Variant report

Variant	rs773115
Chromosome Location	chr12:56398454-56398455
allele	A/C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:2)
CpG islands
(count:0)
Chromatin interactive
region (count:6)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:2 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	POLR2A	chr12:56398249-56399175	HepG2	liver:	n/a	n/a
2	POLR2A	chr12:56398010-56399026	H1-neurons	neurons:	n/a	n/a

No data

(count:6 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr12:56398217..56408038-chr12:56433794..56439966,15	K562	blood:
2	chr12:56388289..56393996-chr12:56394860..56404076,14	K562	blood:
3	chr12:56389364..56393818-chr12:56396293..56409099,19	MCF-7	breast:
4	chr12:56366763..56368279-chr12:56397786..56400423,2	MCF-7	breast:
5	chr12:56386715..56395273-chr12:56398367..56404356,15	MCF-7	breast:
6	chr12:56372898..56375119-chr12:56396371..56398654,2	MCF-7	breast:

No data

Variant related genes	Relation type
IKZF4	TF binding region
ENSG00000257449	Chromatin interaction
ENSG00000197728	Chromatin interaction
ENSG00000111540	Chromatin interaction
ENSG00000139531	Chromatin interaction
ENSG00000237493	Chromatin interaction
ENSG00000185664	Chromatin interaction

Extended variants
information (count: 69 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:65)

rs_ID	r²[population]
rs1045435	1.00[ASN][1000 genomes]
rs10783777	1.00[ASN][1000 genomes]
rs10783778	1.00[ASN][1000 genomes]
rs10876867	1.00[ASN][1000 genomes]
rs1091527	1.00[ASN][1000 genomes]
rs11550558	1.00[ASN][1000 genomes]
rs11835310	1.00[ASN][1000 genomes]
rs11837075	0.87[ASN][1000 genomes]
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	0.88[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1626158	1.00[ASN][1000 genomes]
rs1689511	0.80[AFR][1000 genomes];0.83[AMR][1000 genomes];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1689517	1.00[ASN][1000 genomes]
rs1689518	1.00[ASN][1000 genomes]
rs1701706	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs1702876	0.87[AFR][1000 genomes]
rs17118262	0.94[EUR][1000 genomes]
rs2131569	0.94[EUR][1000 genomes]
rs2271193	1.00[ASN][1000 genomes]
rs2271195	1.00[ASN][1000 genomes]
rs2277340	1.00[ASN][1000 genomes]
rs2456972	0.87[AFR][1000 genomes];0.94[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2640566	1.00[ASN][1000 genomes]
rs2658479	0.93[AFR][1000 genomes];0.94[AMR][1000 genomes];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2661728	1.00[ASN][1000 genomes]
rs2661729	1.00[ASN][1000 genomes]
rs2934152	1.00[ASN][1000 genomes]
rs34228181	0.94[EUR][1000 genomes]
rs34303864	0.94[EUR][1000 genomes]
rs34406511	0.94[EUR][1000 genomes]
rs34485293	0.86[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	0.91[EUR][1000 genomes]
rs35662491	0.80[EUR][1000 genomes]
rs35666826	0.83[EUR][1000 genomes]
rs35961650	0.89[EUR][1000 genomes]
rs4759022	0.94[EUR][1000 genomes]
rs4759239	0.94[AFR][1000 genomes];0.94[AMR][1000 genomes];0.89[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	0.96[EUR][1000 genomes]
rs7300292	1.00[ASN][1000 genomes]
rs7300772	0.84[AFR][1000 genomes];0.91[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs7304690	1.00[ASN][1000 genomes]
rs73338377	1.00[ASN][1000 genomes]
rs73338385	1.00[ASN][1000 genomes]
rs73338396	0.87[ASN][1000 genomes]
rs772919	0.84[AFR][1000 genomes];0.84[EUR][1000 genomes]
rs772922	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs772923	0.94[EUR][1000 genomes]
rs7963590	0.91[EUR][1000 genomes]
rs7970035	1.00[ASN][1000 genomes]
rs7977537	0.89[EUR][1000 genomes]
rs9738143	1.00[ASN][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
rs773115	LOC644166///LOC644191///LOC728937///RPS26	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:105 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:56391600-56398600	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
2	chr12:56391600-56399000	Weak transcription	Primary T cells from cord blood	blood
3	chr12:56391600-56400800	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
4	chr12:56391800-56400600	Weak transcription	Muscle Satellite Cultured Cells	--
5	chr12:56391800-56400600	Weak transcription	NHEK	skin
6	chr12:56392000-56399200	Weak transcription	HUVEC	blood vessel
7	chr12:56392000-56400600	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
8	chr12:56392000-56400600	Weak transcription	Fetal Thymus	thymus
9	chr12:56392000-56400600	Weak transcription	Right Atrium	heart
10	chr12:56392000-56400600	Weak transcription	HMEC	breast
11	chr12:56392000-56400800	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
12	chr12:56392000-56400800	Weak transcription	GM12878-XiMat	blood
13	chr12:56392200-56399800	Weak transcription	Hela-S3	cervix
14	chr12:56392400-56399400	Strong transcription	Fetal Stomach	stomach
15	chr12:56392400-56400800	Weak transcription	Fetal Brain Male	brain
16	chr12:56392600-56399000	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
17	chr12:56393200-56398600	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
18	chr12:56394000-56399200	Weak transcription	Primary T cells fromperipheralblood	blood
19	chr12:56394400-56399400	Strong transcription	Fetal Muscle Trunk	muscle
20	chr12:56395000-56399200	Strong transcription	Breast Myoepithelial Primary Cells	Breast
21	chr12:56395200-56398600	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
22	chr12:56395200-56398800	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
23	chr12:56395200-56398800	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
24	chr12:56395200-56399400	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
25	chr12:56395200-56400000	Strong transcription	Fetal Muscle Leg	muscle
26	chr12:56395400-56398600	Strong transcription	Left Ventricle	heart
27	chr12:56395400-56398800	Strong transcription	Ovary	ovary
28	chr12:56395400-56398800	Strong transcription	Right Ventricle	heart
29	chr12:56395400-56399000	Strong transcription	Brain Angular Gyrus	brain
30	chr12:56395400-56399000	Strong transcription	Brain Cingulate Gyrus	brain
31	chr12:56395400-56399200	Strong transcription	Brain Anterior Caudate	brain
32	chr12:56395600-56398800	Strong transcription	Primary hematopoietic stem cells short term culture	blood
33	chr12:56395600-56398800	Strong transcription	Gastric	stomach
34	chr12:56395600-56399200	Strong transcription	HUES6 Cell Line	embryonic stem cell
35	chr12:56395600-56399200	Strong transcription	Brain Dorsolateral Prefrontal Cortex	brain
36	chr12:56395600-56399200	Strong transcription	Stomach Smooth Muscle	stomach
37	chr12:56395800-56398600	Strong transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
38	chr12:56395800-56398600	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
39	chr12:56395800-56398600	Strong transcription	Duodenum Smooth Muscle	Duodenum
40	chr12:56395800-56398600	Strong transcription	Skeletal Muscle Female	skeletal muscle
41	chr12:56395800-56398600	Strong transcription	Osteobl	bone
42	chr12:56395800-56398800	Strong transcription	Lung	lung
43	chr12:56395800-56398800	Strong transcription	Rectal Smooth Muscle	rectum
44	chr12:56395800-56398800	Strong transcription	Skeletal Muscle Male	skeletal muscle
45	chr12:56395800-56399000	Strong transcription	Primary neutrophils fromperipheralblood	blood
46	chr12:56395800-56399000	Strong transcription	Brain Hippocampus Middle	brain
47	chr12:56395800-56399200	Strong transcription	HUES64 Cell Line	embryonic stem cell
48	chr12:56396000-56399000	Strong transcription	HUES48 Cell Line	embryonic stem cell
49	chr12:56396000-56399000	Strong transcription	Fetal Lung	lung
50	chr12:56396000-56399000	Strong transcription	Spleen	Spleen

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