Variant report

Variant	rs646782
Chromosome Location	chr12:50482211-50482212
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr12:50475132..50479699-chr12:50479828..50484275,5	K562	blood:
2	chr12:50478595..50483647-chr12:50502911..50507517,7	K562	blood:
3	chr12:50478759..50480659-chr12:50481009..50483998,3	K562	blood:
4	chr12:50481586..50483446-chr12:50561055..50562611,2	MCF-7	breast:
5	chr12:50475972..50484033-chr12:50500850..50507517,14	K562	blood:
6	chr12:50477567..50484756-chr12:50559008..50565131,16	MCF-7	breast:
7	chr12:50468886..50470594-chr12:50481318..50483189,2	K562	blood:

Variant related genes	Relation type
ENSG00000272368	Chromatin interaction
ENSG00000178449	Chromatin interaction
ENSG00000139624	Chromatin interaction
ENSG00000110881	Chromatin interaction
ENSG00000066117	Chromatin interaction

Extended variants
information (count: 38 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:33)

rs_ID	r²[population]
rs1044370	0.92[CEU][hapmap];1.00[CHB][hapmap]
rs1862043	1.00[CHB][hapmap]
rs1979702	0.92[CEU][hapmap]
rs2178173	1.00[CHB][hapmap]
rs2272391	0.96[CEU][hapmap];0.82[EUR][1000 genomes]
rs2358538	1.00[CHB][hapmap]
rs578470	0.80[EUR][1000 genomes]
rs6580729	1.00[CHB][hapmap]
rs706790	0.81[EUR][1000 genomes]
rs706791	0.96[CEU][hapmap];1.00[CHB][hapmap];0.86[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs706792	0.96[CEU][hapmap];1.00[CHB][hapmap];0.86[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs706793	1.00[CEU][hapmap];1.00[CHB][hapmap];0.86[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs7136570	1.00[CHB][hapmap]
rs7279	1.00[CHB][hapmap]
rs7297421	1.00[CHB][hapmap]
rs7302981	1.00[CHB][hapmap]
rs7308356	0.88[CHB][hapmap]
rs7532	1.00[CHB][hapmap]
rs835592	0.96[CEU][hapmap];0.81[EUR][1000 genomes]
rs836170	0.92[AMR][1000 genomes];0.93[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs836171	0.92[AMR][1000 genomes];0.93[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs836172	1.00[CEU][hapmap];1.00[CHB][hapmap];0.80[YRI][hapmap];0.85[AFR][1000 genomes];0.98[AMR][1000 genomes];0.95[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs836173	0.98[AMR][1000 genomes];0.95[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs836174	0.98[AMR][1000 genomes];0.95[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs836176	0.96[AMR][1000 genomes];0.95[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs836177	1.00[CEU][hapmap];1.00[CHB][hapmap];0.96[AMR][1000 genomes];0.95[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs836179	1.00[CHB][hapmap];0.84[AMR][1000 genomes];0.82[ASN][1000 genomes]
rs836180	0.80[CEU][hapmap];1.00[CHB][hapmap];0.82[AMR][1000 genomes];0.82[ASN][1000 genomes]
rs836181	0.81[AMR][1000 genomes];0.82[ASN][1000 genomes]
rs836188	0.82[EUR][1000 genomes]
rs836189	0.82[EUR][1000 genomes]
rs844347	0.96[CEU][hapmap];0.82[EUR][1000 genomes]
rs860698	1.00[CEU][hapmap];1.00[CHB][hapmap];0.91[AMR][1000 genomes];0.82[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:5 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1045327	chr12:49975040-50551375	Strong transcription Weak transcription Enhancers Genic enhancers Flanking Active TSS Active TSS Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	170 gene(s)	inside rSNPs	diseases
2	nsv541490	chr12:49975040-50551375	Weak transcription Transcr. at gene 5' and 3' Enhancers Genic enhancers Active TSS Strong transcription Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	170 gene(s)	inside rSNPs	diseases
3	nsv530671	chr12:50233858-50708991	Flanking Active TSS Active TSS Enhancers Weak transcription Genic enhancers Bivalent/Poised TSS Strong transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	117 gene(s)	inside rSNPs	diseases
4	esv3392138	chr12:50394642-50645326	Flanking Bivalent TSS/Enh Active TSS Flanking Active TSS Enhancers Weak transcription Strong transcription Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	66 gene(s)	inside rSNPs	diseases
5	nsv558840	chr12:50449976-50523964	Enhancers Active TSS Genic enhancers Weak transcription Flanking Active TSS Strong transcription Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	42 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs646782	LASS5	cis	multi-tissue	Pritchard
rs646782	CERS5	cis	Nerve Tibial	GTEx

Chromatin state (count:127 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:50479600-50482400	Weak transcription	Ovary	ovary
2	chr12:50479800-50488200	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
3	chr12:50480000-50482400	Weak transcription	Fetal Kidney	kidney
4	chr12:50480000-50482600	Weak transcription	Pancreatic Islets	Pancreatic Islet
5	chr12:50480000-50483600	Weak transcription	Right Ventricle	heart
6	chr12:50480000-50485400	Weak transcription	Stomach Mucosa	stomach
7	chr12:50480000-50486000	Strong transcription	Colon Smooth Muscle	Colon
8	chr12:50480000-50494800	Strong transcription	Rectal Mucosa Donor 29	rectum
9	chr12:50480000-50496400	Weak transcription	Right Atrium	heart
10	chr12:50480200-50482400	Genic enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
11	chr12:50480200-50482400	Weak transcription	Primary T killer memory cells from peripheral blood	blood
12	chr12:50480200-50482600	Genic enhancers	Cortex derived primary cultured neurospheres	brain
13	chr12:50480200-50482600	Genic enhancers	Fetal Adrenal Gland	Adrenal Gland
14	chr12:50480200-50483000	Genic enhancers	HepG2	liver
15	chr12:50480200-50483000	Genic enhancers	NH-A	brain
16	chr12:50480200-50484200	Genic enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
17	chr12:50480200-50484800	Strong transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
18	chr12:50480200-50489400	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
19	chr12:50480200-50494800	Strong transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
20	chr12:50480200-50494800	Strong transcription	HUES48 Cell Line	embryonic stem cell
21	chr12:50480200-50496200	Strong transcription	Fetal Muscle Trunk	muscle
22	chr12:50480200-50496600	Strong transcription	Primary hematopoietic stem cells short term culture	blood
23	chr12:50480200-50496600	Strong transcription	Thymus	Thymus
24	chr12:50480200-50496800	Strong transcription	Fetal Stomach	stomach
25	chr12:50480400-50482400	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
26	chr12:50480400-50482400	Strong transcription	Liver	Liver
27	chr12:50480400-50482600	Transcr. at gene 5' and 3'	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
28	chr12:50480400-50482600	Genic enhancers	Fetal Brain Female	brain
29	chr12:50480400-50482600	Strong transcription	Placenta Amnion	Placenta Amnion
30	chr12:50480400-50482800	Genic enhancers	Brain Anterior Caudate	brain
31	chr12:50480400-50483200	Genic enhancers	Skeletal Muscle Female	skeletal muscle
32	chr12:50480400-50486400	Strong transcription	K562	blood
33	chr12:50480400-50493800	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
34	chr12:50480400-50494400	Strong transcription	H1 Cell Line	embryonic stem cell
35	chr12:50480400-50494400	Strong transcription	iPS-20b Cell Line	embryonic stem cell
36	chr12:50480400-50494600	Strong transcription	iPS-18 Cell Line	embryonic stem cell
37	chr12:50480400-50494800	Strong transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
38	chr12:50480400-50494800	Strong transcription	Duodenum Mucosa	Duodenum
39	chr12:50480400-50494800	Strong transcription	Fetal Intestine Large	intestine
40	chr12:50480400-50494800	Strong transcription	Placenta	Placenta
41	chr12:50480400-50495600	Strong transcription	Stomach Smooth Muscle	stomach
42	chr12:50480400-50495800	Strong transcription	Primary T cells fromperipheralblood	blood
43	chr12:50480400-50496000	Strong transcription	Monocytes-CD14+_RO01746	blood
44	chr12:50480400-50496200	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
45	chr12:50480400-50496200	Strong transcription	A549	lung
46	chr12:50480400-50496600	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
47	chr12:50480400-50496600	Strong transcription	HUES6 Cell Line	embryonic stem cell
48	chr12:50480400-50496600	Strong transcription	Primary T cells from cord blood	blood
49	chr12:50480400-50496600	Strong transcription	Fetal Lung	lung
50	chr12:50480600-50482400	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung

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