Variant report

Variant	rs10019691
Chromosome Location	chr4:26989028-26989029
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	chr4:26876720..26878835-chr4:26986672..26989304,2	MCF-7	breast:

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

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

rs_ID	r²[population]
rs10007132	0.99[ASN][1000 genomes]
rs10010180	0.87[EUR][1000 genomes]
rs1012550	0.87[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10939147	0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12152700	0.92[AFR][1000 genomes];0.83[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs12331378	0.82[AMR][1000 genomes];0.99[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	0.88[ASN][1000 genomes]
rs16878671	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28572642	0.82[ASN][1000 genomes]
rs28668622	0.86[EUR][1000 genomes]
rs2871256	0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3762900	0.82[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs4692136	0.84[AMR][1000 genomes];0.81[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6833149	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6838936	0.92[AFR][1000 genomes];0.82[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs6855865	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6856381	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7669818	0.85[EUR][1000 genomes]
rs7679403	0.93[AFR][1000 genomes]
rs7681802	0.96[AFR][1000 genomes];0.83[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs7700108	0.91[AFR][1000 genomes]
rs9291487	0.91[AFR][1000 genomes]
rs9998009	0.97[ASN][1000 genomes]
rs9998971	0.91[AFR][1000 genomes];0.85[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
rs10019691	STIM2	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:63 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:26961800-26994000	Weak transcription	Monocytes-CD14+_RO01746	blood
2	chr4:26963600-26994200	Weak transcription	Sigmoid Colon	Sigmoid Colon
3	chr4:26966600-26994600	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
4	chr4:26975800-27003200	Weak transcription	Aorta	Aorta
5	chr4:26978000-26994600	Weak transcription	Fetal Stomach	stomach
6	chr4:26978400-27019200	Weak transcription	Fetal Intestine Small	intestine
7	chr4:26980400-26994800	Weak transcription	Breast Myoepithelial Primary Cells	Breast
8	chr4:26980400-27019400	Weak transcription	Left Ventricle	heart
9	chr4:26984800-26989400	Enhancers	Primary T helper cells fromperipheralblood	blood
10	chr4:26984800-26993400	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
11	chr4:26984800-26993400	Weak transcription	Brain Hippocampus Middle	brain
12	chr4:26985400-26989600	Enhancers	Primary T helper naive cells fromperipheralblood	blood
13	chr4:26985400-27019400	Weak transcription	Esophagus	oesophagus
14	chr4:26986000-26994400	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
15	chr4:26986200-26989400	Enhancers	Primary T helper naive cells from peripheral blood	blood
16	chr4:26986200-26989600	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
17	chr4:26986200-26994400	Weak transcription	Right Atrium	heart
18	chr4:26986400-26989400	Enhancers	Primary T killer naive cells fromperipheralblood	blood
19	chr4:26986400-26989400	Enhancers	HSMMtube	muscle
20	chr4:26986400-26994600	Weak transcription	Small Intestine	intestine
21	chr4:26986600-26989200	Enhancers	Primary T helper 17 cells PMA-I stimulated	--
22	chr4:26986600-26989200	Enhancers	GM12878-XiMat	blood
23	chr4:26987000-26989400	Enhancers	Primary T killer memory cells from peripheral blood	blood
24	chr4:26987200-26989600	Enhancers	Primary B cells from peripheral blood	blood
25	chr4:26987800-26994000	Weak transcription	Primary hematopoietic stem cells	blood
26	chr4:26987800-26994000	Weak transcription	Muscle Satellite Cultured Cells	--
27	chr4:26987800-26994000	Weak transcription	Osteobl	bone
28	chr4:26988000-26989800	Enhancers	Primary T helper cells PMA-I stimulated	--
29	chr4:26988400-26989400	Enhancers	ES-I3 Cell Line	embryonic stem cell
30	chr4:26988400-26989600	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
31	chr4:26988400-26994600	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
32	chr4:26988400-26998000	Weak transcription	Dnd41	blood
33	chr4:26988600-26989400	Enhancers	HUES6 Cell Line	embryonic stem cell
34	chr4:26988600-26989400	Enhancers	Fetal Muscle Leg	muscle
35	chr4:26988600-26990000	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
36	chr4:26988800-26989200	Enhancers	iPS-20b Cell Line	embryonic stem cell
37	chr4:26988800-26989200	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
38	chr4:26988800-26989200	Weak transcription	Ovary	ovary
39	chr4:26988800-26989200	Enhancers	Pancreas	Pancrea
40	chr4:26988800-26989400	Enhancers	H1 Cell Line	embryonic stem cell
41	chr4:26988800-26989400	Enhancers	H9 Cell Line	embryonic stem cell
42	chr4:26988800-26989400	Enhancers	HUES64 Cell Line	embryonic stem cell
43	chr4:26988800-26989400	Enhancers	iPS-18 Cell Line	embryonic stem cell
44	chr4:26988800-26989400	Enhancers	Psoas Muscle	Psoas
45	chr4:26988800-26990000	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
46	chr4:26988800-26994000	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
47	chr4:26989000-26989200	Genic enhancers	Primary B cells from cord blood	blood
48	chr4:26989000-26989400	Enhancers	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
49	chr4:26989000-26989400	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
50	chr4:26989000-26989400	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung

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