Variant report

Variant	rs749292
Chromosome Location	chr15:51558731-51558732
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	chr15:51551577..51554113-chr15:51554957..51559127,3	MCF-7	breast:

Extended variants
information (count: 48 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:38)

rs_ID	r²[population]
rs10519299	1.00[CEU][hapmap];0.81[CHB][hapmap];0.91[CHD][hapmap];1.00[GIH][hapmap];0.90[JPT][hapmap];0.87[MEX][hapmap];1.00[TSI][hapmap];0.83[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs1062033	0.85[CEU][hapmap];0.81[EUR][1000 genomes]
rs11632903	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];0.80[LWK][hapmap];1.00[MEX][hapmap];0.86[MKK][hapmap];0.98[TSI][hapmap];0.86[YRI][hapmap];0.90[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11632926	0.94[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs11636403	0.89[CEU][hapmap];0.82[GIH][hapmap];0.90[TSI][hapmap];0.84[EUR][1000 genomes]
rs11636639	0.92[AFR][1000 genomes];0.99[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11856927	0.81[CEU][hapmap]
rs12050767	1.00[CEU][hapmap];1.00[CHB][hapmap];0.98[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.96[MEX][hapmap];0.84[MKK][hapmap];0.98[TSI][hapmap];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12050772	0.85[CEU][hapmap]
rs12901187	1.00[CEU][hapmap];0.84[GIH][hapmap];0.91[TSI][hapmap];0.93[EUR][1000 genomes]
rs12907866	0.85[CEU][hapmap];0.81[EUR][1000 genomes]
rs12908960	0.85[CEU][hapmap];0.81[EUR][1000 genomes]
rs12910259	0.84[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs17523527	0.80[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs17523541	0.85[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs17601876	0.85[CEU][hapmap];0.98[TSI][hapmap];0.84[EUR][1000 genomes]
rs2414100	0.92[AFR][1000 genomes];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2414101	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];0.87[LWK][hapmap];0.96[MEX][hapmap];0.86[MKK][hapmap];0.98[TSI][hapmap];0.86[YRI][hapmap];0.91[AFR][1000 genomes];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs28440805	0.91[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs28490942	0.90[AFR][1000 genomes];0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs28518777	0.99[EUR][1000 genomes]
rs28520437	0.85[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs28637352	0.91[AFR][1000 genomes];0.87[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28674681	0.90[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2899474	0.88[AFR][1000 genomes];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs34712049	0.92[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34784350	0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs35939475	0.85[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs3889391	1.00[CEU][hapmap];0.82[GIH][hapmap];0.91[TSI][hapmap];0.80[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs4545755	0.96[CEU][hapmap];0.84[GIH][hapmap];0.81[TSI][hapmap];0.89[EUR][1000 genomes]
rs4774584	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];0.96[MEX][hapmap];0.83[MKK][hapmap];0.98[TSI][hapmap];0.86[YRI][hapmap];0.88[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6493494	1.00[CEU][hapmap];0.84[GIH][hapmap];0.91[TSI][hapmap];0.94[EUR][1000 genomes]
rs7181429	1.00[ASW][hapmap];1.00[CHB][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.90[AFR][1000 genomes];0.92[AMR][1000 genomes];0.91[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs8028111	0.85[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs8029537	0.98[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs8038715	0.88[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs8039089	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];0.87[LWK][hapmap];0.96[MEX][hapmap];0.86[MKK][hapmap];1.00[TSI][hapmap];0.86[YRI][hapmap];0.90[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs8042086	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];0.87[LWK][hapmap];0.96[MEX][hapmap];0.86[MKK][hapmap];1.00[TSI][hapmap];0.86[YRI][hapmap];0.89[AFR][1000 genomes];0.91[AMR][1000 genomes];0.95[EUR][1000 genomes];0.93[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:10 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1047443	chr15:50744781-51647023	Strong transcription Active TSS Weak transcription Genic enhancers Enhancers Flanking Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	82 gene(s)	inside rSNPs	diseases
2	nsv569399	chr15:50874964-51562198	Flanking Active TSS Transcr. at gene 5' and 3' Weak transcription Strong transcription Enhancers Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats Genic enhancers Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	70 gene(s)	inside rSNPs	diseases
3	nsv569400	chr15:50874964-51767265	ZNF genes & repeats Weak transcription Strong transcription Active TSS Flanking Active TSS Bivalent/Poised TSS Bivalent Enhancer Enhancers Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	80 gene(s)	inside rSNPs	diseases
4	nsv1049644	chr15:51265447-51560445	Strong transcription Enhancers Bivalent Enhancer Weak transcription Flanking Active TSS ZNF genes & repeats Active TSS Bivalent/Poised TSS Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	11 gene(s)	inside rSNPs	diseases
5	esv34532	chr15:51276128-51752856	Flanking Active TSS Weak transcription Strong transcription Enhancers Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	21 gene(s)	inside rSNPs	diseases
6	esv2758382	chr15:51282257-51830339	Enhancers Bivalent/Poised TSS Weak transcription Bivalent Enhancer Strong transcription Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	22 gene(s)	inside rSNPs	diseases
7	esv2760031	chr15:51282257-51830339	Weak transcription Enhancers Strong transcription Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh Flanking Active TSS Active TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	22 gene(s)	inside rSNPs	diseases
8	nsv471243	chr15:51345485-52018096	Weak transcription Enhancers Active TSS Flanking Active TSS Genic enhancers Strong transcription Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	39 gene(s)	inside rSNPs	diseases
9	esv2757600	chr15:51352249-51783981	Weak transcription Bivalent Enhancer Enhancers Strong transcription Active TSS Flanking Bivalent TSS/Enh Flanking Active TSS Genic enhancers Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	21 gene(s)	inside rSNPs	diseases
10	nsv904215	chr15:51542193-51673125	Active TSS Enhancers Bivalent Enhancer Flanking Active TSS Weak transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS Strong transcription Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA	11 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs749292	LYSMD2	cis	parietal	SCAN
rs749292	TMOD2	cis	cerebellum	SCAN

Chromatin state (count:31 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:51524800-51574000	Weak transcription	HepG2	liver
2	chr15:51555000-51559000	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
3	chr15:51555800-51559000	Enhancers	NHDF-Ad	bronchial
4	chr15:51555800-51559200	Genic enhancers	Placenta	Placenta
5	chr15:51557200-51559000	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
6	chr15:51557600-51559000	Enhancers	HSMMtube	muscle
7	chr15:51557800-51558800	Bivalent Enhancer	Fetal Muscle Leg	muscle
8	chr15:51557800-51559200	Bivalent Enhancer	Fetal Stomach	stomach
9	chr15:51558000-51558800	Enhancers	Brain Germinal Matrix	brain
10	chr15:51558400-51558800	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
11	chr15:51558400-51558800	Enhancers	Brain Hippocampus Middle	brain
12	chr15:51558400-51558800	Enhancers	Brain Inferior Temporal Lobe	brain
13	chr15:51558400-51558800	Enhancers	Brain Dorsolateral Prefrontal Cortex	brain
14	chr15:51558400-51558800	Enhancers	Brain Substantia Nigra	brain
15	chr15:51558400-51558800	Bivalent Enhancer	Stomach Smooth Muscle	stomach
16	chr15:51558400-51559000	Enhancers	Cortex derived primary cultured neurospheres	brain
17	chr15:51558400-51559000	Bivalent Enhancer	Adipose Nuclei	Adipose
18	chr15:51558400-51559000	Enhancers	Fetal Brain Male	brain
19	chr15:51558400-51559400	Enhancers	Spleen	Spleen
20	chr15:51558400-51559800	Active TSS	Brain Cingulate Gyrus	brain
21	chr15:51558600-51558800	Bivalent Enhancer	H9 Derived Neuron Cultured Cells	ES cell derived
22	chr15:51558600-51558800	Bivalent Enhancer	Foreskin Melanocyte Primary Cells skin01	Skin
23	chr15:51558600-51558800	Enhancers	Brain Anterior Caudate	brain
24	chr15:51558600-51558800	Bivalent Enhancer	Colonic Mucosa	Colon
25	chr15:51558600-51558800	Enhancers	Fetal Brain Female	brain
26	chr15:51558600-51559000	Bivalent Enhancer	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
27	chr15:51558600-51559000	Bivalent Enhancer	Skeletal Muscle Male	skeletal muscle
28	chr15:51558600-51559000	Enhancers	HSMM	muscle
29	chr15:51558600-51559200	Bivalent Enhancer	ES-UCSF4 Cell Line	embryonic stem cell
30	chr15:51558600-51560000	Flanking Active TSS	Ganglion Eminence derived primary cultured neurospheres	brain
31	chr15:51558600-51560200	Flanking Active TSS	Foreskin Fibroblast Primary Cells skin02	Skin

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