Variant report

Variant	rs1144397
Chromosome Location	chr11:102682285-102682286
allele	G/T
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	CTCF	chr11:102682280-102682430	HCPEpiC	choroid plexus:	n/a	n/a
2	GATA3	chr11:102681669-102682334	SK-N-SH	brain:	n/a	chr11:102682160-102682172 chr11:102682116-102682126 chr11:102682104-102682113 chr11:102682158-102682174 chr11:102682163-102682173
3	GATA2	chr11:102681754-102682348	HUVEC	blood vessel:	n/a	chr11:102682160-102682172 chr11:102682116-102682126 chr11:102682104-102682113 chr11:102682158-102682174 chr11:102682163-102682173
4	SMC3	chr11:102681606-102682328	SK-N-SH	brain:	n/a	n/a

Variant related genes	Relation type
ENSG00000256035	TF binding region

Extended variants
information (count: 41 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:40)

rs_ID	r²[population]
rs1010698	0.90[CHB][hapmap];0.97[CHD][hapmap];0.94[JPT][hapmap];0.91[MEX][hapmap];0.86[ASN][1000 genomes]
rs10791596	0.83[AMR][1000 genomes];0.95[ASN][1000 genomes]
rs10895364	0.92[ASN][1000 genomes]
rs10895365	0.93[ASN][1000 genomes]
rs11225434	0.94[ASN][1000 genomes]
rs1144396	0.95[CHB][hapmap];0.97[CHD][hapmap];0.94[JPT][hapmap];0.90[MEX][hapmap];0.97[ASN][1000 genomes]
rs12801529	0.93[ASN][1000 genomes]
rs12804136	0.94[ASN][1000 genomes]
rs2097248	0.95[ASN][1000 genomes]
rs2155013	0.90[CHB][hapmap];0.97[CHD][hapmap];0.94[JPT][hapmap];0.91[MEX][hapmap];0.86[ASN][1000 genomes]
rs2212637	0.92[ASN][1000 genomes]
rs4754884	0.90[CHB][hapmap];0.94[JPT][hapmap];0.86[ASN][1000 genomes]
rs484915	0.81[MEX][hapmap]
rs485200	0.81[AFR][1000 genomes]
rs502174	0.84[CHB][hapmap];1.00[JPT][hapmap]
rs519166	0.81[AFR][1000 genomes]
rs520540	0.90[CHB][hapmap];0.94[JPT][hapmap];0.86[ASN][1000 genomes]
rs565082	0.86[AMR][1000 genomes];0.98[ASN][1000 genomes]
rs575027	0.86[ASN][1000 genomes]
rs591058	0.90[CHB][hapmap];0.97[CHD][hapmap];0.88[JPT][hapmap];0.91[MEX][hapmap];0.86[ASN][1000 genomes]
rs595840	0.86[ASN][1000 genomes]
rs602128	0.90[CHB][hapmap];0.88[JPT][hapmap];0.85[ASN][1000 genomes]
rs617819	0.85[ASN][1000 genomes]
rs632478	0.85[ASN][1000 genomes]
rs632581	0.81[AFR][1000 genomes]
rs633962	0.86[ASN][1000 genomes]
rs635746	0.86[ASN][1000 genomes]
rs639752	0.90[CHB][hapmap];0.97[CHD][hapmap];0.94[JPT][hapmap];0.91[MEX][hapmap];0.86[ASN][1000 genomes]
rs645419	0.90[CHB][hapmap];0.97[CHD][hapmap];0.88[JPT][hapmap];0.86[MEX][hapmap];0.85[ASN][1000 genomes]
rs6590993	0.93[ASN][1000 genomes]
rs6590994	0.93[ASN][1000 genomes]
rs666734	0.86[ASN][1000 genomes]
rs678815	0.90[CHB][hapmap];0.88[JPT][hapmap];0.85[ASN][1000 genomes]
rs679620	0.90[CHB][hapmap];0.90[CHD][hapmap];0.88[JPT][hapmap];0.85[ASN][1000 genomes]
rs7117013	0.93[ASN][1000 genomes]
rs7118731	0.90[AMR][1000 genomes];0.92[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7126392	0.91[ASN][1000 genomes]
rs756544	0.94[ASN][1000 genomes]
rs7926920	0.90[CHB][hapmap];0.97[CHD][hapmap];0.94[JPT][hapmap];1.00[MEX][hapmap];0.93[ASN][1000 genomes]
rs7946057	0.93[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	nsv898335	chr11:102682285-102866158	Enhancers Flanking Active TSS Active TSS Weak transcription Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	9 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs1144397	TMEM123	cis	lymphoblastoid	seeQTL
rs1144397	GRIA4	cis	cerebellum	SCAN

Chromatin state (count:9 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr11:102678800-102690000	Weak transcription	Gastric	stomach
2	chr11:102679000-102690400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
3	chr11:102681000-102682600	Enhancers	Stomach Mucosa	stomach
4	chr11:102681600-102682600	Enhancers	Duodenum Mucosa	Duodenum
5	chr11:102681600-102682600	Enhancers	Fetal Intestine Small	intestine
6	chr11:102681600-102682600	Enhancers	NHEK	skin
7	chr11:102681600-102682800	Enhancers	Fetal Intestine Large	intestine
8	chr11:102681800-102683800	Weak transcription	HMEC	breast
9	chr11:102682200-102685000	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin

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