Variant report

Variant	rs1057908
Chromosome Location	chr12:49230035-49230036
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	POLR2A	chr12:49229786-49230235	SK-N-MC	brain:	n/a	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr12:49228181..49230534-chr12:49244450..49246157,2	MCF-7	breast:

Variant related genes	Relation type
DDX23	TF binding region
ENSG00000174243	Chromatin interaction

Extended variants
information (count: 14 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:13)

rs_ID	r²[population]
rs1045340	0.84[CEU][hapmap];1.00[CHB][hapmap];0.98[CHD][hapmap];0.93[GIH][hapmap];0.94[JPT][hapmap];0.86[MEX][hapmap];0.95[TSI][hapmap];0.91[AMR][1000 genomes];0.92[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs10875879	0.81[AFR][1000 genomes];0.94[AMR][1000 genomes];0.90[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs10875880	0.96[ASN][1000 genomes]
rs11168753	0.83[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs2446972	0.83[JPT][hapmap]
rs2453469	0.83[LWK][hapmap]
rs2453471	0.89[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];0.90[LWK][hapmap];0.95[MEX][hapmap];1.00[MKK][hapmap];0.91[TSI][hapmap];0.88[AFR][1000 genomes];0.94[AMR][1000 genomes];0.92[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2453472	0.89[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];0.89[LWK][hapmap];0.95[MEX][hapmap];1.00[MKK][hapmap];0.93[TSI][hapmap];0.88[AFR][1000 genomes];0.94[AMR][1000 genomes];0.92[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2453482	0.90[AFR][1000 genomes];0.90[AMR][1000 genomes];0.90[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs59128273	0.93[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs61941108	0.97[ASN][1000 genomes]
rs7164	0.89[CEU][hapmap];0.95[CHB][hapmap];0.95[CHD][hapmap];0.95[GIH][hapmap];0.86[JPT][hapmap];0.91[MEX][hapmap];0.93[TSI][hapmap];0.88[AMR][1000 genomes];0.91[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs954	0.92[ASN][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	nsv826363	chr12:49177227-49250989	Flanking Active TSS Flanking Bivalent TSS/Enh Weak transcription Enhancers Active TSS Strong transcription Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	43 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs1057908	PLEKHA9	cis	parietal	SCAN

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:49213000-49231200	Weak transcription	Right Atrium	heart
2	chr12:49214600-49234800	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
3	chr12:49215200-49243800	Strong transcription	Fetal Stomach	stomach
4	chr12:49215400-49235400	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
5	chr12:49215600-49240000	Strong transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
6	chr12:49215800-49235000	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
7	chr12:49216200-49235400	Strong transcription	Fetal Muscle Leg	muscle
8	chr12:49216200-49240200	Strong transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
9	chr12:49216800-49234200	Strong transcription	Ganglion Eminence derived primary cultured neurospheres	brain
10	chr12:49216800-49235400	Strong transcription	Fetal Intestine Large	intestine
11	chr12:49216800-49238600	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
12	chr12:49216800-49240000	Strong transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
13	chr12:49216800-49240000	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
14	chr12:49216800-49244600	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
15	chr12:49217000-49234200	Strong transcription	Ovary	ovary
16	chr12:49217000-49234400	Strong transcription	Sigmoid Colon	Sigmoid Colon
17	chr12:49217000-49234400	Strong transcription	Stomach Smooth Muscle	stomach
18	chr12:49217000-49234800	Strong transcription	Placenta Amnion	Placenta Amnion
19	chr12:49217000-49235200	Strong transcription	Fetal Muscle Trunk	muscle
20	chr12:49217000-49243800	Strong transcription	Fetal Intestine Small	intestine
21	chr12:49217200-49234400	Strong transcription	Rectal Mucosa Donor 29	rectum
22	chr12:49217200-49235000	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
23	chr12:49217200-49235400	Strong transcription	Adipose Nuclei	Adipose
24	chr12:49217200-49235600	Strong transcription	Placenta	Placenta
25	chr12:49217400-49235000	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
26	chr12:49217400-49235200	Strong transcription	Brain Germinal Matrix	brain
27	chr12:49217400-49235200	Strong transcription	Thymus	Thymus
28	chr12:49217400-49235400	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
29	chr12:49217400-49241000	Strong transcription	Duodenum Smooth Muscle	Duodenum
30	chr12:49217600-49234800	Strong transcription	Brain Dorsolateral Prefrontal Cortex	brain
31	chr12:49217800-49235000	Strong transcription	Brain Inferior Temporal Lobe	brain
32	chr12:49218000-49234400	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
33	chr12:49218000-49235000	Strong transcription	Dnd41	blood
34	chr12:49218200-49241200	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
35	chr12:49218400-49235400	Strong transcription	HUES6 Cell Line	embryonic stem cell
36	chr12:49219000-49234200	Strong transcription	Primary T cells from cord blood	blood
37	chr12:49219000-49234800	Strong transcription	HUES48 Cell Line	embryonic stem cell
38	chr12:49219800-49234200	Strong transcription	Gastric	stomach
39	chr12:49220000-49234600	Strong transcription	HUVEC	blood vessel
40	chr12:49220000-49235000	Strong transcription	Duodenum Mucosa	Duodenum
41	chr12:49220000-49235400	Strong transcription	Fetal Thymus	thymus
42	chr12:49220000-49239800	Strong transcription	Spleen	Spleen
43	chr12:49220000-49240000	Strong transcription	H1 Cell Line	embryonic stem cell
44	chr12:49220000-49241200	Strong transcription	Lung	lung
45	chr12:49220200-49232400	Strong transcription	Right Ventricle	heart
46	chr12:49220200-49235000	Strong transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
47	chr12:49220200-49235600	Strong transcription	Primary hematopoietic stem cells short term culture	blood
48	chr12:49220400-49234000	Strong transcription	iPS DF 6.9 Cell Line	embryonic stem cell
49	chr12:49220400-49235400	Strong transcription	Skeletal Muscle Male	skeletal muscle
50	chr12:49220400-49235600	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--

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