Variant report

Variant	rs16878653
Chromosome Location	chr4:26965306-26965307
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr4:26963208..26966058-chr4:26966686..26968937,2	K562	blood:
2	chr4:26965180..26966816-chr4:26968853..26972336,3	K562	blood:
3	chr4:26947300..26949972-chr4:26965034..26967382,2	K562	blood:

Extended variants
information (count: 25 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:21)

rs_ID	r²[population]
rs10007132	0.82[CEU][hapmap];1.00[CHB][hapmap];0.94[JPT][hapmap];0.86[ASN][1000 genomes]
rs10010180	0.95[CEU][hapmap]
rs10019691	0.88[ASN][1000 genomes]
rs1012550	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs10939143	0.81[ASN][1000 genomes]
rs10939147	0.91[CEU][hapmap];0.91[CHB][hapmap];0.86[CHD][hapmap];0.95[GIH][hapmap];0.84[JPT][hapmap];0.86[MEX][hapmap];0.82[TSI][hapmap];0.88[ASN][1000 genomes]
rs12152700	0.95[CEU][hapmap]
rs12331378	0.82[CEU][hapmap];1.00[CHB][hapmap];0.94[JPT][hapmap];0.86[ASN][1000 genomes]
rs13115054	0.82[CEU][hapmap];0.95[CHB][hapmap];0.94[JPT][hapmap];0.99[ASN][1000 genomes]
rs13140015	0.86[ASN][1000 genomes]
rs16878671	0.88[ASN][1000 genomes]
rs2871256	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.88[ASN][1000 genomes]
rs3762900	0.95[CEU][hapmap]
rs4692136	0.82[CEU][hapmap];0.95[CHB][hapmap];0.94[JPT][hapmap];0.87[ASN][1000 genomes]
rs6833149	0.87[ASN][1000 genomes]
rs6855865	1.00[CEU][hapmap];0.95[CHB][hapmap];0.90[CHD][hapmap];0.91[GIH][hapmap];1.00[JPT][hapmap];0.90[TSI][hapmap];0.86[ASN][1000 genomes]
rs6856381	0.87[ASN][1000 genomes]
rs7695335	0.81[CEU][hapmap]
rs7700108	0.91[CEU][hapmap]
rs9291487	0.95[CEU][hapmap]
rs9998009	1.00[CHB][hapmap];0.97[CHD][hapmap];0.94[JPT][hapmap];0.88[TSI][hapmap];0.88[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	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:3)

SNP	Gene	Cis/trans	Tissue	Source
rs16878653	STIM2	cis	normal skin	skin_eQTL
rs16878653	STIM2	cis	uninvolved skin	skin_eQTL
rs16878653	STIM2	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:64 , 50 per page) page: 1 2

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	chr4:26938600-26969000	Weak transcription	Gastric	stomach
5	chr4:26938800-26965600	Weak transcription	NHLF	lung
6	chr4:26939200-26969000	Weak transcription	Pancreas	Pancrea
7	chr4:26944400-26965600	Weak transcription	Brain Anterior Caudate	brain
8	chr4:26949200-26965600	Weak transcription	NH-A	brain
9	chr4:26950000-26980200	Weak transcription	Spleen	Spleen
10	chr4:26950200-26979400	Weak transcription	Ovary	ovary
11	chr4:26952600-26965600	Weak transcription	Psoas Muscle	Psoas
12	chr4:26955600-26965600	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
13	chr4:26955600-26965600	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
14	chr4:26955600-26965600	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
15	chr4:26955600-26965600	Weak transcription	Muscle Satellite Cultured Cells	--
16	chr4:26955600-26965600	Weak transcription	Brain Cingulate Gyrus	brain
17	chr4:26955600-26965600	Weak transcription	Duodenum Mucosa	Duodenum
18	chr4:26955600-26966400	Weak transcription	Primary hematopoietic stem cells	blood
19	chr4:26956000-26966400	Weak transcription	Pancreatic Islets	Pancreatic Islet
20	chr4:26957400-26966600	Weak transcription	Small Intestine	intestine
21	chr4:26958000-26965600	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
22	chr4:26958600-26965600	Weak transcription	Brain Angular Gyrus	brain
23	chr4:26958600-26965800	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
24	chr4:26959000-26966400	Weak transcription	Liver	Liver
25	chr4:26959200-26977600	Weak transcription	Fetal Thymus	thymus
26	chr4:26961000-26977200	Weak transcription	Fetal Intestine Small	intestine
27	chr4:26961200-26965600	Weak transcription	HSMM	muscle
28	chr4:26961400-26965600	Weak transcription	Primary T killer memory cells from peripheral blood	blood
29	chr4:26961400-26966000	Weak transcription	GM12878-XiMat	blood
30	chr4:26961600-26965600	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
31	chr4:26961600-26966000	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
32	chr4:26961600-26967000	Weak transcription	iPS-15b Cell Line	embryonic stem cell
33	chr4:26961600-26967400	Weak transcription	iPS-20b Cell Line	embryonic stem cell
34	chr4:26961600-26967600	Weak transcription	Dnd41	blood
35	chr4:26961600-26969600	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
36	chr4:26961600-26973400	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
37	chr4:26961600-26977200	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
38	chr4:26961800-26965600	Weak transcription	Brain Hippocampus Middle	brain
39	chr4:26961800-26966000	Weak transcription	Brain Substantia Nigra	brain
40	chr4:26961800-26966400	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
41	chr4:26961800-26966400	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
42	chr4:26961800-26966400	Weak transcription	HUES64 Cell Line	embryonic stem cell
43	chr4:26961800-26966600	Weak transcription	HUES6 Cell Line	embryonic stem cell
44	chr4:26961800-26967200	Weak transcription	iPS-18 Cell Line	embryonic stem cell
45	chr4:26961800-26967400	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
46	chr4:26961800-26975800	Weak transcription	Primary T helper cells fromperipheralblood	blood
47	chr4:26961800-26980200	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
48	chr4:26961800-26994000	Weak transcription	Monocytes-CD14+_RO01746	blood
49	chr4:26962000-26975200	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
50	chr4:26963200-26967400	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood

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