Variant report

Variant	rs12739186
Chromosome Location	chr1:94315669-94315670
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr1:94311804..94314669-chr1:94314970..94317163,2	MCF-7	breast:
2	chr1:94315633..94319063-chr1:94342848..94345734,4	K562	blood:
3	chr1:94313358..94316025-chr1:94316812..94319394,2	MCF-7	breast:
4	chr1:94309833..94313487-chr1:94314841..94317688,5	K562	blood:
5	chr1:94307315..94310834-chr1:94315340..94316960,3	MCF-7	breast:

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-FNBP1L-2	chr1:94312708-94317158	NONHSAT004550

Variant related genes	Relation type
ENSG00000211575	Chromatin interaction
ENSG00000067334	Chromatin interaction
ENSG00000137936	Chromatin interaction
ENSG00000260464	Chromatin interaction

Extended variants
information (count: 51 )
Associated
traits (count: 10 )

rSNPs within LD-proxies of this variant (count:49)

rs_ID	r²[population]
rs10489602	0.98[AFR][1000 genomes];0.90[AMR][1000 genomes];0.91[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs10489604	0.86[AFR][1000 genomes];0.90[AMR][1000 genomes];0.94[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs10782966	0.89[EUR][1000 genomes]
rs10782967	0.89[EUR][1000 genomes]
rs11165020	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs11165024	0.86[AFR][1000 genomes];0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12027630	0.86[AFR][1000 genomes];0.92[AMR][1000 genomes];0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12122113	0.89[AMR][1000 genomes];0.91[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs12134359	0.87[EUR][1000 genomes]
rs12137687	0.98[AFR][1000 genomes];0.90[AMR][1000 genomes];0.91[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs12140446	0.84[EUR][1000 genomes]
rs12143274	0.90[AMR][1000 genomes];0.91[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs12143279	0.98[AFR][1000 genomes];0.90[AMR][1000 genomes];0.91[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs12563731	0.86[AFR][1000 genomes];0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12565614	0.82[AFR][1000 genomes];0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12566531	0.86[AFR][1000 genomes];0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12734571	0.86[AFR][1000 genomes];0.92[AMR][1000 genomes];0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12745990	0.98[AFR][1000 genomes];0.90[AMR][1000 genomes];0.91[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs12752298	0.83[EUR][1000 genomes]
rs1398798	0.81[EUR][1000 genomes]
rs1884018	0.86[AFR][1000 genomes];0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2143990	0.82[AFR][1000 genomes];0.90[EUR][1000 genomes]
rs2235971	0.82[AFR][1000 genomes];0.89[AMR][1000 genomes];0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2391322	0.86[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2747039	0.83[AFR][1000 genomes];0.89[EUR][1000 genomes]
rs2747041	0.83[AFR][1000 genomes];0.89[EUR][1000 genomes]
rs2747043	0.86[AFR][1000 genomes];0.90[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs2747045	0.86[AFR][1000 genomes];0.90[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs2747050	0.83[AFR][1000 genomes];0.83[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs2818160	0.83[AFR][1000 genomes];0.89[EUR][1000 genomes]
rs2818162	0.83[AFR][1000 genomes];0.89[EUR][1000 genomes]
rs2818164	0.81[AFR][1000 genomes];0.90[EUR][1000 genomes]
rs2818169	0.86[AFR][1000 genomes];0.90[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs3000471	0.86[AFR][1000 genomes];0.83[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs3747965	0.83[AFR][1000 genomes];0.89[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4075523	0.89[EUR][1000 genomes]
rs4141736	0.89[AMR][1000 genomes];0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs4141737	0.84[AFR][1000 genomes];0.89[AMR][1000 genomes];0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs4240955	0.89[EUR][1000 genomes]
rs4240956	0.89[EUR][1000 genomes]
rs4314890	0.89[EUR][1000 genomes]
rs4350209	0.80[EUR][1000 genomes]
rs4847253	0.84[EUR][1000 genomes]
rs4847265	0.85[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs6664719	0.86[AFR][1000 genomes];0.92[AMR][1000 genomes];0.94[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6685747	0.98[AFR][1000 genomes];0.90[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs7364910	0.83[AFR][1000 genomes];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs8179391	0.89[EUR][1000 genomes]
rs871854	0.84[EUR][1000 genomes]

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	esv1822452	chr1:94278128-94320233	Enhancers Weak transcription Flanking Active TSS Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Strong transcription Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA	121 gene(s)	inside rSNPs	diseases
2	nsv998755	chr1:94294015-94341712	Flanking Active TSS Active TSS Genic enhancers Enhancers Weak transcription Strong transcription Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA	121 gene(s)	inside rSNPs	diseases

mRNA abundance (count:10)

SNP	Gene	Cis/trans	Tissue	Source
rs12739186	RP11-488P3.1	cis	Heart Left Ventricle	GTEx
rs12739186	RP11-488P3.1	cis	Esophagus Muscularis	GTEx
rs12739186	RP11-488P3.1	cis	Thyroid	GTEx
rs12739186	RP11-488P3.1	cis	Adipose Subcutaneous	GTEx
rs12739186	RP11-488P3.1	cis	Muscle Skeletal	GTEx
rs12739186	RP11-488P3.1	cis	Artery Tibial	GTEx
rs12739186	RP11-488P3.1	cis	Stomach	GTEx
rs12739186	RP11-488P3.1	cis	Nerve Tibial	GTEx
rs12739186	RP11-488P3.1	cis	lung	GTEx
rs12739186	RP11-488P3.1	cis	Skin Sun Exposed Lower leg	GTEx

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:94314000-94316000	Weak transcription	Primary B cells from peripheral blood	blood
2	chr1:94314000-94316000	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
3	chr1:94314000-94316000	Weak transcription	Rectal Mucosa Donor 31	rectum
4	chr1:94314000-94316000	Weak transcription	Skeletal Muscle Female	skeletal muscle
5	chr1:94314000-94316200	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
6	chr1:94314200-94316000	Weak transcription	Skeletal Muscle Male	skeletal muscle
7	chr1:94314200-94316200	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
8	chr1:94314200-94316200	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
9	chr1:94314200-94316200	Weak transcription	Adipose Nuclei	Adipose
10	chr1:94314200-94316200	Weak transcription	Brain Hippocampus Middle	brain
11	chr1:94314200-94316200	Weak transcription	Rectal Mucosa Donor 29	rectum
12	chr1:94314200-94316200	Weak transcription	K562	blood
13	chr1:94314200-94317000	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
14	chr1:94314200-94332800	Weak transcription	Brain Cingulate Gyrus	brain
15	chr1:94314200-94334200	Weak transcription	Primary T helper cells fromperipheralblood	blood
16	chr1:94314200-94334400	Weak transcription	Brain Substantia Nigra	brain
17	chr1:94314400-94316000	Weak transcription	Primary T helper cells PMA-I stimulated	--
18	chr1:94314400-94316000	Weak transcription	Brain Anterior Caudate	brain
19	chr1:94314400-94316000	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
20	chr1:94314400-94316200	Weak transcription	Brain Inferior Temporal Lobe	brain
21	chr1:94314400-94316200	Weak transcription	Hela-S3	cervix
22	chr1:94314600-94316200	Weak transcription	Rectal Smooth Muscle	rectum
23	chr1:94315600-94316800	Enhancers	Primary T cells fromperipheralblood	blood

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