Variant report

Variant	rs1682593
Chromosome Location	chr12:83348764-83348765
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	chr12:83079278..83081926-chr12:83348191..83350037,2	MCF-7	breast:
2	chr12:83341035..83343546-chr12:83347635..83350159,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000179104	Chromatin interaction

Extended variants
information (count: 44 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:35)

rs_ID	r²[population]
rs10746259	0.88[JPT][hapmap]
rs10746261	0.88[JPT][hapmap]
rs10862525	0.85[ASN][1000 genomes]
rs10862526	0.92[CHB][hapmap];1.00[JPT][hapmap];0.94[ASN][1000 genomes]
rs10862527	0.92[CHB][hapmap];1.00[CHD][hapmap];0.88[GIH][hapmap];1.00[JPT][hapmap];0.94[ASN][1000 genomes]
rs10862528	0.98[ASN][1000 genomes]
rs10862529	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10862530	0.92[CHB][hapmap];1.00[CHD][hapmap];0.92[GIH][hapmap];1.00[JPT][hapmap];0.99[ASN][1000 genomes]
rs10862532	0.89[ASN][1000 genomes]
rs12297736	0.86[JPT][hapmap];0.87[ASN][1000 genomes]
rs12320912	0.87[ASN][1000 genomes]
rs12809082	0.82[JPT][hapmap]
rs1471781	0.87[ASN][1000 genomes]
rs1484991	0.82[JPT][hapmap]
rs1625397	0.99[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1682590	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1682592	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1682594	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1682595	0.94[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs17010139	0.82[JPT][hapmap]
rs17010268	0.88[JPT][hapmap];0.86[ASN][1000 genomes]
rs1796188	1.00[CEU][hapmap];1.00[CHB][hapmap];0.94[JPT][hapmap];0.96[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1796189	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2019384	0.81[JPT][hapmap]
rs2403020	0.92[CHB][hapmap];1.00[CHD][hapmap];0.96[GIH][hapmap];1.00[JPT][hapmap];0.84[MEX][hapmap];0.84[MKK][hapmap];0.89[TSI][hapmap];0.98[ASN][1000 genomes]
rs2403021	0.92[CHB][hapmap];0.94[JPT][hapmap];0.82[AMR][1000 genomes];0.98[ASN][1000 genomes]
rs2403023	1.00[CHB][hapmap];1.00[CHD][hapmap];0.92[GIH][hapmap];0.94[JPT][hapmap];0.99[ASN][1000 genomes]
rs3993374	0.99[ASN][1000 genomes]
rs4346030	0.86[ASN][1000 genomes]
rs4346031	0.98[ASN][1000 genomes]
rs7295699	0.98[ASN][1000 genomes]
rs7957916	0.92[CHB][hapmap];1.00[JPT][hapmap];0.96[ASN][1000 genomes]
rs7965229	0.83[ASN][1000 genomes]
rs7970086	0.92[CHB][hapmap];0.90[CHD][hapmap];0.91[GIH][hapmap];0.94[JPT][hapmap];0.88[ASN][1000 genomes]
rs7971263	1.00[CEU][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:9 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv521849	chr12:83013783-83991479	Weak transcription ZNF genes & repeats Enhancers Strong transcription Active TSS Flanking Active TSS Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh 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	nsv469490	chr12:83089431-83507269	Enhancers Weak transcription Strong transcription ZNF genes & repeats Genic enhancers Flanking Active TSS Bivalent Enhancer Active TSS	TF binding region CpG island Chromatin interactive region	6 gene(s)	inside rSNPs	diseases
3	nsv559542	chr12:83089431-83507269	Weak transcription Enhancers Flanking Active TSS Strong transcription ZNF genes & repeats Active TSS Genic enhancers Bivalent Enhancer	TF binding region CpG island Chromatin interactive region	6 gene(s)	inside rSNPs	diseases
4	esv2758315	chr12:83101045-83357621	Enhancers Weak transcription Strong transcription ZNF genes & repeats Flanking Active TSS Bivalent Enhancer Genic enhancers Active TSS	TF binding region CpG island Chromatin interactive region	2 gene(s)	inside rSNPs	diseases
5	esv2759911	chr12:83101045-83357621	Enhancers Weak transcription Active TSS Genic enhancers ZNF genes & repeats Strong transcription Flanking Active TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region	2 gene(s)	inside rSNPs	diseases
6	nsv832472	chr12:83248283-83419753	Weak transcription ZNF genes & repeats Enhancers Flanking Active TSS Active TSS Genic enhancers Strong transcription Bivalent Enhancer	TF binding region CpG island Chromatin interactive region	4 gene(s)	inside rSNPs	n/a
7	nsv559557	chr12:83334204-83453620	ZNF genes & repeats Weak transcription Enhancers Strong transcription Flanking Active TSS Active TSS Genic enhancers	TF binding region CpG island Chromatin interactive region	4 gene(s)	inside rSNPs	n/a
8	nsv469495	chr12:83339933-83374779	Weak transcription Enhancers Strong transcription ZNF genes & repeats Flanking Active TSS Active TSS	Chromatin interactive region	1 gene(s)	inside rSNPs	n/a
9	nsv559558	chr12:83339933-83374779	Enhancers Weak transcription Strong transcription Flanking Active TSS ZNF genes & repeats Active TSS	Chromatin interactive region	1 gene(s)	inside rSNPs	n/a

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs1682593	SLC6A15	cis	cerebellum	SCAN

Chromatin state (count:27 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:83342000-83352600	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
2	chr12:83346200-83349200	Enhancers	Fetal Heart	heart
3	chr12:83346400-83349200	Enhancers	Breast Myoepithelial Primary Cells	Breast
4	chr12:83347000-83348800	Weak transcription	HMEC	breast
5	chr12:83347000-83367200	Weak transcription	Gastric	stomach
6	chr12:83347000-83379600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
7	chr12:83347200-83349400	Enhancers	NHEK	skin
8	chr12:83347600-83349400	Enhancers	Brain Substantia Nigra	brain
9	chr12:83347800-83349200	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
10	chr12:83347800-83349400	Enhancers	Brain Cingulate Gyrus	brain
11	chr12:83348000-83349000	Enhancers	Brain Germinal Matrix	brain
12	chr12:83348000-83349200	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
13	chr12:83348000-83349200	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
14	chr12:83348000-83349200	Enhancers	Brain Hippocampus Middle	brain
15	chr12:83348000-83349200	Enhancers	Brain Inferior Temporal Lobe	brain
16	chr12:83348000-83349200	Enhancers	Stomach Mucosa	stomach
17	chr12:83348000-83349400	Enhancers	Colon Smooth Muscle	Colon
18	chr12:83348200-83349400	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
19	chr12:83348200-83349400	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
20	chr12:83348400-83349200	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
21	chr12:83348400-83349200	Enhancers	Foreskin Melanocyte Primary Cells skin01	Skin
22	chr12:83348400-83349200	Enhancers	Rectal Smooth Muscle	rectum
23	chr12:83348400-83349400	Enhancers	Primary monocytes fromperipheralblood	blood
24	chr12:83348400-83349400	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
25	chr12:83348400-83349400	Enhancers	Monocytes-CD14+_RO01746	blood
26	chr12:83348400-83349600	Enhancers	Placenta Amnion	Placenta Amnion
27	chr12:83348600-83358000	Weak transcription	Fetal Lung	lung

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