Variant report

Variant	rs6448488
Chromosome Location	chr4:26950987-26950988
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr4:26857143..26859433-chr4:26950614..26952186,2	K562	blood:

Variant related genes	Relation type
ENSG00000109689	Chromatin interaction

Extended variants
information (count: 57 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:46)

rs_ID	r²[population]
rs10029307	0.95[CHB][hapmap];0.95[JPT][hapmap];0.93[ASN][1000 genomes]
rs11729927	0.81[AMR][1000 genomes];0.95[ASN][1000 genomes]
rs11730235	1.00[CHB][hapmap];0.96[JPT][hapmap];0.95[ASN][1000 genomes]
rs11734308	0.97[ASN][1000 genomes]
rs11737218	0.95[CHB][hapmap];0.95[JPT][hapmap];0.87[ASN][1000 genomes]
rs11943948	0.84[ASN][1000 genomes]
rs12641261	0.86[ASN][1000 genomes]
rs12644073	0.95[CHB][hapmap];0.95[JPT][hapmap];0.91[ASN][1000 genomes]
rs12646473	0.93[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs12650172	0.95[CHB][hapmap];0.96[JPT][hapmap];0.86[ASN][1000 genomes]
rs13138942	0.89[CHB][hapmap];0.95[JPT][hapmap];0.85[ASN][1000 genomes]
rs16878655	0.87[CEU][hapmap]
rs28497454	0.93[ASN][1000 genomes]
rs28520489	0.88[ASN][1000 genomes]
rs34996346	0.85[ASN][1000 genomes]
rs3792685	1.00[CEU][hapmap];0.95[CHB][hapmap];0.95[JPT][hapmap];0.82[YRI][hapmap];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs3924178	0.91[CHB][hapmap];0.91[JPT][hapmap]
rs4274829	0.84[ASN][1000 genomes]
rs4407490	0.95[JPT][hapmap]
rs4505809	0.91[CHB][hapmap];0.95[JPT][hapmap];0.85[ASN][1000 genomes]
rs4519790	0.95[CHB][hapmap];0.91[JPT][hapmap];0.84[ASN][1000 genomes]
rs4532223	0.84[ASN][1000 genomes]
rs4557250	0.84[ASN][1000 genomes]
rs4557251	0.80[AMR][1000 genomes];0.81[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs57663175	0.84[AFR][1000 genomes];0.88[AMR][1000 genomes];0.91[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs57686546	0.80[AMR][1000 genomes];0.85[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs58968032	0.87[ASN][1000 genomes]
rs60890366	0.98[AMR][1000 genomes];0.93[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs61047003	0.96[ASN][1000 genomes]
rs62302474	0.82[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs62302532	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs62302533	1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62302535	0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6448479	0.84[ASN][1000 genomes]
rs6448484	0.85[ASN][1000 genomes]
rs6815719	0.95[CHB][hapmap];0.95[JPT][hapmap];0.86[ASN][1000 genomes]
rs6833053	0.95[CHB][hapmap];0.95[JPT][hapmap];0.86[ASN][1000 genomes]
rs6833895	0.84[ASN][1000 genomes]
rs6835631	0.88[CEU][hapmap];0.91[CHB][hapmap];1.00[JPT][hapmap];0.94[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6844153	0.93[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.87[AMR][1000 genomes];0.93[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6853032	0.85[ASN][1000 genomes]
rs73116683	0.98[ASN][1000 genomes]
rs73811400	0.87[ASN][1000 genomes]
rs73813220	0.94[ASN][1000 genomes]
rs7655686	0.91[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs9790789	0.91[CHB][hapmap];0.95[JPT][hapmap];0.85[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:11 , 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
6	esv1000535	chr4:26944042-26955394	Weak transcription Enhancers ZNF genes & repeats Strong transcription	Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
7	esv1812289	chr4:26945149-26957436	ZNF genes & repeats Enhancers Weak transcription Flanking Active TSS Strong transcription	Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
8	esv1808465	chr4:26945149-26957489	Weak transcription Enhancers Strong transcription ZNF genes & repeats Flanking Active TSS	Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
9	nsv593873	chr4:26950265-26957385	Weak transcription Enhancers ZNF genes & repeats Flanking Active TSS Strong transcription	Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
10	nsv593874	chr4:26950265-26957436	Weak transcription ZNF genes & repeats Enhancers Flanking Active TSS Strong transcription	Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
11	nsv593875	chr4:26950265-26957489	Weak transcription Enhancers Strong transcription ZNF genes & repeats Flanking Active TSS	Chromatin interactive region	1 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs6448488		cis	Lymphoblastoid	GTEx
rs6448488	STIM2	cis	multi-tissue	Pritchard
rs6448488	STIM2	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:34 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:26911600-26965800	Weak transcription	HMEC	breast
2	chr4:26923200-26965800	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
3	chr4:26923200-26977200	Weak transcription	Thymus	Thymus
4	chr4:26923400-26954400	Weak transcription	HSMM	muscle
5	chr4:26923400-26960600	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
6	chr4:26924400-26955200	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
7	chr4:26938600-26969000	Weak transcription	Gastric	stomach
8	chr4:26938800-26965600	Weak transcription	NHLF	lung
9	chr4:26939000-26954000	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
10	chr4:26939200-26969000	Weak transcription	Pancreas	Pancrea
11	chr4:26942000-26961000	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
12	chr4:26943200-26955000	Weak transcription	Primary T helper cells fromperipheralblood	blood
13	chr4:26944000-26952000	Weak transcription	Primary T cells from cord blood	blood
14	chr4:26944200-26952000	Weak transcription	Fetal Stomach	stomach
15	chr4:26944200-26952800	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
16	chr4:26944400-26965600	Weak transcription	Brain Anterior Caudate	brain
17	chr4:26945200-26952000	Weak transcription	Breast Myoepithelial Primary Cells	Breast
18	chr4:26945200-26954600	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
19	chr4:26945200-26956800	Weak transcription	Brain Angular Gyrus	brain
20	chr4:26945400-26954600	Weak transcription	Primary T killer memory cells from peripheral blood	blood
21	chr4:26947600-26951600	Weak transcription	Primary B cells from peripheral blood	blood
22	chr4:26948400-26952200	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
23	chr4:26948400-26952200	Weak transcription	Primary T helper cells PMA-I stimulated	--
24	chr4:26948800-26952800	Strong transcription	Primary B cells from cord blood	blood
25	chr4:26949000-26952000	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
26	chr4:26949200-26965600	Weak transcription	NH-A	brain
27	chr4:26949400-26952000	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
28	chr4:26949400-26963400	Weak transcription	Lung	lung
29	chr4:26950000-26951400	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
30	chr4:26950000-26980200	Weak transcription	Spleen	Spleen
31	chr4:26950200-26951200	Weak transcription	Cortex derived primary cultured neurospheres	brain
32	chr4:26950200-26954200	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
33	chr4:26950200-26979400	Weak transcription	Ovary	ovary
34	chr4:26950400-26959600	Weak transcription	Monocytes-CD14+_RO01746	blood

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