Variant report

Variant	rs4759239
Chromosome Location	chr12:56420395-56420396
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:0)
CpG islands
(count:0)
Chromatin interactive
region (count:9)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

(count:9 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr12:56387127..56392729-chr12:56419203..56425417,17	MCF-7	breast:
2	chr12:56107674..56111560-chr12:56417665..56420637,3	MCF-7	breast:
3	chr12:56400024..56405744-chr12:56418580..56425265,13	MCF-7	breast:
4	chr12:56419317..56422414-chr12:56434888..56438037,4	K562	blood:
5	chr12:56417053..56422414-chr12:56432550..56437155,7	K562	blood:
6	chr12:56418586..56420915-chr12:56435116..56437578,2	MCF-7	breast:
7	chr12:56385051..56386875-chr12:56418911..56420935,2	K562	blood:
8	chr12:56350151..56351741-chr12:56420142..56422270,2	MCF-7	breast:
9	chr12:56418842..56421090-chr12:56423782..56426240,2	MCF-7	breast:

No data

Variant related genes	Relation type
ENSG00000139531	Chromatin interaction
ENSG00000185664	Chromatin interaction
ENSG00000135441	Chromatin interaction
ENSG00000257449	Chromatin interaction
ENSG00000255990	Chromatin interaction
ENSG00000258311	Chromatin interaction
ENSG00000197728	Chromatin interaction
ENSG00000123411	Chromatin interaction
ENSG00000135424	Chromatin interaction

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

rSNPs within LD-proxies of this variant (count:40)

rs_ID	r²[population]
rs12099979	0.94[EUR][1000 genomes]
rs12810011	0.94[EUR][1000 genomes]
rs12815302	0.89[EUR][1000 genomes]
rs12815387	0.94[EUR][1000 genomes]
rs12815488	0.94[EUR][1000 genomes]
rs12818756	0.94[EUR][1000 genomes]
rs12831468	0.94[EUR][1000 genomes]
rs1614219	0.84[AFR][1000 genomes];0.94[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs1689511	0.86[AFR][1000 genomes];0.89[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs1701706	0.89[AFR][1000 genomes];0.94[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs1702876	0.85[AFR][1000 genomes]
rs17118262	0.94[EUR][1000 genomes]
rs2131569	0.94[EUR][1000 genomes]
rs2456972	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs2658479	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs34228181	0.94[EUR][1000 genomes]
rs34303864	0.94[EUR][1000 genomes]
rs34406511	0.94[EUR][1000 genomes]
rs34485293	0.93[EUR][1000 genomes]
rs34507011	0.93[EUR][1000 genomes]
rs34602183	0.91[EUR][1000 genomes]
rs34650555	0.94[EUR][1000 genomes]
rs34921584	0.94[EUR][1000 genomes]
rs35485002	0.98[EUR][1000 genomes]
rs35662491	0.80[EUR][1000 genomes]
rs35666826	0.83[EUR][1000 genomes]
rs35961650	1.00[EUR][1000 genomes]
rs4759022	0.94[EUR][1000 genomes]
rs71459334	0.94[EUR][1000 genomes]
rs71459336	0.93[EUR][1000 genomes]
rs71459339	0.94[EUR][1000 genomes]
rs71459342	0.83[EUR][1000 genomes]
rs7298818	0.89[EUR][1000 genomes]
rs7300772	0.89[AFR][1000 genomes];0.97[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs772919	0.89[AFR][1000 genomes];0.95[EUR][1000 genomes]
rs772922	0.93[AFR][1000 genomes];0.94[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs772923	0.94[EUR][1000 genomes]
rs773115	0.94[AFR][1000 genomes];0.94[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs7963590	0.83[EUR][1000 genomes]
rs7977537	0.89[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1051961	chr12:56262220-56629427	Weak transcription Enhancers Strong transcription Flanking Bivalent TSS/Enh Flanking Active TSS Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	284 gene(s)	inside rSNPs	diseases
2	nsv832424	chr12:56275226-56466917	Enhancers Flanking Active TSS Active TSS Weak transcription Strong transcription Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	121 gene(s)	inside rSNPs	diseases
3	nsv1043988	chr12:56348185-56534900	Weak transcription Flanking Active TSS Enhancers Genic enhancers Active TSS Strong transcription Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	189 gene(s)	inside rSNPs	diseases
4	nsv832427	chr12:56392545-56512774	Weak transcription Strong transcription Genic enhancers Enhancers Flanking Active TSS Transcr. at gene 5' and 3' Active TSS Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	152 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs4759239	LOC644166///LOC644191///LOC728937///RPS26	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:117 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:56402200-56434800	Weak transcription	Psoas Muscle	Psoas
2	chr12:56402400-56422400	Weak transcription	Osteobl	bone
3	chr12:56402400-56423000	Weak transcription	Muscle Satellite Cultured Cells	--
4	chr12:56406000-56422800	Weak transcription	HSMM	muscle
5	chr12:56409400-56435000	Weak transcription	Stomach Mucosa	stomach
6	chr12:56409800-56422600	Weak transcription	Liver	Liver
7	chr12:56415400-56422400	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
8	chr12:56415600-56426200	Weak transcription	Aorta	Aorta
9	chr12:56415800-56420600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
10	chr12:56415800-56420600	Weak transcription	Esophagus	oesophagus
11	chr12:56415800-56422400	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
12	chr12:56415800-56422400	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
13	chr12:56416000-56420600	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
14	chr12:56416000-56420600	Weak transcription	Brain Substantia Nigra	brain
15	chr12:56416000-56420600	Weak transcription	Pancreatic Islets	Pancreatic Islet
16	chr12:56416000-56420600	Weak transcription	Right Ventricle	heart
17	chr12:56416000-56421200	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
18	chr12:56416000-56421200	Weak transcription	Rectal Mucosa Donor 29	rectum
19	chr12:56416000-56422800	Weak transcription	NH-A	brain
20	chr12:56416000-56426000	Weak transcription	Rectal Mucosa Donor 31	rectum
21	chr12:56416000-56434800	Weak transcription	Primary B cells from cord blood	blood
22	chr12:56416000-56434800	Weak transcription	Primary B cells from peripheral blood	blood
23	chr12:56416000-56435000	Weak transcription	Right Atrium	heart
24	chr12:56416200-56420600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
25	chr12:56416200-56420600	Weak transcription	Duodenum Mucosa	Duodenum
26	chr12:56416200-56420600	Weak transcription	Thymus	Thymus
27	chr12:56416200-56420800	Weak transcription	H9 Cell Line	embryonic stem cell
28	chr12:56416200-56420800	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
29	chr12:56416200-56420800	Weak transcription	NHLF	lung
30	chr12:56416200-56421000	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
31	chr12:56416200-56421600	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
32	chr12:56416200-56421600	Weak transcription	Spleen	Spleen
33	chr12:56416200-56422600	Weak transcription	NHDF-Ad	bronchial
34	chr12:56416200-56425800	Weak transcription	Small Intestine	intestine
35	chr12:56416200-56426000	Weak transcription	ES-I3 Cell Line	embryonic stem cell
36	chr12:56416200-56426000	Weak transcription	Colonic Mucosa	Colon
37	chr12:56416200-56434800	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
38	chr12:56416400-56420600	Weak transcription	iPS-15b Cell Line	embryonic stem cell
39	chr12:56416400-56420600	Weak transcription	Primary monocytes fromperipheralblood	blood
40	chr12:56416400-56421400	Weak transcription	Primary T helper cells PMA-I stimulated	--
41	chr12:56416400-56421400	Weak transcription	Monocytes-CD14+_RO01746	blood
42	chr12:56416400-56421600	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
43	chr12:56416400-56431000	Weak transcription	Primary T killer memory cells from peripheral blood	blood
44	chr12:56416600-56420800	Weak transcription	Primary T helper cells fromperipheralblood	blood
45	chr12:56416600-56422800	Weak transcription	HepG2	liver
46	chr12:56416600-56431000	Weak transcription	Primary T helper naive cells from peripheral blood	blood
47	chr12:56417400-56430800	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
48	chr12:56417600-56422200	Strong transcription	iPS-20b Cell Line	embryonic stem cell
49	chr12:56417800-56423200	Strong transcription	Brain Inferior Temporal Lobe	brain
50	chr12:56417800-56430600	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived

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