
26	chr11:76261400-76268600	Weak transcription	Fetal Muscle Leg	muscle
27	chr11:76261400-76270000	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
28	chr11:76261400-76279200	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
29	chr11:76261600-76270800	Weak transcription	Fetal Muscle Trunk	muscle
30	chr11:76262000-76270600	Weak transcription	Placenta	Placenta
31	chr11:76262000-76270800	Weak transcription	Hela-S3	cervix
32	chr11:76262000-76271000	Weak transcription	Primary T cells fromperipheralblood	blood
33	chr11:76262200-76270600	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
34	chr11:76262600-76270200	Weak transcription	Osteobl	bone
35	chr11:76264200-76266800	Weak transcription	ES-I3 Cell Line	embryonic stem cell
36	chr11:76264400-76268600	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
37	chr11:76265000-76267200	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
38	chr11:76265400-76270000	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
39	chr11:76265800-76270800	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
40	chr11:76266000-76266800	Enhancers	Rectal Mucosa Donor 29	rectum
41	chr11:76266000-76270000	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
42	chr11:76266000-76270200	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
43	chr11:76266400-76267000	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
44	chr11:76266600-76266800	Enhancers	Small Intestine	intestine
45	chr11:76266600-76267000	Weak transcription	Aorta	Aorta

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links