Variant report

Variant	rs12872114
Chromosome Location	chr13:80020616-80020617
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 10 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:8)

rs_ID	r²[population]
rs12585625	0.86[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs12877278	0.84[EUR][1000 genomes]
rs1408049	0.81[TSI][hapmap]
rs2760106	0.81[TSI][hapmap]
rs2783122	0.81[TSI][hapmap]
rs71445304	0.81[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs7334344	0.90[AFR][1000 genomes];0.84[AMR][1000 genomes]
rs987284	0.81[TSI][hapmap]

Variant overlapped rSNPs/rCNVs (count:2 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv832657	chr13:79904978-80099108	Active TSS Weak transcription Enhancers Strong transcription Flanking Active TSS Genic enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	34 gene(s)	inside rSNPs	diseases
2	nsv523979	chr13:79979679-80120263	Strong transcription Enhancers Active TSS Weak transcription Flanking Active TSS Bivalent/Poised TSS ZNF genes & repeats Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	29 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs12872114	MICAL1	trans	parietal	SCAN
rs12872114	RBM26	Cis_1M	lymphoblastoid	RTeQTL
rs12872114	SLAIN1	cis	cerebellum	SCAN

Chromatin state (count:21 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr13:80010200-80025600	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
2	chr13:80016200-80025800	Weak transcription	H1 Cell Line	embryonic stem cell
3	chr13:80019600-80021000	Enhancers	ES-I3 Cell Line	embryonic stem cell
4	chr13:80019800-80020800	Enhancers	Sigmoid Colon	Sigmoid Colon
5	chr13:80019800-80021000	Enhancers	Dnd41	blood
6	chr13:80019800-80021200	Enhancers	Primary T helper cells PMA-I stimulated	--
7	chr13:80020000-80020800	Enhancers	Fetal Thymus	thymus
8	chr13:80020200-80020800	Enhancers	Primary T cells fromperipheralblood	blood
9	chr13:80020200-80020800	Enhancers	Primary T helper naive cells fromperipheralblood	blood
10	chr13:80020200-80021600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
11	chr13:80020200-80021600	Enhancers	Primary T cells from cord blood	blood
12	chr13:80020200-80024200	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
13	chr13:80020600-80020800	Enhancers	iPS-18 Cell Line	embryonic stem cell
14	chr13:80020600-80020800	Enhancers	Primary T cells effector/memory enriched fromperipheralblood	blood
15	chr13:80020600-80020800	Enhancers	Primary T killer naive cells fromperipheralblood	blood
16	chr13:80020600-80021000	Enhancers	HUES64 Cell Line	embryonic stem cell
17	chr13:80020600-80021000	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
18	chr13:80020600-80021000	Enhancers	Primary T helper cells fromperipheralblood	blood
19	chr13:80020600-80021200	Enhancers	Primary T helper 17 cells PMA-I stimulated	--
20	chr13:80020600-80023200	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
21	chr13:80020600-80034000	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell

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