Variant report

Variant	rs638903
Chromosome Location	chr11:120983264-120983265
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 12 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:11)

rs_ID	r²[population]
rs1783777	0.98[ASN][1000 genomes]
rs1783778	1.00[CHB][hapmap];0.97[CHD][hapmap];0.89[GIH][hapmap];0.95[JPT][hapmap];0.92[LWK][hapmap];0.94[MKK][hapmap];0.98[ASN][1000 genomes]
rs1784281	0.98[ASN][1000 genomes]
rs3016242	0.98[ASN][1000 genomes]
rs504626	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.96[GIH][hapmap];0.85[JPT][hapmap];1.00[MEX][hapmap];0.96[TSI][hapmap];0.96[AMR][1000 genomes];0.94[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs538741	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.87[MEX][hapmap];0.95[TSI][hapmap];0.94[AMR][1000 genomes];0.95[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs538936	0.96[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.96[TSI][hapmap];0.96[AMR][1000 genomes];0.95[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs592529	0.96[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];0.98[GIH][hapmap];0.94[JPT][hapmap];0.87[MEX][hapmap];0.91[TSI][hapmap];0.92[AMR][1000 genomes];0.94[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs638775	1.00[CHB][hapmap];1.00[JPT][hapmap];0.97[ASN][1000 genomes]
rs681311	1.00[CHB][hapmap];1.00[CHD][hapmap];0.87[GIH][hapmap];0.85[JPT][hapmap];0.96[ASN][1000 genomes]
rs684384	1.00[CHB][hapmap];1.00[CHD][hapmap];0.89[GIH][hapmap];0.95[JPT][hapmap];0.98[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	nsv524	chr11:120963503-121008167	Weak transcription ZNF genes & repeats Enhancers Strong transcription Bivalent Enhancer Flanking Active TSS Genic enhancers Active TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region	1 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs638903	CXCR5	cis	cerebellum	SCAN
rs638903	TMEM25	cis	parietal	SCAN
rs638903	CRTAM	cis	parietal	SCAN

Chromatin state (count:37 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr11:120971800-120983600	Weak transcription	H9 Cell Line	embryonic stem cell
2	chr11:120975800-121005600	Weak transcription	Right Ventricle	heart
3	chr11:120976400-120984200	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
4	chr11:120976600-120992200	Weak transcription	Stomach Smooth Muscle	stomach
5	chr11:120976600-120998400	Weak transcription	Brain Anterior Caudate	brain
6	chr11:120976800-120983600	Weak transcription	Skeletal Muscle Male	skeletal muscle
7	chr11:120977600-120983600	Weak transcription	HSMMtube	muscle
8	chr11:120979200-120983600	Enhancers	Fetal Lung	lung
9	chr11:120980000-120983800	Enhancers	Fetal Brain Male	brain
10	chr11:120980000-120991000	Weak transcription	Aorta	Aorta
11	chr11:120980600-120998400	Weak transcription	Fetal Brain Female	brain
12	chr11:120981400-120992400	Weak transcription	Brain Germinal Matrix	brain
13	chr11:120981600-120983400	Enhancers	Fetal Muscle Leg	muscle
14	chr11:120982200-120983400	Enhancers	Duodenum Mucosa	Duodenum
15	chr11:120982200-120984200	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
16	chr11:120982600-120983600	Weak transcription	Fetal Muscle Trunk	muscle
17	chr11:120982600-120983600	Weak transcription	Lung	lung
18	chr11:120982600-120983600	Weak transcription	Skeletal Muscle Female	skeletal muscle
19	chr11:120983000-120983400	Enhancers	iPS-18 Cell Line	embryonic stem cell
20	chr11:120983000-120983400	Enhancers	Liver	Liver
21	chr11:120983000-120983800	Enhancers	Breast Myoepithelial Primary Cells	Breast
22	chr11:120983000-120984000	Enhancers	H1 Cell Line	embryonic stem cell
23	chr11:120983200-120983400	Bivalent Enhancer	Primary T cells fromperipheralblood	blood
24	chr11:120983200-120983400	Enhancers	Primary T helper naive cells from peripheral blood	blood
25	chr11:120983200-120983400	Bivalent Enhancer	Primary T helper cells PMA-I stimulated	--
26	chr11:120983200-120983400	Flanking Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
27	chr11:120983200-120983400	Enhancers	Brain Substantia Nigra	brain
28	chr11:120983200-120983400	Enhancers	Fetal Stomach	stomach
29	chr11:120983200-120983400	Flanking Bivalent TSS/Enh	GM12878-XiMat	blood
30	chr11:120983200-120983400	Bivalent Enhancer	HUVEC	blood vessel
31	chr11:120983200-120983800	Enhancers	HUES48 Cell Line	embryonic stem cell
32	chr11:120983200-120983800	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
33	chr11:120983200-120983800	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
34	chr11:120983200-120983800	Enhancers	Brain Hippocampus Middle	brain
35	chr11:120983200-120983800	Enhancers	Fetal Adrenal Gland	Adrenal Gland
36	chr11:120983200-120983800	Enhancers	Fetal Heart	heart
37	chr11:120983200-120983800	Bivalent Enhancer	Osteobl	bone

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