Variant report

Variant	rs1468195
Chromosome Location	chr12:47808682-47808683
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-FAM113B-4	chr12:47808467-47809015	XLOC_009728

Extended variants
information (count: 7 )
Associated
traits (count: 5 )

rSNPs within LD-proxies of this variant (count:6)

rs_ID	r²[population]
rs10748471	0.92[CEU][hapmap];1.00[CHB][hapmap];0.94[JPT][hapmap];0.98[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10881106	0.81[CEU][hapmap];0.95[MEX][hapmap];0.89[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs1155457	0.83[AMR][1000 genomes]
rs12814601	0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1919725	0.97[AFR][1000 genomes];0.99[AMR][1000 genomes];0.95[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2005690	0.87[AMR][1000 genomes];0.88[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	nsv558785	chr12:47740440-48044011	Enhancers Weak transcription Flanking Active TSS Strong transcription ZNF genes & repeats Active TSS Genic enhancers Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA	17 gene(s)	inside rSNPs	diseases

mRNA abundance (count:5)

SNP	Gene	Cis/trans	Tissue	Source
rs1468195	HDAC7	cis	cerebellum	SCAN
rs1468195	RAPGEF3	cis	parietal	SCAN
rs1468195	TMEM117	cis	cerebellum	SCAN
rs1468195	SLC38A4	cis	cerebellum	SCAN
rs1468195	CCDC65	cis	parietal	SCAN

Chromatin state (count:23 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:47800000-47808800	Enhancers	Fetal Brain Male	brain
2	chr12:47802200-47809000	Enhancers	Primary T helper cells PMA-I stimulated	--
3	chr12:47802200-47820000	Weak transcription	Aorta	Aorta
4	chr12:47805200-47808800	Weak transcription	Brain Anterior Caudate	brain
5	chr12:47806200-47809200	Enhancers	Primary T helper 17 cells PMA-I stimulated	--
6	chr12:47806600-47809200	Weak transcription	A549	lung
7	chr12:47807600-47809000	Enhancers	Breast Myoepithelial Primary Cells	Breast
8	chr12:47807800-47809000	Weak transcription	Primary T helper naive cells from peripheral blood	blood
9	chr12:47808000-47818800	Weak transcription	Hela-S3	cervix
10	chr12:47808200-47809000	Enhancers	Cortex derived primary cultured neurospheres	brain
11	chr12:47808200-47809200	Enhancers	Fetal Brain Female	brain
12	chr12:47808200-47812800	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
13	chr12:47808200-47813000	Weak transcription	Osteobl	bone
14	chr12:47808400-47808800	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
15	chr12:47808400-47809000	Enhancers	H1 Cell Line	embryonic stem cell
16	chr12:47808400-47809000	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
17	chr12:47808400-47809000	Enhancers	iPS-18 Cell Line	embryonic stem cell
18	chr12:47808400-47809000	Enhancers	Primary T cells fromperipheralblood	blood
19	chr12:47808600-47809000	Enhancers	HUES48 Cell Line	embryonic stem cell
20	chr12:47808600-47809200	Enhancers	Primary T killer memory cells from peripheral blood	blood
21	chr12:47808600-47809400	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
22	chr12:47808600-47813000	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
23	chr12:47808600-47816000	Weak transcription	Colon Smooth Muscle	Colon

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