Variant report

Variant	rs12641290
Chromosome Location	chr4:27050213-27050214
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr4:27050056..27050609-chr4:27320044..27320989,2	K562	blood:
2	chr4:27049663..27050552-chr4:27320144..27321043,3	MCF-7	breast:
3	chr4:27049630..27050564-chr4:27086025..27086924,3	K562	blood:
4	chr4:27048431..27052730-chr4:27053495..27057145,5	K562	blood:
5	chr4:27049831..27050640-chr4:27086186..27086987,2	MCF-7	breast:

Extended variants
information (count: 14 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:11)

rs_ID	r²[population]
rs11734522	0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12642922	0.91[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs12649969	0.86[ASN][1000 genomes]
rs16878719	0.96[AMR][1000 genomes];0.92[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs16878720	0.92[AMR][1000 genomes];0.92[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs62299310	0.91[AMR][1000 genomes];0.92[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs62299311	0.88[AMR][1000 genomes];0.90[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs62299312	0.88[AMR][1000 genomes];0.94[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7654400	0.97[ASN][1000 genomes]
rs7676191	0.84[AMR][1000 genomes];0.91[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7681425	0.97[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:3 , 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

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs12641290	STIM2	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:85 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:27045800-27050400	Weak transcription	Left Ventricle	heart
2	chr4:27049800-27050400	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
3	chr4:27049800-27050400	Active TSS	Brain Substantia Nigra	brain
4	chr4:27049800-27050400	Active TSS	Fetal Lung	lung
5	chr4:27049800-27050400	Active TSS	HSMM	muscle
6	chr4:27049800-27050400	Enhancers	K562	blood
7	chr4:27049800-27050400	Active TSS	NHDF-Ad	bronchial
8	chr4:27049800-27050600	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
9	chr4:27049800-27050600	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
10	chr4:27049800-27050600	Enhancers	iPS-18 Cell Line	embryonic stem cell
11	chr4:27049800-27050600	Bivalent Enhancer	Primary T cells fromperipheralblood	blood
12	chr4:27049800-27050800	Enhancers	Primary T killer naive cells fromperipheralblood	blood
13	chr4:27050000-27050400	Enhancers	Primary B cells from peripheral blood	blood
14	chr4:27050000-27050400	Active TSS	Cortex derived primary cultured neurospheres	brain
15	chr4:27050000-27050400	Active TSS	Fetal Brain Female	brain
16	chr4:27050000-27050400	Bivalent/Poised TSS	Ovary	ovary
17	chr4:27050000-27050400	Active TSS	Skeletal Muscle Female	skeletal muscle
18	chr4:27050000-27050400	Bivalent/Poised TSS	HSMMtube	muscle
19	chr4:27050000-27050600	Bivalent Enhancer	Primary T helper memory cells from peripheral blood 1	blood
20	chr4:27050000-27050800	Active TSS	Brain Cingulate Gyrus	brain
21	chr4:27050000-27050800	Active TSS	Brain Hippocampus Middle	brain
22	chr4:27050200-27050400	Bivalent/Poised TSS	IMR90 fetal lung fibroblasts Cell Line	lung
23	chr4:27050200-27050400	Flanking Bivalent TSS/Enh	Primary neutrophils fromperipheralblood	blood
24	chr4:27050200-27050400	Active TSS	Primary hematopoietic stem cells	blood
25	chr4:27050200-27050400	Bivalent Enhancer	Primary hematopoietic stem cells short term culture	blood
26	chr4:27050200-27050400	Flanking Active TSS	Primary T helper naive cells from peripheral blood	blood
27	chr4:27050200-27050400	Flanking Active TSS	Primary T helper naive cells fromperipheralblood	blood
28	chr4:27050200-27050400	Bivalent/Poised TSS	Primary T killer memory cells from peripheral blood	blood
29	chr4:27050200-27050400	Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
30	chr4:27050200-27050400	Active TSS	Foreskin Melanocyte Primary Cells skin03	Skin
31	chr4:27050200-27050400	Active TSS	Brain Inferior Temporal Lobe	brain
32	chr4:27050200-27050400	Active TSS	Duodenum Mucosa	Duodenum
33	chr4:27050200-27050400	Active TSS	Fetal Intestine Large	intestine
34	chr4:27050200-27050400	Active TSS	Fetal Kidney	kidney
35	chr4:27050200-27050400	Active TSS	Fetal Muscle Leg	muscle
36	chr4:27050200-27050400	Bivalent/Poised TSS	Psoas Muscle	Psoas
37	chr4:27050200-27050400	Flanking Active TSS	Rectal Mucosa Donor 29	rectum
38	chr4:27050200-27050400	Active TSS	Rectal Mucosa Donor 31	rectum
39	chr4:27050200-27050400	Bivalent/Poised TSS	NH-A	brain
40	chr4:27050200-27050400	Bivalent/Poised TSS	Osteobl	bone
41	chr4:27050200-27050600	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
42	chr4:27050200-27050600	Enhancers	HUES48 Cell Line	embryonic stem cell
43	chr4:27050200-27050600	Flanking Bivalent TSS/Enh	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
44	chr4:27050200-27050600	Flanking Bivalent TSS/Enh	Primary B cells from cord blood	blood
45	chr4:27050200-27050600	Bivalent/Poised TSS	Primary T cells from cord blood	blood
46	chr4:27050200-27050600	Bivalent Enhancer	Primary T helper 17 cells PMA-I stimulated	--
47	chr4:27050200-27050600	Flanking Bivalent TSS/Enh	Primary T regulatory cells fromperipheralblood	blood
48	chr4:27050200-27050600	Flanking Bivalent TSS/Enh	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
49	chr4:27050200-27050600	Flanking Bivalent TSS/Enh	Muscle Satellite Cultured Cells	--
50	chr4:27050200-27050600	Active TSS	Ganglion Eminence derived primary cultured neurospheres	brain

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