Variant report

Variant	rs4392258
Chromosome Location	chr2:86552577-86552578
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr2:86551461..86553165-chr2:86556623..86558513,2	MCF-7	breast:

Extended variants
information (count: 53 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:52)

rs_ID	r²[population]
rs10189492	0.85[ASN][1000 genomes]
rs10200186	0.87[AFR][1000 genomes];0.99[ASN][1000 genomes]
rs10200526	0.87[AFR][1000 genomes];0.99[ASN][1000 genomes]
rs10200619	1.00[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10520415	0.86[AFR][1000 genomes];0.96[ASN][1000 genomes]
rs11127026	0.87[AFR][1000 genomes];0.99[ASN][1000 genomes]
rs11127028	0.85[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs11127029	0.90[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs11674249	0.81[AMR][1000 genomes];0.81[ASN][1000 genomes]
rs11675942	0.81[AMR][1000 genomes]
rs11685863	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11691122	0.89[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs12052607	0.83[AMR][1000 genomes]
rs12472390	0.85[ASN][1000 genomes]
rs12472676	0.99[ASN][1000 genomes]
rs12478575	0.87[AFR][1000 genomes];0.99[ASN][1000 genomes]
rs12478653	0.87[AFR][1000 genomes];0.99[ASN][1000 genomes]
rs12620833	0.83[ASN][1000 genomes]
rs12622200	0.86[AFR][1000 genomes];0.96[ASN][1000 genomes]
rs12714179	0.83[AFR][1000 genomes];0.99[ASN][1000 genomes]
rs12714180	0.87[AFR][1000 genomes];0.99[ASN][1000 genomes]
rs12999029	0.96[ASN][1000 genomes]
rs13017338	0.86[AFR][1000 genomes];0.93[ASN][1000 genomes]
rs13020869	0.82[AFR][1000 genomes];0.99[ASN][1000 genomes]
rs13421310	0.83[AFR][1000 genomes];0.96[ASN][1000 genomes]
rs17738096	0.99[ASN][1000 genomes]
rs1863051	0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1863052	0.97[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1863059	0.84[AMR][1000 genomes]
rs2278105	0.81[ASN][1000 genomes]
rs2303359	0.81[AMR][1000 genomes]
rs2367233	0.89[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs34048420	0.87[AFR][1000 genomes];0.99[ASN][1000 genomes]
rs34069316	0.87[AFR][1000 genomes];0.99[ASN][1000 genomes]
rs35160687	0.81[ASN][1000 genomes]
rs35281683	0.87[AFR][1000 genomes];0.99[ASN][1000 genomes]
rs35370705	0.85[ASN][1000 genomes]
rs35494267	0.81[AMR][1000 genomes]
rs35762338	0.83[AFR][1000 genomes];0.99[ASN][1000 genomes]
rs4832033	0.82[AMR][1000 genomes]
rs6547674	0.92[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs6713456	0.97[ASN][1000 genomes]
rs6714362	0.85[ASN][1000 genomes]
rs6725234	0.82[AMR][1000 genomes]
rs6728029	0.85[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs6738585	0.82[AMR][1000 genomes]
rs67407963	0.86[AFR][1000 genomes];0.97[ASN][1000 genomes]
rs6746198	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs67903513	0.99[ASN][1000 genomes]
rs7560886	0.81[AMR][1000 genomes]
rs7571424	1.00[ASN][1000 genomes]
rs7593440	1.00[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[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	esv3412938	chr2:86370969-86867936	Strong transcription Enhancers Genic enhancers Weak transcription Flanking Bivalent TSS/Enh Active TSS Flanking Active TSS ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	77 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs4392258	IMMT	cis	Whole Blood	GTEx
rs4392258	IMMT	Cis_1M	lymphoblastoid	RTeQTL
rs4392258	MRPL35	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:13 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:86533200-86563000	Weak transcription	Brain Germinal Matrix	brain
2	chr2:86536200-86559800	Weak transcription	HSMMtube	muscle
3	chr2:86537600-86563000	Weak transcription	Brain Anterior Caudate	brain
4	chr2:86542200-86559400	Weak transcription	Stomach Smooth Muscle	stomach
5	chr2:86543000-86556800	Weak transcription	Skeletal Muscle Female	skeletal muscle
6	chr2:86546800-86555000	Weak transcription	Left Ventricle	heart
7	chr2:86547400-86553200	Weak transcription	Colon Smooth Muscle	Colon
8	chr2:86549200-86563000	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
9	chr2:86550200-86554000	Weak transcription	Right Atrium	heart
10	chr2:86551000-86555800	Weak transcription	Fetal Intestine Small	intestine
11	chr2:86551600-86559200	Weak transcription	Fetal Brain Male	brain
12	chr2:86552200-86563800	Weak transcription	Aorta	Aorta
13	chr2:86552400-86556800	Weak transcription	Fetal Brain Female	brain

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