Variant report

Variant	rs28668622
Chromosome Location	chr4:27029173-27029174
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 32 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:28)

rs_ID	r²[population]
rs10010180	0.90[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10019691	0.86[EUR][1000 genomes]
rs10433805	0.84[ASN][1000 genomes]
rs10939147	0.86[EUR][1000 genomes]
rs12152700	0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs16878671	0.86[EUR][1000 genomes]
rs28570016	0.82[AFR][1000 genomes];0.84[AMR][1000 genomes];0.83[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2871256	0.85[EUR][1000 genomes]
rs2871258	0.87[ASN][1000 genomes]
rs35499018	0.85[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs3762900	0.91[AFR][1000 genomes];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4692142	0.81[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs6448491	0.87[ASN][1000 genomes]
rs6830950	0.81[AMR][1000 genomes];0.83[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6833149	0.87[EUR][1000 genomes]
rs6838936	0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6855865	0.87[EUR][1000 genomes]
rs6856381	0.87[EUR][1000 genomes]
rs7669818	0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7679403	0.84[AMR][1000 genomes];0.83[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7680613	0.87[ASN][1000 genomes]
rs7681802	0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7693687	0.84[ASN][1000 genomes]
rs7695335	0.81[AMR][1000 genomes];0.82[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7700108	0.82[AMR][1000 genomes];0.90[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs9291487	0.90[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs9995206	0.90[AMR][1000 genomes]
rs9998971	0.87[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv470021	chr4:26721578-27067027	Active TSS Strong transcription Enhancers Weak transcription Flanking Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Genic enhancers Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	16 gene(s)	inside rSNPs	diseases
2	nsv461312	chr4:26844674-27078376	Enhancers Weak transcription Active TSS Flanking Active TSS Bivalent/Poised TSS Strong transcription ZNF genes & repeats Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases
3	nsv593872	chr4:26844674-27078376	Enhancers Weak transcription ZNF genes & repeats Flanking Active TSS Strong transcription Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases
4	nsv1000568	chr4:26886920-27049554	Strong transcription Weak transcription Enhancers Active TSS ZNF genes & repeats Genic enhancers Flanking Active TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region	2 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs28668622	STIM2	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:17 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:27001200-27029600	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
2	chr4:27012000-27029200	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
3	chr4:27023200-27030800	Weak transcription	Primary neutrophils fromperipheralblood	blood
4	chr4:27024800-27031800	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
5	chr4:27025000-27031000	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
6	chr4:27025000-27032000	Weak transcription	HSMMtube	muscle
7	chr4:27025600-27030600	Weak transcription	Monocytes-CD14+_RO01746	blood
8	chr4:27026000-27030400	Weak transcription	HSMM	muscle
9	chr4:27026800-27030000	Weak transcription	Primary monocytes fromperipheralblood	blood
10	chr4:27026800-27030200	Weak transcription	Breast Myoepithelial Primary Cells	Breast
11	chr4:27026800-27031200	Weak transcription	Primary B cells from cord blood	blood
12	chr4:27027000-27029400	Weak transcription	Primary T cells fromperipheralblood	blood
13	chr4:27027400-27030000	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
14	chr4:27029000-27029200	Enhancers	HUES6 Cell Line	embryonic stem cell
15	chr4:27029000-27029200	Enhancers	Primary B cells from peripheral blood	blood
16	chr4:27029000-27029200	Enhancers	Esophagus	oesophagus
17	chr4:27029000-27029200	Enhancers	Spleen	Spleen

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