Variant report

Variant	rs6815719
Chromosome Location	chr4:26881854-26881855
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr4:26879279..26881991-chr4:26883787..26885649,2	K562	blood:
2	chr4:26860902..26863056-chr4:26879948..26882121,2	K562	blood:
3	chr4:26875079..26876908-chr4:26880652..26882305,2	K562	blood:
4	chr4:26861238..26864586-chr4:26879222..26882735,4	MCF-7	breast:
5	chr4:26863853..26865538-chr4:26880691..26883360,2	K562	blood:
6	chr4:26860284..26863900-chr4:26879948..26882544,3	K562	blood:

Variant related genes	Relation type
ENSG00000248340	Chromatin interaction
ENSG00000109689	Chromatin interaction
ENSG00000240005	Chromatin interaction

Extended variants
information (count: 53 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:49)

rs_ID	r²[population]
rs10023256	0.81[ASW][hapmap]
rs10029307	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.93[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];0.91[LWK][hapmap];1.00[MEX][hapmap];0.90[MKK][hapmap];0.96[TSI][hapmap];0.83[YRI][hapmap];0.85[AFR][1000 genomes];0.96[AMR][1000 genomes];0.94[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs11729927	0.84[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs11730235	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.89[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs11734308	0.81[AMR][1000 genomes];0.80[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs11737218	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];0.85[LWK][hapmap];1.00[MEX][hapmap];0.94[MKK][hapmap];1.00[TSI][hapmap];0.83[YRI][hapmap];0.86[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs11943948	0.94[ASN][1000 genomes]
rs12641261	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12644073	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.93[CHD][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.89[MKK][hapmap];0.96[TSI][hapmap];0.83[YRI][hapmap];0.87[AFR][1000 genomes];0.96[AMR][1000 genomes];0.94[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs12646473	0.95[CHB][hapmap];0.95[JPT][hapmap];0.98[ASN][1000 genomes]
rs12650172	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13116341	0.88[ASN][1000 genomes]
rs13138942	0.82[CHB][hapmap];1.00[JPT][hapmap];0.96[ASN][1000 genomes]
rs13139464	0.90[ASN][1000 genomes]
rs28497454	0.82[AFR][1000 genomes];0.91[AMR][1000 genomes];0.87[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs28520489	0.87[AFR][1000 genomes];0.96[AMR][1000 genomes];0.94[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs34996346	0.96[ASN][1000 genomes]
rs3792685	0.90[CHB][hapmap];0.98[CHD][hapmap];0.91[JPT][hapmap];0.84[ASN][1000 genomes]
rs3924178	0.85[CHB][hapmap];0.93[CHD][hapmap];0.95[JPT][hapmap];0.88[ASN][1000 genomes]
rs4274829	0.94[ASN][1000 genomes]
rs4407490	0.88[CHD][hapmap];0.91[JPT][hapmap];0.87[ASN][1000 genomes]
rs4505809	0.85[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.96[ASN][1000 genomes]
rs4519790	0.90[CHB][hapmap];0.95[CHD][hapmap];0.95[JPT][hapmap];0.94[ASN][1000 genomes]
rs4532223	0.94[ASN][1000 genomes]
rs4557250	0.94[ASN][1000 genomes]
rs4557251	0.93[ASN][1000 genomes]
rs57663175	0.92[ASN][1000 genomes]
rs57686546	0.91[ASN][1000 genomes]
rs58075729	0.87[ASN][1000 genomes]
rs58968032	0.92[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs60890366	0.88[ASN][1000 genomes]
rs61047003	0.83[AMR][1000 genomes];0.83[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs62302532	0.87[ASN][1000 genomes]
rs62302533	0.86[ASN][1000 genomes]
rs62302535	0.85[ASN][1000 genomes]
rs6448479	0.95[ASN][1000 genomes]
rs6448484	0.96[ASN][1000 genomes]
rs6448488	0.95[CHB][hapmap];0.95[JPT][hapmap];0.86[ASN][1000 genomes]
rs6833053	0.94[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.93[TSI][hapmap];0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6833895	0.95[ASN][1000 genomes]
rs6835631	0.85[CHB][hapmap];0.97[CHD][hapmap];0.95[JPT][hapmap];0.88[ASN][1000 genomes]
rs6844153	0.95[CHB][hapmap];0.98[CHD][hapmap];0.95[JPT][hapmap];0.88[ASN][1000 genomes]
rs6853032	0.94[ASN][1000 genomes]
rs73116683	0.82[AMR][1000 genomes];0.89[ASN][1000 genomes]
rs73811400	0.92[AFR][1000 genomes];0.96[AMR][1000 genomes];0.89[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs73813220	0.92[ASN][1000 genomes]
rs7655686	0.93[ASN][1000 genomes]
rs9654110	0.81[ASW][hapmap]
rs9790789	0.85[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.96[ASN][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	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

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs6815719	STIM2	Cis_1M	lymphoblastoid	RTeQTL
rs6815719		cis	Lymphoblastoid	GTEx
rs6815719	STIM2	cis	lymphoblastoid	seeQTL
rs6815719	STIM2	cis	multi-tissue	Pritchard

Chromatin state (count:48 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:26864400-26886600	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
2	chr4:26864600-26885600	Weak transcription	Thymus	Thymus
3	chr4:26867200-26884200	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
4	chr4:26869800-26886000	Weak transcription	Fetal Stomach	stomach
5	chr4:26873000-26886200	Weak transcription	Skeletal Muscle Male	skeletal muscle
6	chr4:26873400-26883600	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
7	chr4:26875600-26904600	Weak transcription	Brain Anterior Caudate	brain
8	chr4:26875800-26888200	Weak transcription	Adipose Nuclei	Adipose
9	chr4:26876400-26885600	Weak transcription	Fetal Lung	lung
10	chr4:26877400-26882800	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
11	chr4:26878000-26885400	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
12	chr4:26878600-26885600	Enhancers	Primary T helper naive cells fromperipheralblood	blood
13	chr4:26878600-26885800	Enhancers	Primary T helper cells fromperipheralblood	blood
14	chr4:26879200-26882200	Enhancers	Primary T cells fromperipheralblood	blood
15	chr4:26879200-26882200	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
16	chr4:26879200-26885400	Enhancers	Primary T regulatory cells fromperipheralblood	blood
17	chr4:26879200-26885400	Enhancers	Primary T killer naive cells fromperipheralblood	blood
18	chr4:26879400-26882000	Flanking Active TSS	Primary T helper cells PMA-I stimulated	--
19	chr4:26880200-26882000	Enhancers	Primary T killer memory cells from peripheral blood	blood
20	chr4:26880200-26882200	Enhancers	Primary T cells from cord blood	blood
21	chr4:26880200-26884200	Weak transcription	Cortex derived primary cultured neurospheres	brain
22	chr4:26880200-26885000	Weak transcription	Primary hematopoietic stem cells	blood
23	chr4:26880200-26885000	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
24	chr4:26880200-26885600	Enhancers	Primary T helper naive cells from peripheral blood	blood
25	chr4:26880400-26884000	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
26	chr4:26880600-26882200	Enhancers	K562	blood
27	chr4:26880600-26884800	Weak transcription	Primary hematopoietic stem cells short term culture	blood
28	chr4:26880600-26885600	Weak transcription	Fetal Muscle Leg	muscle
29	chr4:26880600-26902400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
30	chr4:26880600-26921600	Weak transcription	Fetal Muscle Trunk	muscle
31	chr4:26880800-26882000	Enhancers	Stomach Mucosa	stomach
32	chr4:26880800-26882200	Enhancers	Primary T helper 17 cells PMA-I stimulated	--
33	chr4:26880800-26885200	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
34	chr4:26881000-26882600	Strong transcription	Primary B cells from cord blood	blood
35	chr4:26881200-26882000	Enhancers	Fetal Heart	heart
36	chr4:26881400-26882000	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
37	chr4:26881400-26882000	Enhancers	Pancreas	Pancrea
38	chr4:26881400-26882000	Enhancers	Sigmoid Colon	Sigmoid Colon
39	chr4:26881400-26882000	Enhancers	Small Intestine	intestine
40	chr4:26881400-26885600	Enhancers	Primary B cells from peripheral blood	blood
41	chr4:26881800-26882000	Enhancers	Dnd41	blood
42	chr4:26881800-26882200	Weak transcription	Liver	Liver
43	chr4:26881800-26883400	Weak transcription	Breast Myoepithelial Primary Cells	Breast
44	chr4:26881800-26884000	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
45	chr4:26881800-26885200	Weak transcription	Pancreatic Islets	Pancreatic Islet
46	chr4:26881800-26885600	Weak transcription	Rectal Mucosa Donor 31	rectum
47	chr4:26881800-26886800	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
48	chr4:26881800-26896200	Weak transcription	HMEC	breast

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