Variant report

Variant	rs2393084
Chromosome Location	chr12:117229598-117229599
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 27 )
Associated
traits (count: 1 )

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

rs_ID	r²[population]
rs10047539	0.81[CHD][hapmap]
rs10735096	1.00[CHB][hapmap];0.89[CHD][hapmap]
rs10774887	1.00[CHB][hapmap];0.89[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs10850715	1.00[CHB][hapmap];0.89[CHD][hapmap];0.88[ASN][1000 genomes]
rs11068175	1.00[CHB][hapmap];0.88[ASN][1000 genomes]
rs1565988	0.88[ASN][1000 genomes]
rs2101868	0.91[ASN][1000 genomes]
rs2393085	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3926590	1.00[CHB][hapmap]
rs4301877	1.00[CHB][hapmap]
rs4612912	1.00[CHB][hapmap]
rs4767445	1.00[CHB][hapmap]
rs4767448	1.00[CHB][hapmap]
rs4767449	1.00[CHB][hapmap];0.89[CHD][hapmap];0.88[ASN][1000 genomes]
rs4767450	1.00[CHB][hapmap];0.88[ASN][1000 genomes]
rs4767452	0.88[ASN][1000 genomes]
rs4767460	0.81[CHD][hapmap]
rs6490086	1.00[CHB][hapmap]
rs6490093	0.81[CHD][hapmap]
rs7135526	0.88[ASN][1000 genomes]
rs7304747	0.81[CHD][hapmap]
rs7306658	0.88[ASN][1000 genomes]
rs7313399	1.00[CHB][hapmap];0.88[ASN][1000 genomes]
rs7314309	1.00[CHB][hapmap];0.89[CHD][hapmap];0.88[ASN][1000 genomes]
rs7980144	1.00[CHB][hapmap]
rs9300333	0.88[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	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:1)

SNP	Gene	Cis/trans	Tissue	Source
rs2393084	MED13L	cis	parietal	SCAN

Chromatin state (count:40 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:117198000-117256200	Weak transcription	Hela-S3	cervix
2	chr12:117198200-117233600	Weak transcription	Fetal Stomach	stomach
3	chr12:117198200-117236600	Weak transcription	A549	lung
4	chr12:117198600-117233600	Weak transcription	Right Atrium	heart
5	chr12:117209800-117232600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
6	chr12:117216800-117229600	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
7	chr12:117221200-117236800	Weak transcription	Brain Hippocampus Middle	brain
8	chr12:117222000-117230200	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
9	chr12:117222000-117248000	Weak transcription	iPS-15b Cell Line	embryonic stem cell
10	chr12:117222200-117231000	Weak transcription	Fetal Brain Male	brain
11	chr12:117222200-117235400	Weak transcription	Thymus	Thymus
12	chr12:117222400-117236600	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
13	chr12:117222400-117236800	Weak transcription	iPS-20b Cell Line	embryonic stem cell
14	chr12:117222600-117236600	Weak transcription	Brain Angular Gyrus	brain
15	chr12:117222600-117236600	Weak transcription	Brain Anterior Caudate	brain
16	chr12:117222800-117236600	Weak transcription	Brain Inferior Temporal Lobe	brain
17	chr12:117222800-117236600	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
18	chr12:117223400-117234400	Weak transcription	H9 Cell Line	embryonic stem cell
19	chr12:117223600-117231800	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
20	chr12:117223600-117246200	Weak transcription	H1 Cell Line	embryonic stem cell
21	chr12:117223800-117230000	Weak transcription	GM12878-XiMat	blood
22	chr12:117225000-117236600	Weak transcription	Primary B cells from cord blood	blood
23	chr12:117225000-117237600	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
24	chr12:117225200-117236600	Weak transcription	HUES64 Cell Line	embryonic stem cell
25	chr12:117225200-117236800	Weak transcription	Brain Cingulate Gyrus	brain
26	chr12:117225200-117256200	Weak transcription	ES-I3 Cell Line	embryonic stem cell
27	chr12:117225400-117234000	Weak transcription	Brain Germinal Matrix	brain
28	chr12:117225600-117233000	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
29	chr12:117225600-117235400	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
30	chr12:117227000-117249200	Weak transcription	Primary T cells from cord blood	blood
31	chr12:117227400-117235400	Weak transcription	Dnd41	blood
32	chr12:117227600-117234800	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
33	chr12:117228000-117235600	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
34	chr12:117228400-117256400	Weak transcription	HUES48 Cell Line	embryonic stem cell
35	chr12:117229000-117234000	Weak transcription	Fetal Brain Female	brain
36	chr12:117229000-117235600	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
37	chr12:117229200-117231200	Weak transcription	HUES6 Cell Line	embryonic stem cell
38	chr12:117229200-117256200	Weak transcription	iPS-18 Cell Line	embryonic stem cell
39	chr12:117229400-117229800	Strong transcription	Fetal Thymus	thymus
40	chr12:117229400-117230800	Weak transcription	Cortex derived primary cultured neurospheres	brain

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