Variant report

Variant	rs10774890
Chromosome Location	chr12:117256698-117256699
allele	A/C
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:15)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

(count:15 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr12:117255787..117257433-chr12:117297351..117300001,2	K562	blood:
2	chr12:117255552..117257189-chr12:117266755..117268584,2	K562	blood:
3	chr12:117253820..117255367-chr12:117255716..117257267,2	K562	blood:
4	chr12:117242162..117243909-chr12:117254243..117257229,2	K562	blood:
5	chr12:117245789..117252962-chr12:117254340..117258603,11	K562	blood:
6	chr12:117255729..117257748-chr12:117292292..117294428,2	MCF-7	breast:
7	chr12:117249993..117252950-chr12:117255244..117258293,4	MCF-7	breast:
8	chr12:117255625..117260515-chr12:117260953..117265280,7	K562	blood:
9	chr12:117251777..117254967-chr12:117255465..117258181,5	MCF-7	breast:
10	chr12:117175650..117178418-chr12:117255455..117257271,2	MCF-7	breast:
11	chr12:117211331..117213827-chr12:117255904..117257677,2	MCF-7	breast:
12	chr12:117255053..117257426-chr12:117349302..117351380,2	K562	blood:
13	chr12:117256194..117258778-chr12:117314042..117315845,3	MCF-7	breast:
14	chr12:117255957..117259131-chr12:117261216..117264613,4	MCF-7	breast:
15	chr12:117256689..117258680-chr12:117270250..117272345,2	MCF-7	breast:

No data

Variant related genes	Relation type
ENSG00000135119	Chromatin interaction
ENSG00000111412	Chromatin interaction

Extended variants
information (count: 27 )
Associated
traits (count: 3 )

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

rs_ID	r²[population]
rs10047539	0.81[TSI][hapmap]
rs10735097	1.00[CEU][hapmap];0.81[EUR][1000 genomes]
rs10735098	0.89[CEU][hapmap];1.00[CHB][hapmap];0.96[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.95[TSI][hapmap];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10774889	1.00[CEU][hapmap]
rs10850720	0.84[AFR][1000 genomes];0.88[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs10850723	0.81[EUR][1000 genomes]
rs1495933	0.88[ASW][hapmap];1.00[CEU][hapmap];0.85[CHB][hapmap];0.93[CHD][hapmap];0.96[GIH][hapmap];0.89[JPT][hapmap];0.88[LWK][hapmap];1.00[MEX][hapmap];0.93[MKK][hapmap];1.00[TSI][hapmap];0.85[AFR][1000 genomes];0.91[AMR][1000 genomes];0.99[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2393107	1.00[CEU][hapmap];0.81[EUR][1000 genomes]
rs2393108	0.89[JPT][hapmap]
rs4238048	0.81[EUR][1000 genomes]
rs4326894	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4480639	0.88[AFR][1000 genomes];0.96[AMR][1000 genomes];0.94[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4767454	0.81[EUR][1000 genomes]
rs4767457	1.00[CEU][hapmap];0.92[EUR][1000 genomes]
rs4767458	1.00[CEU][hapmap];0.81[EUR][1000 genomes]
rs4767460	0.88[CEU][hapmap]
rs6490093	0.89[CEU][hapmap];0.81[EUR][1000 genomes]
rs7304747	0.80[CEU][hapmap]
rs7313014	0.81[ASN][1000 genomes]
rs7315763	0.87[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs903772	0.89[JPT][hapmap]
rs903774	0.89[JPT][hapmap]
rs924072	1.00[CEU][hapmap];0.92[CHB][hapmap];1.00[JPT][hapmap];0.88[AFR][1000 genomes];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs924075	0.89[CEU][hapmap];1.00[CHB][hapmap];0.96[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.95[TSI][hapmap];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs924078	1.00[ASW][hapmap];0.89[CEU][hapmap];1.00[CHB][hapmap];0.96[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.97[LWK][hapmap];1.00[MEX][hapmap];0.98[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs987560	0.81[EUR][1000 genomes]

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

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv832523	chr12:117090343-117273810	Strong transcription Flanking Active TSS Weak transcription Enhancers Active TSS Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	19 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs10774890	MAPKAPK5	cis	parietal	SCAN
rs10774890	RNFT2	cis	parietal	SCAN
rs10774890	TBX5	cis	cerebellum	SCAN

Chromatin state (count:126 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:117255600-117256800	Flanking Active TSS	Thymus	Thymus
2	chr12:117255600-117257000	Flanking Active TSS	Fetal Thymus	thymus
3	chr12:117255800-117257200	Flanking Active TSS	Primary B cells from cord blood	blood
4	chr12:117255800-117257200	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
5	chr12:117256000-117256800	Flanking Active TSS	Primary T helper naive cells from peripheral blood	blood
6	chr12:117256000-117256800	Flanking Active TSS	Brain Cingulate Gyrus	brain
7	chr12:117256000-117256800	Flanking Active TSS	K562	blood
8	chr12:117256000-117257000	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Female	--
9	chr12:117256200-117256800	Flanking Active TSS	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
10	chr12:117256200-117256800	Flanking Active TSS	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
11	chr12:117256200-117256800	Flanking Active TSS	IMR90 fetal lung fibroblasts Cell Line	lung
12	chr12:117256200-117256800	Flanking Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
13	chr12:117256200-117256800	Flanking Active TSS	Primary T helper naive cells fromperipheralblood	blood
14	chr12:117256200-117256800	Flanking Active TSS	Primary T helper 17 cells PMA-I stimulated	--
15	chr12:117256200-117256800	Flanking Active TSS	Primary T regulatory cells fromperipheralblood	blood
16	chr12:117256200-117256800	Flanking Active TSS	Cortex derived primary cultured neurospheres	brain
17	chr12:117256200-117256800	Flanking Active TSS	Foreskin Fibroblast Primary Cells skin02	Skin
18	chr12:117256200-117256800	Flanking Active TSS	Foreskin Melanocyte Primary Cells skin01	Skin
19	chr12:117256200-117256800	Flanking Active TSS	Brain Anterior Caudate	brain
20	chr12:117256200-117256800	Flanking Active TSS	Brain Hippocampus Middle	brain
21	chr12:117256200-117256800	Flanking Active TSS	Brain Dorsolateral Prefrontal Cortex	brain
22	chr12:117256200-117256800	Flanking Active TSS	Colon Smooth Muscle	Colon
23	chr12:117256200-117256800	Flanking Active TSS	Fetal Brain Male	brain
24	chr12:117256200-117256800	Flanking Active TSS	Fetal Brain Female	brain
25	chr12:117256200-117256800	Flanking Active TSS	Left Ventricle	heart
26	chr12:117256200-117256800	Flanking Active TSS	Psoas Muscle	Psoas
27	chr12:117256200-117256800	Flanking Active TSS	Rectal Smooth Muscle	rectum
28	chr12:117256200-117256800	Flanking Active TSS	Right Ventricle	heart
29	chr12:117256200-117256800	Flanking Active TSS	A549	lung
30	chr12:117256200-117256800	Flanking Active TSS	Hela-S3	cervix
31	chr12:117256200-117256800	Flanking Active TSS	HepG2	liver
32	chr12:117256200-117256800	Flanking Active TSS	NHDF-Ad	bronchial
33	chr12:117256200-117256800	Flanking Active TSS	NHLF	lung
34	chr12:117256200-117257000	Flanking Active TSS	H9 Derived Neuron Cultured Cells	ES cell derived
35	chr12:117256200-117257000	Transcr. at gene 5' and 3'	iPS DF 19.11 Cell Line	embryonic stem cell
36	chr12:117256200-117257000	Flanking Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
37	chr12:117256200-117257000	Flanking Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
38	chr12:117256200-117257000	Flanking Active TSS	Primary monocytes fromperipheralblood	blood
39	chr12:117256200-117257000	Flanking Active TSS	Primary B cells from peripheral blood	blood
40	chr12:117256200-117257000	Flanking Active TSS	Primary T cells from cord blood	blood
41	chr12:117256200-117257000	Flanking Active TSS	Primary hematopoietic stem cells short term culture	blood
42	chr12:117256200-117257000	Flanking Active TSS	Primary T helper cells PMA-I stimulated	--
43	chr12:117256200-117257000	Flanking Active TSS	Primary T helper cells fromperipheralblood	blood
44	chr12:117256200-117257000	Flanking Active TSS	Primary Natural Killer cells fromperipheralblood	blood
45	chr12:117256200-117257000	Flanking Active TSS	Primary T killer naive cells fromperipheralblood	blood
46	chr12:117256200-117257000	Flanking Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
47	chr12:117256200-117257000	Flanking Active TSS	Muscle Satellite Cultured Cells	--
48	chr12:117256200-117257000	Flanking Active TSS	Foreskin Melanocyte Primary Cells skin03	Skin
49	chr12:117256200-117257000	Flanking Active TSS	Adipose Nuclei	Adipose
50	chr12:117256200-117257000	Flanking Active TSS	Liver	Liver

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