Variant report

Variant	rs12642922
Chromosome Location	chr4:27027618-27027619
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 19 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:15)

rs_ID	r²[population]
rs10939146	0.89[AMR][1000 genomes];0.90[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11734522	0.84[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs12641290	0.91[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs12641862	0.82[ASN][1000 genomes]
rs12646473	0.86[CEU][hapmap]
rs16878655	1.00[ASW][hapmap];0.93[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.97[GIH][hapmap];0.84[JPT][hapmap];0.90[LWK][hapmap];0.93[MEX][hapmap];1.00[MKK][hapmap];0.92[TSI][hapmap];0.89[YRI][hapmap];0.81[AMR][1000 genomes];0.83[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs16878719	0.91[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs16878720	0.83[AMR][1000 genomes]
rs3792685	0.93[CEU][hapmap];0.93[GIH][hapmap];0.80[MEX][hapmap];0.80[TSI][hapmap]
rs62299310	0.81[AMR][1000 genomes]
rs62299311	0.83[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs62299312	0.83[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs6448488	0.93[CEU][hapmap]
rs6835631	0.82[CEU][hapmap];0.90[GIH][hapmap]
rs6844153	0.86[CEU][hapmap];0.90[GIH][hapmap];0.84[TSI][hapmap]

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:2)

SNP	Gene	Cis/trans	Tissue	Source
rs12642922	STIM2	Cis_1M	lymphoblastoid	RTeQTL
rs12642922	STIM2	cis	lymphoblastoid	seeQTL

Chromatin state (count:40 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:26995000-27028200	Weak transcription	Pancreas	Pancrea
2	chr4:27001200-27029600	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
3	chr4:27012000-27029200	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
4	chr4:27018000-27028000	Weak transcription	Right Ventricle	heart
5	chr4:27018600-27029000	Weak transcription	HUES6 Cell Line	embryonic stem cell
6	chr4:27018800-27028800	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
7	chr4:27020000-27028200	Weak transcription	GM12878-XiMat	blood
8	chr4:27022800-27028600	Weak transcription	Right Atrium	heart
9	chr4:27023200-27030800	Weak transcription	Primary neutrophils fromperipheralblood	blood
10	chr4:27024400-27028600	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
11	chr4:27024600-27028400	Weak transcription	Thymus	Thymus
12	chr4:27024600-27028600	Weak transcription	Spleen	Spleen
13	chr4:27024600-27028800	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
14	chr4:27024600-27029000	Weak transcription	Esophagus	oesophagus
15	chr4:27024800-27028000	Weak transcription	Fetal Intestine Small	intestine
16	chr4:27024800-27028000	Weak transcription	Fetal Stomach	stomach
17	chr4:27024800-27031800	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
18	chr4:27025000-27028000	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
19	chr4:27025000-27028600	Weak transcription	Primary hematopoietic stem cells short term culture	blood
20	chr4:27025000-27028600	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
21	chr4:27025000-27028600	Weak transcription	Sigmoid Colon	Sigmoid Colon
22	chr4:27025000-27031000	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
23	chr4:27025000-27032000	Weak transcription	HSMMtube	muscle
24	chr4:27025400-27028200	Weak transcription	Fetal Thymus	thymus
25	chr4:27025400-27028400	Weak transcription	Primary T helper cells PMA-I stimulated	--
26	chr4:27025400-27028400	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
27	chr4:27025400-27028800	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
28	chr4:27025400-27028800	Weak transcription	NH-A	brain
29	chr4:27025600-27028200	Weak transcription	Primary T helper naive cells from peripheral blood	blood
30	chr4:27025600-27029000	Weak transcription	Fetal Intestine Large	intestine
31	chr4:27025600-27030600	Weak transcription	Monocytes-CD14+_RO01746	blood
32	chr4:27026000-27030400	Weak transcription	HSMM	muscle
33	chr4:27026800-27028600	Weak transcription	Brain Inferior Temporal Lobe	brain
34	chr4:27026800-27029000	Weak transcription	Primary B cells from peripheral blood	blood
35	chr4:27026800-27029000	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
36	chr4:27026800-27030000	Weak transcription	Primary monocytes fromperipheralblood	blood
37	chr4:27026800-27030200	Weak transcription	Breast Myoepithelial Primary Cells	Breast
38	chr4:27026800-27031200	Weak transcription	Primary B cells from cord blood	blood
39	chr4:27027000-27029400	Weak transcription	Primary T cells fromperipheralblood	blood
40	chr4:27027400-27030000	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood

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