Variant report

Variant	rs10939147
Chromosome Location	chr4:26997475-26997476
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	chr4:26900718..26903532-chr4:26996706..26999074,2	K562	blood:

Extended variants
information (count: 30 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:26)

rs_ID	r²[population]
rs10007132	0.91[CHB][hapmap];0.96[YRI][hapmap];0.82[AFR][1000 genomes];0.99[ASN][1000 genomes]
rs10010180	0.86[CEU][hapmap];0.96[YRI][hapmap];0.89[AFR][1000 genomes];0.87[EUR][1000 genomes]
rs10019691	0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1012550	0.91[CEU][hapmap];0.91[CHB][hapmap];0.84[JPT][hapmap];0.87[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10433805	0.92[YRI][hapmap]
rs12152700	0.87[CEU][hapmap];0.88[EUR][1000 genomes]
rs12331378	0.95[CHB][hapmap];0.92[YRI][hapmap];0.83[AMR][1000 genomes];0.99[ASN][1000 genomes]
rs13115054	0.87[CHB][hapmap];0.86[ASN][1000 genomes]
rs13140015	0.81[AMR][1000 genomes];0.82[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs16878653	0.91[CEU][hapmap];0.91[CHB][hapmap];0.86[CHD][hapmap];0.95[GIH][hapmap];0.84[JPT][hapmap];0.86[MEX][hapmap];0.82[TSI][hapmap];0.88[ASN][1000 genomes]
rs16878671	0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28572642	0.82[ASN][1000 genomes]
rs28668622	0.86[EUR][1000 genomes]
rs2871256	0.91[CEU][hapmap];0.87[CHB][hapmap];0.84[JPT][hapmap];0.85[YRI][hapmap];0.83[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3762900	0.87[CEU][hapmap];0.86[EUR][1000 genomes]
rs4692136	0.87[CHB][hapmap];0.81[AMR][1000 genomes];0.81[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6833149	0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6838936	0.87[EUR][1000 genomes]
rs6855865	0.91[CEU][hapmap];0.87[CHB][hapmap];0.86[CHD][hapmap];0.91[GIH][hapmap];0.84[JPT][hapmap];0.91[MEX][hapmap];1.00[MKK][hapmap];0.92[TSI][hapmap];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6856381	0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7669818	0.85[EUR][1000 genomes]
rs7681802	0.87[EUR][1000 genomes]
rs7700108	0.82[CEU][hapmap]
rs9291487	0.87[CEU][hapmap]
rs9998009	0.91[CHB][hapmap];0.83[CHD][hapmap];0.82[MEX][hapmap];0.92[YRI][hapmap];0.81[AMR][1000 genomes];0.97[ASN][1000 genomes]
rs9998971	0.85[EUR][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:3)

SNP	Gene	Cis/trans	Tissue	Source
rs10939147	STIM2	cis	uninvolved skin	skin_eQTL
rs10939147	STIM2	Cis_1M	lymphoblastoid	RTeQTL
rs10939147	STIM2	cis	normal skin	skin_eQTL

Chromatin state (count:69 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:26975800-27003200	Weak transcription	Aorta	Aorta
2	chr4:26978400-27019200	Weak transcription	Fetal Intestine Small	intestine
3	chr4:26980400-27019400	Weak transcription	Left Ventricle	heart
4	chr4:26985400-27019400	Weak transcription	Esophagus	oesophagus
5	chr4:26988400-26998000	Weak transcription	Dnd41	blood
6	chr4:26989000-27010000	Weak transcription	Thymus	Thymus
7	chr4:26989000-27010400	Weak transcription	Fetal Thymus	thymus
8	chr4:26989400-27024800	Weak transcription	Psoas Muscle	Psoas
9	chr4:26989600-27027000	Weak transcription	HepG2	liver
10	chr4:26993400-26997800	Enhancers	Primary T cells from cord blood	blood
11	chr4:26994200-27004600	Weak transcription	Rectal Mucosa Donor 31	rectum
12	chr4:26994800-26999000	Enhancers	Primary T helper cells PMA-I stimulated	--
13	chr4:26994800-27002600	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
14	chr4:26994800-27004600	Weak transcription	Primary T cells fromperipheralblood	blood
15	chr4:26994800-27005200	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
16	chr4:26994800-27011000	Weak transcription	Duodenum Mucosa	Duodenum
17	chr4:26995000-27002600	Weak transcription	Fetal Kidney	kidney
18	chr4:26995000-27002600	Weak transcription	Fetal Muscle Leg	muscle
19	chr4:26995000-27004000	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
20	chr4:26995000-27004200	Weak transcription	Primary monocytes fromperipheralblood	blood
21	chr4:26995000-27004600	Weak transcription	Primary hematopoietic stem cells	blood
22	chr4:26995000-27004600	Weak transcription	Small Intestine	intestine
23	chr4:26995000-27019000	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
24	chr4:26995000-27028200	Weak transcription	Pancreas	Pancrea
25	chr4:26995200-27004600	Weak transcription	HMEC	breast
26	chr4:26995200-27006600	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
27	chr4:26995400-26997800	Enhancers	Cortex derived primary cultured neurospheres	brain
28	chr4:26995400-27001000	Weak transcription	Muscle Satellite Cultured Cells	--
29	chr4:26995400-27001800	Weak transcription	Skeletal Muscle Male	skeletal muscle
30	chr4:26995400-27009800	Weak transcription	Adipose Nuclei	Adipose
31	chr4:26995600-26997600	Enhancers	Primary B cells from cord blood	blood
32	chr4:26995600-26999200	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
33	chr4:26995600-27000800	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
34	chr4:26995600-27001000	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
35	chr4:26995600-27004600	Weak transcription	NH-A	brain
36	chr4:26995600-27004800	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
37	chr4:26996000-26998800	Enhancers	HUES48 Cell Line	embryonic stem cell
38	chr4:26996200-26998400	Weak transcription	Breast Myoepithelial Primary Cells	Breast
39	chr4:26996200-27004200	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
40	chr4:26996200-27015400	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
41	chr4:26996400-27005400	Weak transcription	Primary neutrophils fromperipheralblood	blood
42	chr4:26996400-27007600	Weak transcription	Brain Angular Gyrus	brain
43	chr4:26996400-27026200	Weak transcription	H9 Cell Line	embryonic stem cell
44	chr4:26996600-27000800	Weak transcription	HSMMtube	muscle
45	chr4:26996600-27004600	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
46	chr4:26996600-27007600	Weak transcription	Ovary	ovary
47	chr4:26996600-27011800	Weak transcription	Brain Anterior Caudate	brain
48	chr4:26996600-27018400	Weak transcription	Fetal Intestine Large	intestine
49	chr4:26996600-27019200	Weak transcription	Sigmoid Colon	Sigmoid Colon
50	chr4:26996800-27001800	Weak transcription	Fetal Lung	lung

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