Variant report

Variant	rs12644232
Chromosome Location	chr4:26932453-26932454
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	chr4:26915845..26917465-chr4:26932098..26934843,2	K562	blood:

Extended variants
information (count: 34 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:29)

rs_ID	r²[population]
rs10002654	0.80[EUR][1000 genomes]
rs10023256	0.80[JPT][hapmap]
rs10470822	0.80[EUR][1000 genomes]
rs10939142	0.80[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs10939144	0.91[GIH][hapmap];0.86[TSI][hapmap];0.87[EUR][1000 genomes]
rs13129075	0.89[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs17555311	0.87[CHB][hapmap];0.94[JPT][hapmap];0.91[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs28454570	0.83[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs28704572	0.84[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4259045	0.81[ASN][1000 genomes]
rs4519791	0.82[TSI][hapmap];0.82[EUR][1000 genomes]
rs4575981	0.81[ASN][1000 genomes]
rs4692131	0.89[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs4692132	0.80[JPT][hapmap]
rs4692137	0.85[CEU][hapmap];0.86[GIH][hapmap];0.82[TSI][hapmap]
rs6448478	1.00[JPT][hapmap]
rs6448482	0.81[ASN][1000 genomes]
rs6448483	0.81[ASN][1000 genomes]
rs6448485	0.82[CEU][hapmap];0.92[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs6448487	0.81[CEU][hapmap];0.94[CHB][hapmap];0.94[JPT][hapmap];0.82[AMR][1000 genomes];0.93[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6831605	0.81[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.83[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6847438	0.82[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[AMR][1000 genomes];0.91[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs725981	0.88[CHB][hapmap];0.97[CHD][hapmap];0.85[GIH][hapmap];0.89[JPT][hapmap];0.86[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs7658174	1.00[ASW][hapmap];0.82[CEU][hapmap];0.94[CHB][hapmap];0.97[CHD][hapmap];0.95[GIH][hapmap];0.94[JPT][hapmap];0.90[LWK][hapmap];0.95[MEX][hapmap];0.93[MKK][hapmap];0.98[TSI][hapmap];0.90[YRI][hapmap];0.92[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7666651	0.92[CHB][hapmap];0.93[JPT][hapmap];0.84[AMR][1000 genomes];0.98[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs7672936	0.82[TSI][hapmap];0.81[EUR][1000 genomes]
rs7692953	1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9654110	0.80[JPT][hapmap]
rs9998368	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]

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:3)

SNP	Gene	Cis/trans	Tissue	Source
rs12644232	STIM2	cis	uninvolved skin	skin_eQTL
rs12644232	STIM2	cis	cerebellum	SCAN
rs12644232	STIM2	cis	Whole Blood	GTEx

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:26907200-26937800	Weak transcription	Stomach Mucosa	stomach
2	chr4:26911600-26965800	Weak transcription	HMEC	breast
3	chr4:26914600-26936800	Weak transcription	Small Intestine	intestine
4	chr4:26914800-26932600	Weak transcription	Spleen	Spleen
5	chr4:26914800-26942200	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
6	chr4:26918200-26938400	Weak transcription	Psoas Muscle	Psoas
7	chr4:26918400-26939800	Weak transcription	Fetal Heart	heart
8	chr4:26919600-26932800	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
9	chr4:26922600-26932600	Weak transcription	Brain Substantia Nigra	brain
10	chr4:26922800-26941400	Weak transcription	Brain Hippocampus Middle	brain
11	chr4:26923000-26940200	Weak transcription	Sigmoid Colon	Sigmoid Colon
12	chr4:26923000-26942400	Weak transcription	Fetal Brain Male	brain
13	chr4:26923000-26942400	Weak transcription	Left Ventricle	heart
14	chr4:26923200-26939400	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
15	chr4:26923200-26941400	Weak transcription	Brain Inferior Temporal Lobe	brain
16	chr4:26923200-26942400	Weak transcription	Brain Angular Gyrus	brain
17	chr4:26923200-26965800	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
18	chr4:26923200-26977200	Weak transcription	Thymus	Thymus
19	chr4:26923400-26954400	Weak transcription	HSMM	muscle
20	chr4:26923400-26960600	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
21	chr4:26923600-26936000	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
22	chr4:26923800-26943800	Weak transcription	Fetal Lung	lung
23	chr4:26924400-26932600	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
24	chr4:26924400-26932600	Weak transcription	Brain Cingulate Gyrus	brain
25	chr4:26924400-26936000	Weak transcription	Primary T helper naive cells from peripheral blood	blood
26	chr4:26924400-26936200	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
27	chr4:26924400-26936400	Weak transcription	Primary B cells from cord blood	blood
28	chr4:26924400-26936400	Weak transcription	Primary T helper cells PMA-I stimulated	--
29	chr4:26924400-26938200	Weak transcription	GM12878-XiMat	blood
30	chr4:26924400-26938400	Weak transcription	Ovary	ovary
31	chr4:26924400-26940200	Weak transcription	Rectal Mucosa Donor 31	rectum
32	chr4:26924400-26940600	Weak transcription	Rectal Mucosa Donor 29	rectum
33	chr4:26924400-26955200	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
34	chr4:26924600-26932600	Weak transcription	Primary T helper cells fromperipheralblood	blood
35	chr4:26924600-26932600	Weak transcription	Cortex derived primary cultured neurospheres	brain
36	chr4:26924600-26936800	Weak transcription	Primary B cells from peripheral blood	blood
37	chr4:26924600-26936800	Weak transcription	Primary T cells from cord blood	blood
38	chr4:26924600-26936800	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
39	chr4:26924600-26938400	Weak transcription	Primary T cells fromperipheralblood	blood
40	chr4:26924600-26938400	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
41	chr4:26924600-26940000	Weak transcription	Breast Myoepithelial Primary Cells	Breast
42	chr4:26929800-26938400	Weak transcription	Pancreas	Pancrea
43	chr4:26931800-26936600	Weak transcription	Primary T killer memory cells from peripheral blood	blood
44	chr4:26932000-26936200	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
45	chr4:26932200-26932600	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
46	chr4:26932200-26933000	Enhancers	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
47	chr4:26932400-26932800	Enhancers	iPS-18 Cell Line	embryonic stem cell
48	chr4:26932400-26933000	Enhancers	Primary T killer naive cells fromperipheralblood	blood
49	chr4:26932400-26933000	Enhancers	K562	blood
50	chr4:26932400-26933200	Enhancers	HUES64 Cell Line	embryonic stem cell

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