Variant report

Variant	rs4768940
Chromosome Location	chr12:51220761-51220762
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr12:51212786..51214358-chr12:51219133..51221117,2	K562	blood:
2	chr12:51218257..51221554-chr12:51475850..51478812,3	MCF-7	breast:
3	chr12:51216774..51221510-chr12:51379576..51384198,5	MCF-7	breast:
4	chr12:51220629..51223236-chr12:51418576..51421161,3	MCF-7	breast:
5	chr12:51218193..51220790-chr12:51416290..51419028,2	K562	blood:
6	chr12:51216775..51221102-chr12:51419333..51421670,3	K562	blood:
7	chr12:51219096..51220890-chr12:51222074..51224257,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000110911	Chromatin interaction
ENSG00000110925	Chromatin interaction

Extended variants
information (count: 28 )
Associated
traits (count: 2 )

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

rs_ID	r²[population]
rs10783389	0.84[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs10876081	0.80[AMR][1000 genomes];0.80[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs10876089	0.80[AMR][1000 genomes];0.84[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs10876090	0.82[EUR][1000 genomes]
rs10876094	0.81[AFR][1000 genomes];0.83[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs10876095	0.80[AMR][1000 genomes];0.90[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs10876096	0.86[AFR][1000 genomes];0.80[AMR][1000 genomes];0.90[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs10876097	0.86[AFR][1000 genomes];0.80[AMR][1000 genomes];0.91[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs11169544	0.80[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs11169552	0.80[AMR][1000 genomes];0.80[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs11169554	0.80[AMR][1000 genomes];0.82[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs11169560	0.83[AFR][1000 genomes];0.84[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs11169561	0.83[AFR][1000 genomes];0.84[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs12424860	0.80[AMR][1000 genomes];0.82[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs1344958	0.81[AFR][1000 genomes];0.86[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs3809319	0.80[AMR][1000 genomes];0.84[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs4026593	0.86[AFR][1000 genomes];0.80[AMR][1000 genomes];0.91[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs4768866	0.80[EUR][1000 genomes]
rs4768917	0.80[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs4768921	0.80[AMR][1000 genomes];0.82[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs4768922	0.84[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs4768923	0.83[AFR][1000 genomes];0.86[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs4768924	0.92[AFR][1000 genomes];0.88[AMR][1000 genomes];0.92[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4768925	0.92[AFR][1000 genomes];0.90[AMR][1000 genomes];0.90[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs73094900	0.80[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs73096846	0.80[AMR][1000 genomes];0.84[EUR][1000 genomes];0.83[ASN][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	esv3414501	chr12:51174503-51534707	Strong transcription Weak transcription Genic enhancers Enhancers Active TSS Flanking Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	67 gene(s)	inside rSNPs	diseases
2	nsv899078	chr12:51213433-51286750	Weak transcription Enhancers Strong transcription Flanking Active TSS ZNF genes & repeats Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs4768940	LASS5	cis	brain	BrainEAC
rs4768940	DIP2B	cis	Thyroid	GTEx

Chromatin state (count:19 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:51200600-51222200	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
2	chr12:51205000-51228200	Weak transcription	Gastric	stomach
3	chr12:51210200-51222000	Weak transcription	Esophagus	oesophagus
4	chr12:51210600-51222000	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
5	chr12:51210600-51223400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
6	chr12:51211000-51222000	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
7	chr12:51211000-51222000	Weak transcription	Brain Cingulate Gyrus	brain
8	chr12:51213200-51222200	Weak transcription	Fetal Muscle Leg	muscle
9	chr12:51213400-51221800	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
10	chr12:51213400-51222600	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
11	chr12:51213800-51222800	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
12	chr12:51218800-51223400	Enhancers	Breast Myoepithelial Primary Cells	Breast
13	chr12:51219200-51221800	Weak transcription	HMEC	breast
14	chr12:51219200-51223000	Weak transcription	Brain Anterior Caudate	brain
15	chr12:51219400-51222400	Weak transcription	Brain Substantia Nigra	brain
16	chr12:51219600-51222200	Weak transcription	Fetal Muscle Trunk	muscle
17	chr12:51219600-51222400	Weak transcription	Skeletal Muscle Female	skeletal muscle
18	chr12:51219600-51222800	Weak transcription	Thymus	Thymus
19	chr12:51220200-51222200	Weak transcription	Skeletal Muscle Male	skeletal muscle

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