Variant report

Variant	rs7306864
Chromosome Location	chr12:104440069-104440070
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr12:104437965..104440233-chr12:104457193..104459611,2	MCF-7	breast:
2	chr12:104438711..104441073-chr12:104451682..104453689,2	K562	blood:
3	chr12:104438680..104440536-chr12:104458293..104460022,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000120820	Chromatin interaction
ENSG00000111727	Chromatin interaction

Extended variants
information (count: 17 )
Associated
traits (count: 3 )

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

rs_ID	r²[population]
rs12318096	1.00[CEU][hapmap];0.90[YRI][hapmap]
rs1437503	0.90[YRI][hapmap]
rs17035135	1.00[ASW][hapmap];1.00[CEU][hapmap];0.81[GIH][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.90[YRI][hapmap];0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs17035297	1.00[MEX][hapmap]
rs55997300	0.86[AFR][1000 genomes]
rs58131303	1.00[EUR][1000 genomes]
rs58937971	0.89[EUR][1000 genomes]
rs6539118	1.00[EUR][1000 genomes]
rs6539119	1.00[CEU][hapmap];1.00[EUR][1000 genomes]
rs7132060	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs7294791	1.00[EUR][1000 genomes]
rs7303182	0.85[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs7315363	1.00[YRI][hapmap];0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs7315396	1.00[CEU][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs7960212	1.00[CEU][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:2 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv560039	chr12:104177668-104455340	Strong transcription Enhancers Weak transcription Flanking Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS Genic enhancers Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	63 gene(s)	inside rSNPs	diseases
2	nsv427922	chr12:104325583-104523096	Enhancers Strong transcription Weak transcription Flanking Active TSS Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	30 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs7306864	TSPO	trans	lymphoblastoid	seeQTL
rs7306864	JAM3	trans	lymphoblastoid	seeQTL
rs7306864	FOXG1	trans	lymphoblastoid	seeQTL

Chromatin state (count:35 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:104408800-104442200	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
2	chr12:104435000-104442000	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
3	chr12:104435800-104441600	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
4	chr12:104436800-104440200	Weak transcription	Aorta	Aorta
5	chr12:104437600-104442000	Enhancers	Breast Myoepithelial Primary Cells	Breast
6	chr12:104438000-104440600	Weak transcription	Fetal Brain Female	brain
7	chr12:104438400-104441800	Enhancers	Colon Smooth Muscle	Colon
8	chr12:104438800-104440400	Enhancers	Rectal Smooth Muscle	rectum
9	chr12:104438800-104440600	Enhancers	Fetal Heart	heart
10	chr12:104438800-104440800	Enhancers	Duodenum Smooth Muscle	Duodenum
11	chr12:104439000-104440200	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
12	chr12:104439000-104440400	Enhancers	Fetal Lung	lung
13	chr12:104439200-104442000	Weak transcription	Fetal Muscle Trunk	muscle
14	chr12:104439400-104440200	Weak transcription	Ovary	ovary
15	chr12:104439400-104440600	Enhancers	Stomach Smooth Muscle	stomach
16	chr12:104439400-104441200	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
17	chr12:104439400-104442000	Weak transcription	Adipose Nuclei	Adipose
18	chr12:104439400-104442200	Weak transcription	Skeletal Muscle Male	skeletal muscle
19	chr12:104439400-104442600	Weak transcription	Right Atrium	heart
20	chr12:104439400-104443400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
21	chr12:104439400-104443400	Weak transcription	Left Ventricle	heart
22	chr12:104439400-104443400	Weak transcription	Lung	lung
23	chr12:104439400-104443400	Weak transcription	Right Ventricle	heart
24	chr12:104439400-104443800	Weak transcription	Primary hematopoietic stem cells short term culture	blood
25	chr12:104439600-104440800	Weak transcription	Fetal Muscle Leg	muscle
26	chr12:104439600-104441800	Weak transcription	HMEC	breast
27	chr12:104439600-104442000	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
28	chr12:104439600-104442200	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
29	chr12:104439600-104442400	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
30	chr12:104439600-104442400	Weak transcription	Fetal Stomach	stomach
31	chr12:104439600-104442400	Weak transcription	HSMM	muscle
32	chr12:104439600-104442400	Weak transcription	HSMMtube	muscle
33	chr12:104439600-104443400	Weak transcription	Psoas Muscle	Psoas
34	chr12:104440000-104442400	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
35	chr12:104440000-104443400	Weak transcription	Cortex derived primary cultured neurospheres	brain

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