Variant report

Variant	rs6856381
Chromosome Location	chr4:27011621-27011622
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 30 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:26)

rs_ID	r²[population]
rs10007132	0.98[ASN][1000 genomes]
rs10010180	0.86[EUR][1000 genomes]
rs10019691	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1012550	0.86[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs10939147	0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12152700	0.93[AFR][1000 genomes];0.83[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs12331378	0.82[AMR][1000 genomes];0.98[ASN][1000 genomes]
rs13115054	0.86[ASN][1000 genomes]
rs13140015	0.84[AMR][1000 genomes];0.82[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs16878653	0.87[ASN][1000 genomes]
rs16878671	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs28572642	0.83[ASN][1000 genomes]
rs28668622	0.87[EUR][1000 genomes]
rs2871256	0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs3762900	0.82[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs4692136	0.84[AMR][1000 genomes];0.82[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6833149	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6838936	0.89[AFR][1000 genomes];0.82[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs6855865	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7669818	0.84[EUR][1000 genomes]
rs7679403	0.91[AFR][1000 genomes]
rs7681802	0.93[AFR][1000 genomes];0.83[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs7700108	0.88[AFR][1000 genomes]
rs9291487	0.88[AFR][1000 genomes]
rs9998009	0.96[ASN][1000 genomes]
rs9998971	0.89[AFR][1000 genomes];0.84[EUR][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:1)

SNP	Gene	Cis/trans	Tissue	Source
rs6856381	STIM2	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:99 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:26978400-27019200	Weak transcription	Fetal Intestine Small	intestine
2	chr4:26980400-27019400	Weak transcription	Left Ventricle	heart
3	chr4:26985400-27019400	Weak transcription	Esophagus	oesophagus
4	chr4:26989400-27024800	Weak transcription	Psoas Muscle	Psoas
5	chr4:26989600-27027000	Weak transcription	HepG2	liver
6	chr4:26995000-27019000	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
7	chr4:26995000-27028200	Weak transcription	Pancreas	Pancrea
8	chr4:26996200-27015400	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
9	chr4:26996400-27026200	Weak transcription	H9 Cell Line	embryonic stem cell
10	chr4:26996600-27011800	Weak transcription	Brain Anterior Caudate	brain
11	chr4:26996600-27018400	Weak transcription	Fetal Intestine Large	intestine
12	chr4:26996600-27019200	Weak transcription	Sigmoid Colon	Sigmoid Colon
13	chr4:26996800-27019200	Weak transcription	Duodenum Smooth Muscle	Duodenum
14	chr4:26997400-27019200	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
15	chr4:27001200-27029600	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
16	chr4:27001600-27019000	Weak transcription	Spleen	Spleen
17	chr4:27002000-27019200	Weak transcription	Lung	lung
18	chr4:27002000-27019200	Weak transcription	Skeletal Muscle Female	skeletal muscle
19	chr4:27002200-27013000	Weak transcription	Skeletal Muscle Male	skeletal muscle
20	chr4:27002800-27011800	Weak transcription	Stomach Mucosa	stomach
21	chr4:27002800-27026000	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
22	chr4:27004200-27027200	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
23	chr4:27004800-27025000	Weak transcription	H1 Cell Line	embryonic stem cell
24	chr4:27005000-27018000	Weak transcription	HUES64 Cell Line	embryonic stem cell
25	chr4:27005000-27019400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
26	chr4:27005400-27011800	Enhancers	Osteobl	bone
27	chr4:27005400-27017600	Weak transcription	iPS-20b Cell Line	embryonic stem cell
28	chr4:27005600-27012000	Weak transcription	Rectal Mucosa Donor 31	rectum
29	chr4:27005600-27013400	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
30	chr4:27005600-27019200	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
31	chr4:27005600-27019600	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
32	chr4:27005600-27021800	Weak transcription	Primary T killer memory cells from peripheral blood	blood
33	chr4:27005800-27019400	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
34	chr4:27005800-27019400	Weak transcription	Primary hematopoietic stem cells short term culture	blood
35	chr4:27005800-27019400	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
36	chr4:27006000-27019200	Weak transcription	HMEC	breast
37	chr4:27006000-27020200	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
38	chr4:27006400-27018400	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
39	chr4:27006400-27019400	Weak transcription	Fetal Muscle Trunk	muscle
40	chr4:27006400-27024200	Weak transcription	Small Intestine	intestine
41	chr4:27006600-27026000	Weak transcription	Fetal Kidney	kidney
42	chr4:27006800-27016800	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
43	chr4:27006800-27019200	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
44	chr4:27007000-27025800	Weak transcription	Placenta	Placenta
45	chr4:27007800-27025200	Weak transcription	K562	blood
46	chr4:27007800-27026200	Weak transcription	Gastric	stomach
47	chr4:27008000-27024200	Weak transcription	Brain Substantia Nigra	brain
48	chr4:27008200-27012400	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
49	chr4:27008200-27012400	Enhancers	NHLF	lung
50	chr4:27008200-27013000	Weak transcription	NHEK	skin

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