Variant report

Variant	rs1034762
Chromosome Location	chr12:48389643-48389644
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr12:48346353..48348105-chr12:48388384..48390746,2	MCF-7	breast:
2	chr12:48387141..48389064-chr12:48389409..48391360,2	MCF-7	breast:
3	chr12:48375884..48381022-chr12:48386743..48391938,6	MCF-7	breast:

Variant related genes	Relation type
ENSG00000139219	Chromatin interaction

Extended variants
information (count: 27 )
Associated
traits (count: 2 )

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

rs_ID	r²[population]
rs10783227	0.80[EUR][1000 genomes]
rs10783232	0.81[CEU][hapmap]
rs11612578	0.81[CEU][hapmap]
rs1635526	0.84[CEU][hapmap];0.84[EUR][1000 genomes]
rs1635529	0.83[EUR][1000 genomes]
rs1635534	0.82[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs1635535	0.82[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs1635536	0.93[EUR][1000 genomes]
rs1635550	0.80[CEU][hapmap];0.83[MEX][hapmap];0.84[TSI][hapmap]
rs1793912	0.82[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs1793913	0.82[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs1793915	0.81[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs1793917	0.82[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs1793931	0.87[CEU][hapmap];0.86[EUR][1000 genomes]
rs1793933	0.85[CEU][hapmap];0.86[EUR][1000 genomes]
rs1793955	0.88[EUR][1000 genomes]
rs1793956	0.87[EUR][1000 genomes]
rs1859444	0.81[CEU][hapmap];0.81[EUR][1000 genomes]
rs1990029	0.85[CEU][hapmap]
rs3803183	0.80[EUR][1000 genomes]
rs3803184	0.80[EUR][1000 genomes]
rs3825404	0.81[CEU][hapmap];0.80[EUR][1000 genomes]
rs6580647	0.81[CEU][hapmap]
rs6580649	0.81[CEU][hapmap]
rs6580660	0.81[CEU][hapmap]
rs917055	0.86[ASW][hapmap];0.93[CEU][hapmap];0.81[LWK][hapmap];0.88[MEX][hapmap];1.00[TSI][hapmap];0.94[YRI][hapmap];0.86[AFR][1000 genomes];0.82[AMR][1000 genomes];0.98[EUR][1000 genomes]

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

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv832401	chr12:48347453-48477999	Weak transcription Enhancers Bivalent Enhancer Genic enhancers Active TSS Flanking Bivalent TSS/Enh Strong transcription Bivalent/Poised TSS Flanking Active TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	29 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs1034762	ZNF641	cis	Whole Blood	GTEx
rs1034762	SNORA2A	cis	parietal	SCAN

Chromatin state (count:41 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:48376800-48391000	Weak transcription	Fetal Intestine Large	intestine
2	chr12:48382800-48394600	Weak transcription	Breast Myoepithelial Primary Cells	Breast
3	chr12:48383800-48393800	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
4	chr12:48383800-48394400	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
5	chr12:48385200-48391600	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
6	chr12:48386400-48389800	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
7	chr12:48386800-48392800	Strong transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
8	chr12:48387000-48391600	Strong transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
9	chr12:48387600-48390200	Strong transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
10	chr12:48388000-48391400	Enhancers	Fetal Brain Male	brain
11	chr12:48388600-48390400	Enhancers	Brain Germinal Matrix	brain
12	chr12:48388800-48390200	Strong transcription	Fetal Intestine Small	intestine
13	chr12:48389000-48390600	Genic enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
14	chr12:48389000-48390600	Enhancers	Skeletal Muscle Female	skeletal muscle
15	chr12:48389200-48390400	Bivalent Enhancer	Fetal Stomach	stomach
16	chr12:48389200-48390400	Enhancers	Skeletal Muscle Male	skeletal muscle
17	chr12:48389200-48391000	Enhancers	Cortex derived primary cultured neurospheres	brain
18	chr12:48389400-48390000	Enhancers	Foreskin Melanocyte Primary Cells skin01	Skin
19	chr12:48389400-48390000	Enhancers	Psoas Muscle	Psoas
20	chr12:48389400-48390400	Enhancers	Brain Anterior Caudate	brain
21	chr12:48389400-48390600	Enhancers	Fetal Brain Female	brain
22	chr12:48389400-48390600	Enhancers	Fetal Lung	lung
23	chr12:48389400-48390600	Enhancers	Fetal Muscle Leg	muscle
24	chr12:48389400-48390600	Enhancers	HSMMtube	muscle
25	chr12:48389400-48391000	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
26	chr12:48389600-48389800	Bivalent Enhancer	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
27	chr12:48389600-48389800	Enhancers	Brain Dorsolateral Prefrontal Cortex	brain
28	chr12:48389600-48390000	Bivalent Enhancer	Foreskin Fibroblast Primary Cells skin02	Skin
29	chr12:48389600-48390000	Enhancers	Lung	lung
30	chr12:48389600-48390000	Enhancers	Right Atrium	heart
31	chr12:48389600-48390200	Enhancers	Adipose Nuclei	Adipose
32	chr12:48389600-48390200	Bivalent Enhancer	Brain Cingulate Gyrus	brain
33	chr12:48389600-48390200	Enhancers	Placenta	Placenta
34	chr12:48389600-48390400	Bivalent Enhancer	IMR90 fetal lung fibroblasts Cell Line	lung
35	chr12:48389600-48390400	Bivalent Enhancer	Brain Angular Gyrus	brain
36	chr12:48389600-48390400	Bivalent Enhancer	Brain Hippocampus Middle	brain
37	chr12:48389600-48390400	Enhancers	Fetal Muscle Trunk	muscle
38	chr12:48389600-48390400	Enhancers	Gastric	stomach
39	chr12:48389600-48390400	Enhancers	Left Ventricle	heart
40	chr12:48389600-48390400	Enhancers	Ovary	ovary
41	chr12:48389600-48390400	Enhancers	Right Ventricle	heart

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