Variant report

Variant	rs12539530
Chromosome Location	chr7:107976561-107976562
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr7:107975728..107977944-chr7:107990404..107993160,3	MCF-7	breast:
2	chr7:107974215..107977046-chr7:107980359..107982514,2	K562	blood:
3	chr7:107976217..107977976-chr7:107988714..107990446,2	MCF-7	breast:

Extended variants
information (count: 38 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:27)

rs_ID	r²[population]
rs1016149	0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12531089	1.00[CEU][hapmap];1.00[CHB][hapmap];0.81[JPT][hapmap];0.90[AMR][1000 genomes];0.86[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs12539964	0.90[CEU][hapmap];0.83[CHB][hapmap];0.85[TSI][hapmap];0.83[EUR][1000 genomes]
rs13230316	0.95[CEU][hapmap];1.00[CHB][hapmap];0.98[CHD][hapmap];0.91[GIH][hapmap];0.82[JPT][hapmap];1.00[MEX][hapmap];0.88[TSI][hapmap];0.96[AMR][1000 genomes];0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs13242951	0.83[MEX][hapmap]
rs13244715	0.95[CEU][hapmap];1.00[CHB][hapmap];0.98[CHD][hapmap];0.91[GIH][hapmap];0.82[JPT][hapmap];1.00[MEX][hapmap];0.88[TSI][hapmap];0.92[AMR][1000 genomes];0.92[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs16872495	0.83[MEX][hapmap]
rs17155518	0.83[MEX][hapmap]
rs1990712	0.85[CEU][hapmap]
rs2080489	0.99[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2216259	0.90[CEU][hapmap];0.83[CHB][hapmap];0.85[EUR][1000 genomes]
rs2284286	0.92[AMR][1000 genomes];0.92[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2284287	0.95[CEU][hapmap];1.00[CHB][hapmap];0.82[JPT][hapmap];0.92[AMR][1000 genomes];0.90[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2284288	0.95[CEU][hapmap];1.00[CHB][hapmap];0.82[JPT][hapmap];0.92[AMR][1000 genomes];0.92[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2300027	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2395961	0.90[CEU][hapmap];0.83[CHB][hapmap];0.85[EUR][1000 genomes]
rs2395962	0.90[CEU][hapmap];0.83[CHB][hapmap];0.85[TSI][hapmap];0.83[EUR][1000 genomes]
rs34294071	0.96[AFR][1000 genomes];0.88[AMR][1000 genomes];0.87[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs34427132	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35669142	0.85[EUR][1000 genomes]
rs36063908	0.85[EUR][1000 genomes]
rs56102707	0.82[EUR][1000 genomes]
rs6948554	0.92[AMR][1000 genomes];0.86[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs6957056	0.89[AMR][1000 genomes];0.86[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6975557	0.86[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.98[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.84[MKK][hapmap];1.00[TSI][hapmap];0.86[YRI][hapmap];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7804045	0.95[CEU][hapmap];1.00[CHB][hapmap];0.98[CHD][hapmap];0.91[GIH][hapmap];0.82[JPT][hapmap];1.00[MEX][hapmap];0.85[TSI][hapmap];0.92[AMR][1000 genomes];0.93[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7807783	0.93[AFR][1000 genomes];0.82[AMR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:11 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv3348839	chr7:107377311-108286538	Weak transcription Enhancers Flanking Active TSS Genic enhancers ZNF genes & repeats Strong transcription Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	91 gene(s)	inside rSNPs	diseases
2	nsv949344	chr7:107396502-107987085	Weak transcription Enhancers Strong transcription Active TSS Flanking Active TSS Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	25 gene(s)	inside rSNPs	diseases
3	nsv831090	chr7:107786650-108011196	Enhancers Weak transcription Active TSS ZNF genes & repeats Flanking Active TSS Strong transcription Transcr. at gene 5' and 3' Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region	7 gene(s)	inside rSNPs	diseases
4	nsv888942	chr7:107893695-108055858	Weak transcription Enhancers ZNF genes & repeats Flanking Active TSS Strong transcription Active TSS Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region	5 gene(s)	inside rSNPs	diseases
5	nsv888943	chr7:107893695-108058574	Enhancers Weak transcription Active TSS Flanking Active TSS ZNF genes & repeats Strong transcription Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region	5 gene(s)	inside rSNPs	diseases
6	nsv1030425	chr7:107910716-108041036	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	5 gene(s)	inside rSNPs	diseases
7	nsv1019059	chr7:107935905-107995523	Enhancers ZNF genes & repeats Weak transcription Flanking Active TSS Active TSS Bivalent Enhancer Strong transcription Genic enhancers	TF binding region CpG island Chromatin interactive region	5 gene(s)	inside rSNPs	diseases
8	nsv1021783	chr7:107935905-107998281	Weak transcription Enhancers Flanking Active TSS Active TSS Strong transcription ZNF genes & repeats Genic enhancers Bivalent Enhancer	TF binding region CpG island Chromatin interactive region	5 gene(s)	inside rSNPs	diseases
9	esv2761354	chr7:107935905-107998293	Weak transcription Enhancers Flanking Active TSS Active TSS Bivalent Enhancer Genic enhancers ZNF genes & repeats Strong transcription	TF binding region CpG island Chromatin interactive region	5 gene(s)	inside rSNPs	diseases
10	nsv1031824	chr7:107935905-108006038	Enhancers Strong transcription Active TSS Weak transcription Flanking Active TSS ZNF genes & repeats Genic enhancers Bivalent Enhancer	TF binding region CpG island Chromatin interactive region	5 gene(s)	inside rSNPs	diseases
11	nsv1017288	chr7:107939739-108000837	Weak transcription Enhancers Flanking Active TSS ZNF genes & repeats Active TSS Strong transcription Genic enhancers Bivalent Enhancer	TF binding region CpG island Chromatin interactive region	5 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs12539530	LRRN3	cis	cerebellum	SCAN

Chromatin state (count:26 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr7:107967800-107986000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
2	chr7:107969000-107988200	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
3	chr7:107969200-107979800	Weak transcription	Pancreas	Pancrea
4	chr7:107970400-107978800	Weak transcription	Fetal Intestine Small	intestine
5	chr7:107971200-107979600	Weak transcription	HUES64 Cell Line	embryonic stem cell
6	chr7:107971200-107981000	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
7	chr7:107972800-107986000	Weak transcription	Cortex derived primary cultured neurospheres	brain
8	chr7:107974800-107976800	Enhancers	Placenta	Placenta
9	chr7:107975200-107976600	Enhancers	Pancreatic Islets	Pancreatic Islet
10	chr7:107975200-107978800	Weak transcription	Fetal Intestine Large	intestine
11	chr7:107975200-107989000	Weak transcription	Right Atrium	heart
12	chr7:107975600-107976800	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
13	chr7:107975600-107976800	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
14	chr7:107975600-107977200	Enhancers	A549	lung
15	chr7:107975800-107976800	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
16	chr7:107975800-107976800	Enhancers	Fetal Adrenal Gland	Adrenal Gland
17	chr7:107976000-107976600	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
18	chr7:107976000-107976600	Enhancers	HSMM	muscle
19	chr7:107976000-107976800	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
20	chr7:107976000-107976800	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
21	chr7:107976000-107976800	Enhancers	Brain Angular Gyrus	brain
22	chr7:107976000-107976800	Enhancers	HSMMtube	muscle
23	chr7:107976000-107977600	Enhancers	Brain Cingulate Gyrus	brain
24	chr7:107976200-107977000	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
25	chr7:107976400-107977400	Weak transcription	Brain Inferior Temporal Lobe	brain
26	chr7:107976400-107980000	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin

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