Variant report

Variant	rs10939144
Chromosome Location	chr4:26966906-26966907
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr4:26947300..26949972-chr4:26965034..26967382,2	K562	blood:
2	chr4:26963208..26966058-chr4:26966686..26968937,2	K562	blood:
3	chr4:26962657..26964232-chr4:26966255..26969155,2	MCF-7	breast:

Extended variants
information (count: 30 )
Associated
traits (count: 2 )

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

rs_ID	r²[population]
rs10023256	0.81[CEU][hapmap]
rs10470822	0.89[CEU][hapmap]
rs12331333	0.80[CEU][hapmap]
rs12644232	0.91[GIH][hapmap];0.86[TSI][hapmap];0.87[EUR][1000 genomes]
rs13129075	0.82[EUR][1000 genomes]
rs13434709	0.81[CEU][hapmap]
rs17555311	0.92[CEU][hapmap];0.86[EUR][1000 genomes]
rs28454570	0.90[EUR][1000 genomes]
rs28704572	0.89[EUR][1000 genomes]
rs4519791	0.89[CEU][hapmap]
rs4692131	0.81[EUR][1000 genomes]
rs4692132	0.81[CEU][hapmap]
rs4692137	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.98[CHD][hapmap];0.95[GIH][hapmap];0.81[JPT][hapmap];1.00[LWK][hapmap];0.96[MEX][hapmap];0.80[MKK][hapmap];0.91[TSI][hapmap];1.00[YRI][hapmap];0.82[AFR][1000 genomes];0.86[EUR][1000 genomes]
rs6448485	0.96[CEU][hapmap];0.83[EUR][1000 genomes]
rs6448487	0.96[CEU][hapmap];0.86[EUR][1000 genomes]
rs6822297	1.00[ASW][hapmap];0.96[CEU][hapmap];1.00[LWK][hapmap];0.81[TSI][hapmap];1.00[YRI][hapmap]
rs6831605	0.96[CEU][hapmap];0.83[EUR][1000 genomes]
rs6847438	0.96[CEU][hapmap];0.82[EUR][1000 genomes]
rs724624	0.90[ASW][hapmap];0.88[CEU][hapmap];0.95[LWK][hapmap];0.81[MKK][hapmap];1.00[YRI][hapmap]
rs725981	0.85[CEU][hapmap];0.87[MEX][hapmap];0.83[EUR][1000 genomes]
rs7658174	0.96[CEU][hapmap];0.86[GIH][hapmap];0.89[TSI][hapmap];0.88[EUR][1000 genomes]
rs7666651	0.89[EUR][1000 genomes]
rs7672936	0.89[CEU][hapmap]
rs7692953	0.92[CEU][hapmap];0.86[EUR][1000 genomes]
rs9654110	0.81[CEU][hapmap]
rs9998368	0.96[CEU][hapmap];0.88[GIH][hapmap];0.87[MEX][hapmap];0.91[TSI][hapmap];0.86[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:2)

SNP	Gene	Cis/trans	Tissue	Source
rs10939144	STIM2	cis	Whole Blood	GTEx
rs10939144	STIM2	cis	cerebellum	SCAN

Chromatin state (count:54 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:26923200-26977200	Weak transcription	Thymus	Thymus
2	chr4:26938600-26969000	Weak transcription	Gastric	stomach
3	chr4:26939200-26969000	Weak transcription	Pancreas	Pancrea
4	chr4:26950000-26980200	Weak transcription	Spleen	Spleen
5	chr4:26950200-26979400	Weak transcription	Ovary	ovary
6	chr4:26959200-26977600	Weak transcription	Fetal Thymus	thymus
7	chr4:26961000-26977200	Weak transcription	Fetal Intestine Small	intestine
8	chr4:26961600-26967000	Weak transcription	iPS-15b Cell Line	embryonic stem cell
9	chr4:26961600-26967400	Weak transcription	iPS-20b Cell Line	embryonic stem cell
10	chr4:26961600-26967600	Weak transcription	Dnd41	blood
11	chr4:26961600-26969600	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
12	chr4:26961600-26973400	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
13	chr4:26961600-26977200	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
14	chr4:26961800-26967200	Weak transcription	iPS-18 Cell Line	embryonic stem cell
15	chr4:26961800-26967400	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
16	chr4:26961800-26975800	Weak transcription	Primary T helper cells fromperipheralblood	blood
17	chr4:26961800-26980200	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
18	chr4:26961800-26994000	Weak transcription	Monocytes-CD14+_RO01746	blood
19	chr4:26962000-26975200	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
20	chr4:26963200-26967400	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
21	chr4:26963600-26975000	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
22	chr4:26963600-26994200	Weak transcription	Sigmoid Colon	Sigmoid Colon
23	chr4:26963800-26967200	Enhancers	Cortex derived primary cultured neurospheres	brain
24	chr4:26964200-26977200	Weak transcription	Primary T cells fromperipheralblood	blood
25	chr4:26964400-26975000	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
26	chr4:26965200-26967000	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
27	chr4:26965200-26967400	Enhancers	Primary T helper cells PMA-I stimulated	--
28	chr4:26965600-26967000	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
29	chr4:26965600-26967000	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
30	chr4:26965600-26967000	Enhancers	Brain Angular Gyrus	brain
31	chr4:26965600-26967200	Enhancers	Brain Anterior Caudate	brain
32	chr4:26965600-26967600	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
33	chr4:26965600-26968000	Enhancers	Brain Hippocampus Middle	brain
34	chr4:26965800-26967200	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
35	chr4:26966000-26967000	Enhancers	GM12878-XiMat	blood
36	chr4:26966000-26968000	Strong transcription	Primary T cells from cord blood	blood
37	chr4:26966000-26970400	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
38	chr4:26966000-26971000	Weak transcription	Psoas Muscle	Psoas
39	chr4:26966400-26967000	Enhancers	Liver	Liver
40	chr4:26966400-26967000	Enhancers	Pancreatic Islets	Pancreatic Islet
41	chr4:26966400-26967800	Enhancers	HUES64 Cell Line	embryonic stem cell
42	chr4:26966600-26967000	Enhancers	HUES6 Cell Line	embryonic stem cell
43	chr4:26966600-26967000	Enhancers	Primary B cells from peripheral blood	blood
44	chr4:26966600-26967600	Weak transcription	NHDF-Ad	bronchial
45	chr4:26966600-26967600	Weak transcription	Osteobl	bone
46	chr4:26966600-26986400	Weak transcription	HSMM	muscle
47	chr4:26966600-26989000	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
48	chr4:26966600-26994600	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
49	chr4:26966800-26969000	Weak transcription	Primary B cells from cord blood	blood
50	chr4:26966800-26977200	Weak transcription	Breast Myoepithelial Primary Cells	Breast

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