Variant report

Variant	rs12257233
Chromosome Location	chr10:20106794-20106795
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr10:20102006..20103854-chr10:20105528..20107867,2	K562	blood:

Extended variants
information (count: 37 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:29)

rs_ID	r²[population]
rs10764159	0.87[EUR][1000 genomes]
rs10764164	0.81[AMR][1000 genomes];0.88[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs10827885	0.91[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1590963	0.83[ASN][1000 genomes]
rs1977539	0.89[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2481936	0.89[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2481937	0.83[AFR][1000 genomes];0.89[AMR][1000 genomes];0.86[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2481938	0.83[AFR][1000 genomes];0.86[AMR][1000 genomes];0.86[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2481939	0.88[AFR][1000 genomes];0.89[AMR][1000 genomes];0.91[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2884470	0.82[AFR][1000 genomes];0.88[AMR][1000 genomes];0.89[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs333687	0.87[AFR][1000 genomes];0.89[AMR][1000 genomes];0.91[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs333689	0.88[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs333691	0.83[AFR][1000 genomes];0.89[AMR][1000 genomes];0.91[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs333692	0.84[AMR][1000 genomes];0.89[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs420898	0.84[AMR][1000 genomes];0.88[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs442830	0.90[EUR][1000 genomes]
rs447706	0.88[AMR][1000 genomes];0.89[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4748612	0.89[ASN][1000 genomes]
rs6482065	0.93[AFR][1000 genomes];0.93[AMR][1000 genomes];0.93[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7086438	0.81[AFR][1000 genomes];0.81[AMR][1000 genomes];0.91[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs7094033	0.84[AFR][1000 genomes];0.86[AMR][1000 genomes];0.89[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs7906452	0.87[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs7908480	0.91[CHD][hapmap];0.81[JPT][hapmap];0.96[LWK][hapmap];0.88[YRI][hapmap];0.86[ASN][1000 genomes]
rs7911243	0.85[CHB][hapmap];0.84[JPT][hapmap];0.88[ASN][1000 genomes]
rs7912855	0.89[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7914865	0.87[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs7914996	0.88[AFR][1000 genomes];0.86[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs7922577	0.91[MEX][hapmap]
rs989767	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.87[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.94[TSI][hapmap];0.91[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:8 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1049295	chr10:19740296-20509036	Weak transcription Enhancers Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS Strong transcription Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	11 gene(s)	inside rSNPs	diseases
2	esv34306	chr10:19777069-20117944	Enhancers Flanking Active TSS Weak transcription Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Strong transcription ZNF genes & repeats Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases
3	nsv1044794	chr10:20010269-20391329	Enhancers Weak transcription Bivalent/Poised TSS Active TSS Flanking Active TSS Bivalent Enhancer Strong transcription ZNF genes & repeats Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
4	nsv540510	chr10:20010269-20391329	Weak transcription Enhancers Genic enhancers Bivalent/Poised TSS Active TSS Bivalent Enhancer Strong transcription Flanking Bivalent TSS/Enh ZNF genes & repeats Flanking Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
5	nsv1038966	chr10:20010469-20391190	Enhancers Active TSS Flanking Active TSS Weak transcription Strong transcription Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
6	nsv540511	chr10:20010469-20391190	Enhancers Flanking Active TSS Weak transcription Strong transcription Active TSS ZNF genes & repeats Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
7	nsv1037055	chr10:20010469-20651965	Enhancers Bivalent/Poised TSS Weak transcription Genic enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Active TSS Strong transcription Flanking Active TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	8 gene(s)	inside rSNPs	diseases
8	nsv540512	chr10:20010469-20651965	Weak transcription Flanking Active TSS Enhancers Active TSS ZNF genes & repeats Strong transcription Bivalent/Poised TSS Flanking Bivalent TSS/Enh Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	8 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs12257233	PLXDC2	cis	cerebellum	SCAN

Chromatin state (count:106 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr10:20103400-20109000	Active TSS	Brain Anterior Caudate	brain
2	chr10:20103400-20110200	Active TSS	Brain Hippocampus Middle	brain
3	chr10:20103600-20107600	Active TSS	iPS-15b Cell Line	embryonic stem cell
4	chr10:20103800-20107200	Active TSS	Rectal Mucosa Donor 31	rectum
5	chr10:20103800-20107400	Active TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
6	chr10:20103800-20107800	Active TSS	Colon Smooth Muscle	Colon
7	chr10:20103800-20108000	Active TSS	Fetal Adrenal Gland	Adrenal Gland
8	chr10:20103800-20108000	Active TSS	Rectal Smooth Muscle	rectum
9	chr10:20103800-20108600	Active TSS	H9 Cell Line	embryonic stem cell
10	chr10:20103800-20108600	Active TSS	Brain Inferior Temporal Lobe	brain
11	chr10:20103800-20108600	Active TSS	Brain Dorsolateral Prefrontal Cortex	brain
12	chr10:20103800-20108800	Active TSS	Brain Angular Gyrus	brain
13	chr10:20103800-20108800	Active TSS	Duodenum Smooth Muscle	Duodenum
14	chr10:20103800-20109000	Active TSS	Brain Cingulate Gyrus	brain
15	chr10:20103800-20109000	Active TSS	HSMMtube	muscle
16	chr10:20104000-20107400	Active TSS	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
17	chr10:20104000-20107400	Active TSS	HUES48 Cell Line	embryonic stem cell
18	chr10:20104000-20107400	Active TSS	HUES6 Cell Line	embryonic stem cell
19	chr10:20104000-20107400	Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
20	chr10:20104000-20107600	Active TSS	iPS-20b Cell Line	embryonic stem cell
21	chr10:20104000-20107600	Active TSS	iPS DF 6.9 Cell Line	embryonic stem cell
22	chr10:20104000-20107600	Active TSS	Right Ventricle	heart
23	chr10:20104000-20107600	Bivalent/Poised TSS	Skeletal Muscle Male	skeletal muscle
24	chr10:20104000-20107800	Active TSS	ES-WA7 Cell Line	embryonic stem cell
25	chr10:20104000-20107800	Active TSS	Pancreatic Islets	Pancreatic Islet
26	chr10:20104000-20107800	Bivalent/Poised TSS	Osteobl	bone
27	chr10:20104000-20108000	Active TSS	HUES64 Cell Line	embryonic stem cell
28	chr10:20104000-20108000	Active TSS	IMR90 fetal lung fibroblasts Cell Line	lung
29	chr10:20104000-20108000	Flanking Active TSS	Adipose Nuclei	Adipose
30	chr10:20104000-20108000	Active TSS	Aorta	Aorta
31	chr10:20104000-20108000	Active TSS	Psoas Muscle	Psoas
32	chr10:20104000-20108200	Active TSS	H1 Cell Line	embryonic stem cell
33	chr10:20104000-20108200	Active TSS	ES-UCSF4 Cell Line	embryonic stem cell
34	chr10:20104000-20108200	Active TSS	Right Atrium	heart
35	chr10:20104000-20108600	Active TSS	H9 Derived Neuron Cultured Cells	ES cell derived
36	chr10:20104000-20108600	Active TSS	Ovary	ovary
37	chr10:20104200-20106800	Active TSS	Fetal Lung	lung
38	chr10:20104200-20106800	Active TSS	Placenta Amnion	Placenta Amnion
39	chr10:20104200-20107000	Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
40	chr10:20104200-20107000	Flanking Active TSS	Liver	Liver
41	chr10:20104200-20107000	Bivalent/Poised TSS	Thymus	Thymus
42	chr10:20104200-20107200	Active TSS	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
43	chr10:20104200-20107400	Active TSS	iPS-18 Cell Line	embryonic stem cell
44	chr10:20104200-20107400	Active TSS	Small Intestine	intestine
45	chr10:20104200-20107600	Active TSS	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
46	chr10:20104200-20107600	Active TSS	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
47	chr10:20104200-20107600	Active TSS	Esophagus	oesophagus
48	chr10:20104200-20107600	Active TSS	Lung	lung
49	chr10:20104200-20107600	Active TSS	HSMM	muscle
50	chr10:20104200-20108400	Active TSS	Fetal Kidney	kidney

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