Variant report

Variant	rs9998368
Chromosome Location	chr4:26889054-26889055
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 42 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:37)

rs_ID	r²[population]
rs10006403	0.81[CEU][hapmap]
rs10023256	0.85[CEU][hapmap];0.81[JPT][hapmap]
rs10470822	0.92[CEU][hapmap];0.81[AFR][1000 genomes]
rs10939144	0.96[CEU][hapmap];0.88[GIH][hapmap];0.87[MEX][hapmap];0.91[TSI][hapmap];0.86[EUR][1000 genomes]
rs12331333	0.84[CEU][hapmap]
rs12644232	0.80[ASW][hapmap];0.82[CEU][hapmap];0.94[CHB][hapmap];0.83[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];0.95[TSI][hapmap];0.95[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs13129075	0.82[AFR][1000 genomes];0.84[AMR][1000 genomes];0.88[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs13434709	0.85[CEU][hapmap];0.80[JPT][hapmap]
rs17555311	0.96[CEU][hapmap];0.82[CHB][hapmap];0.94[JPT][hapmap];0.90[EUR][1000 genomes]
rs28454570	0.90[AMR][1000 genomes];0.96[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs28704572	0.92[AFR][1000 genomes];0.91[AMR][1000 genomes];0.97[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs3924177	0.94[ASN][1000 genomes]
rs4259045	0.95[ASN][1000 genomes]
rs4376128	0.94[ASN][1000 genomes]
rs4519791	0.93[ASW][hapmap];0.92[CEU][hapmap];0.85[LWK][hapmap];0.87[MEX][hapmap];0.97[MKK][hapmap];0.87[TSI][hapmap];0.88[YRI][hapmap];0.85[AFR][1000 genomes];0.83[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs4575981	0.95[ASN][1000 genomes]
rs4692131	0.99[AFR][1000 genomes];0.96[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4692132	0.85[CEU][hapmap];0.81[JPT][hapmap]
rs4692137	0.96[CEU][hapmap];0.83[GIH][hapmap];0.82[MEX][hapmap];0.87[TSI][hapmap]
rs6448478	0.83[CHB][hapmap];0.82[CHD][hapmap];1.00[JPT][hapmap];0.88[ASN][1000 genomes]
rs6448480	0.87[ASN][1000 genomes]
rs6448481	0.89[ASN][1000 genomes]
rs6448482	0.95[ASN][1000 genomes]
rs6448483	0.95[ASN][1000 genomes]
rs6448485	1.00[CEU][hapmap];0.90[AFR][1000 genomes];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6448487	1.00[CEU][hapmap];0.88[CHB][hapmap];0.95[JPT][hapmap];0.87[AFR][1000 genomes];0.89[AMR][1000 genomes];0.92[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs6822297	0.92[CEU][hapmap];0.81[TSI][hapmap]
rs6830424	0.90[ASN][1000 genomes]
rs6831605	1.00[CEU][hapmap];0.94[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.89[AFR][1000 genomes];0.90[AMR][1000 genomes];0.91[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs6847438	1.00[CEU][hapmap];0.94[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];0.88[AMR][1000 genomes];0.90[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs724624	0.84[CEU][hapmap]
rs725981	1.00[ASW][hapmap];0.89[CEU][hapmap];0.83[CHB][hapmap];0.85[CHD][hapmap];0.85[GIH][hapmap];0.89[JPT][hapmap];1.00[MEX][hapmap];0.88[YRI][hapmap];0.83[AFR][1000 genomes];0.84[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs7658174	0.80[ASW][hapmap];1.00[CEU][hapmap];0.89[CHB][hapmap];0.86[CHD][hapmap];0.92[GIH][hapmap];0.95[JPT][hapmap];0.84[MEX][hapmap];0.98[TSI][hapmap];0.94[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs7666651	1.00[CHB][hapmap];0.93[JPT][hapmap];1.00[YRI][hapmap];0.89[AFR][1000 genomes];0.91[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7672936	0.93[ASW][hapmap];0.92[CEU][hapmap];0.82[MEX][hapmap];0.97[MKK][hapmap];0.87[TSI][hapmap];0.88[YRI][hapmap];0.85[AFR][1000 genomes];0.83[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs7692953	0.96[CEU][hapmap];0.94[CHB][hapmap];1.00[JPT][hapmap];0.84[AMR][1000 genomes];0.92[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs9654110	0.85[CEU][hapmap];0.81[JPT][hapmap]

Variant overlapped rSNPs/rCNVs (count:5 , 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	nsv1001306	chr4:26821511-26955344	Weak transcription Flanking Active TSS Enhancers Genic enhancers Active TSS Strong transcription Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases
3	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
4	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
5	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
rs9998368	STIM2	cis	cerebellum	SCAN
rs9998368	STIM2	cis	Whole Blood	GTEx

Chromatin state (count:52 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:26875600-26904600	Weak transcription	Brain Anterior Caudate	brain
2	chr4:26880600-26902400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
3	chr4:26880600-26921600	Weak transcription	Fetal Muscle Trunk	muscle
4	chr4:26881800-26896200	Weak transcription	HMEC	breast
5	chr4:26882000-26897000	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
6	chr4:26883400-26892800	Enhancers	Breast Myoepithelial Primary Cells	Breast
7	chr4:26885400-26889200	Flanking Active TSS	Primary T regulatory cells fromperipheralblood	blood
8	chr4:26885400-26889200	Flanking Active TSS	Dnd41	blood
9	chr4:26885800-26890800	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
10	chr4:26885800-26903600	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
11	chr4:26886000-26894400	Weak transcription	Skeletal Muscle Female	skeletal muscle
12	chr4:26886000-26896200	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
13	chr4:26886400-26890600	Weak transcription	Cortex derived primary cultured neurospheres	brain
14	chr4:26886600-26899400	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
15	chr4:26886600-26921600	Weak transcription	Fetal Muscle Leg	muscle
16	chr4:26887000-26889200	Enhancers	Brain Substantia Nigra	brain
17	chr4:26887000-26891000	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
18	chr4:26887600-26889200	Flanking Active TSS	Primary T helper cells fromperipheralblood	blood
19	chr4:26887800-26889200	Flanking Active TSS	Primary T helper memory cells from peripheral blood 1	blood
20	chr4:26887800-26889200	Flanking Active TSS	Primary T helper cells PMA-I stimulated	--
21	chr4:26887800-26889200	Flanking Active TSS	Monocytes-CD14+_RO01746	blood
22	chr4:26887800-26889800	Flanking Active TSS	Primary T cells from cord blood	blood
23	chr4:26888000-26889200	Flanking Active TSS	Primary T helper naive cells fromperipheralblood	blood
24	chr4:26888000-26889200	Flanking Active TSS	Primary T helper 17 cells PMA-I stimulated	--
25	chr4:26888000-26889200	Flanking Active TSS	Primary T killer memory cells from peripheral blood	blood
26	chr4:26888000-26889200	Flanking Active TSS	Duodenum Mucosa	Duodenum
27	chr4:26888000-26889200	Enhancers	Rectal Mucosa Donor 31	rectum
28	chr4:26888200-26889200	Enhancers	Primary monocytes fromperipheralblood	blood
29	chr4:26888200-26889200	Enhancers	Sigmoid Colon	Sigmoid Colon
30	chr4:26888200-26889800	Enhancers	Primary hematopoietic stem cells	blood
31	chr4:26888200-26891600	Enhancers	Primary B cells from peripheral blood	blood
32	chr4:26888400-26889200	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
33	chr4:26888400-26889400	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
34	chr4:26888400-26889400	Enhancers	Primary mononuclear cells fromperipheralblood	Blood
35	chr4:26888400-26891200	Weak transcription	Rectal Smooth Muscle	rectum
36	chr4:26888400-26901600	Weak transcription	Brain Inferior Temporal Lobe	brain
37	chr4:26888600-26889200	Active TSS	Primary T cells fromperipheralblood	blood
38	chr4:26888600-26889200	Enhancers	Primary hematopoietic stem cells short term culture	blood
39	chr4:26888600-26889200	Active TSS	Primary Natural Killer cells fromperipheralblood	blood
40	chr4:26888600-26889200	Enhancers	Rectal Mucosa Donor 29	rectum
41	chr4:26888600-26889200	Enhancers	GM12878-XiMat	blood
42	chr4:26888600-26890600	Enhancers	Primary T helper naive cells from peripheral blood	blood
43	chr4:26888600-26890800	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
44	chr4:26888600-26891000	Weak transcription	Small Intestine	intestine
45	chr4:26888600-26899400	Weak transcription	Spleen	Spleen
46	chr4:26889000-26889200	Flanking Active TSS	Primary B cells from cord blood	blood
47	chr4:26889000-26889200	Flanking Active TSS	Primary T helper memory cells from peripheral blood 2	blood
48	chr4:26889000-26889200	Flanking Active TSS	Primary T cells effector/memory enriched fromperipheralblood	blood
49	chr4:26889000-26889200	Flanking Active TSS	Primary T killer naive cells fromperipheralblood	blood
50	chr4:26889000-26889200	Enhancers	Brain Hippocampus Middle	brain

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