Variant report

Variant	rs34448712
Chromosome Location	chr18:12439062-12439063
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:2)
CpG islands
(count:0)
Chromatin interactive
region (count:3)
LncRNA
region (count:4)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:2 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	RCOR1	chr18:12439049-12439095	K562	blood:	n/a	n/a
2	TAL1	chr18:12438927-12439148	K562	blood:	n/a	chr18:12439029-12439047

No data

(count:3 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr18:12436823..12439176-chr18:12440236..12443079,2	K562	blood:
2	chr18:12427958..12434396-chr18:12436312..12440619,6	K562	blood:
3	chr18:12436425..12438277-chr18:12439040..12441425,2	MCF-7	breast:

(count:4 , 50 per page) page: 1

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-SLMO1-1	chr18:12438889-12439075	XLOC_012632
2	lnc-SLMO1-1	chr18:12438889-12439122	NONHSAT058371
3	lnc-SLMO1-1	chr18:12438971-12439105	NONHSAT058374
4	lnc-SLMO1-1	chr18:12438889-12439105	ENSG00000267199.1

No data

Variant related genes	Relation type
ENSG00000267199	TF binding region
ENSG00000267199	Chromatin interaction
ENSG00000256786	Chromatin interaction
ENSG00000267108	Chromatin interaction

Extended variants
information (count: 30 )
Associated
traits (count: 15 )

rSNPs within LD-proxies of this variant (count:20)

rs_ID	r²[population]
rs12959459	0.91[AFR][1000 genomes];0.94[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs12959998	0.91[AFR][1000 genomes];0.94[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs12961307	0.83[AFR][1000 genomes]
rs12971000	0.91[AFR][1000 genomes];0.86[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs17524639	0.91[AFR][1000 genomes];0.89[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs17615525	0.91[AFR][1000 genomes]
rs1977937	0.84[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34054541	0.83[AFR][1000 genomes]
rs34088731	0.83[AFR][1000 genomes]
rs34215298	0.91[AFR][1000 genomes];0.86[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs34460164	0.83[AFR][1000 genomes]
rs34469203	0.91[AFR][1000 genomes];0.89[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs34512782	0.91[AFR][1000 genomes];0.89[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs34620743	0.90[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35532404	0.91[AFR][1000 genomes];0.94[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs35872229	0.86[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs71351482	0.84[AMR][1000 genomes]
rs71351484	0.91[AFR][1000 genomes];0.94[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs71351485	0.91[AFR][1000 genomes];0.94[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs919	0.91[AFR][1000 genomes];0.94[AMR][1000 genomes];0.90[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:10 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1063125	chr18:12046892-12918251	Weak transcription Strong transcription Flanking Bivalent TSS/Enh Active TSS Enhancers Flanking Active TSS Genic enhancers Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	130 gene(s)	inside rSNPs	diseases
2	nsv491873	chr18:12159445-12739784	Weak transcription Flanking Active TSS Strong transcription Enhancers Active TSS Genic enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	79 gene(s)	inside rSNPs	diseases
3	nsv909400	chr18:12201374-12585545	Weak transcription Enhancers Genic enhancers Active TSS Strong transcription Bivalent/Poised TSS ZNF genes & repeats Flanking Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	67 gene(s)	inside rSNPs	diseases
4	esv2758471	chr18:12240681-12499525	Flanking Active TSS Strong transcription ZNF genes & repeats Weak transcription Flanking Bivalent TSS/Enh Active TSS Enhancers Genic enhancers Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	64 gene(s)	inside rSNPs	diseases
5	esv2758714	chr18:12240681-12499525	Flanking Active TSS Weak transcription Strong transcription Active TSS Bivalent Enhancer Genic enhancers Enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	64 gene(s)	inside rSNPs	diseases
6	nsv576496	chr18:12247872-12490502	Weak transcription Flanking Active TSS Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Strong transcription Enhancers Genic enhancers Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	62 gene(s)	inside rSNPs	diseases
7	nsv1060808	chr18:12302792-12514417	Genic enhancers Weak transcription Enhancers Strong transcription Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Active TSS Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	53 gene(s)	inside rSNPs	diseases
8	esv3528039	chr18:12396582-12851293	Flanking Active TSS Weak transcription Enhancers Strong transcription Genic enhancers ZNF genes & repeats Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	36 gene(s)	inside rSNPs	diseases
9	esv3528041	chr18:12396641-12851245	Weak transcription Strong transcription Enhancers ZNF genes & repeats Active TSS Flanking Bivalent TSS/Enh Flanking Active TSS Bivalent Enhancer Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	36 gene(s)	inside rSNPs	diseases
10	esv3380733	chr18:12436852-12441150	Weak transcription Strong transcription Enhancers Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases

mRNA abundance (count:15)

SNP	Gene	Cis/trans	Tissue	Source
rs34448712	AP001029.1	cis	Thyroid	GTEx
rs34448712	SLMO1	cis	Esophagus Muscularis	GTEx
rs34448712	SLMO1	cis	Adipose Subcutaneous	GTEx
rs34448712	RP11-861E21.1	cis	Artery Tibial	GTEx
rs34448712	SLMO1	cis	Thyroid	GTEx
rs34448712	SLMO1	cis	Nerve Tibial	GTEx
rs34448712	AP001029.1	cis	Artery Tibial	GTEx
rs34448712	RP11-861E21.1	cis	Esophagus Muscularis	GTEx
rs34448712	SLMO1	cis	Artery Tibial	GTEx
rs34448712	SLMO1	cis	Esophagus Mucosa	GTEx
rs34448712	SLMO1	cis	lung	GTEx
rs34448712	AP001029.1	cis	Esophagus Muscularis	GTEx
rs34448712	SLMO1	cis	Stomach	GTEx
rs34448712	SLMO1	cis	Artery Aorta	GTEx
rs34448712	AP001029.1	cis	Artery Aorta	GTEx

Chromatin state (count:85 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr18:12420600-12443600	Weak transcription	Sigmoid Colon	Sigmoid Colon
2	chr18:12420600-12477600	Weak transcription	Rectal Mucosa Donor 29	rectum
3	chr18:12421200-12443400	Weak transcription	Skeletal Muscle Male	skeletal muscle
4	chr18:12421200-12447600	Weak transcription	Placenta Amnion	Placenta Amnion
5	chr18:12421200-12452800	Weak transcription	Colonic Mucosa	Colon
6	chr18:12421400-12444200	Weak transcription	Rectal Smooth Muscle	rectum
7	chr18:12421800-12442400	Weak transcription	GM12878-XiMat	blood
8	chr18:12428200-12440200	Strong transcription	Primary hematopoietic stem cells short term culture	blood
9	chr18:12428200-12440600	Strong transcription	Breast Myoepithelial Primary Cells	Breast
10	chr18:12428400-12439600	Weak transcription	Primary B cells from cord blood	blood
11	chr18:12428400-12443400	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
12	chr18:12428600-12443800	Weak transcription	HSMMtube	muscle
13	chr18:12430800-12443400	Weak transcription	A549	lung
14	chr18:12431000-12443400	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
15	chr18:12431000-12443600	Weak transcription	Fetal Heart	heart
16	chr18:12431000-12447600	Weak transcription	NH-A	brain
17	chr18:12431000-12449200	Weak transcription	Pancreas	Pancrea
18	chr18:12431200-12443400	Weak transcription	Fetal Kidney	kidney
19	chr18:12431200-12447800	Weak transcription	NHEK	skin
20	chr18:12431400-12443400	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
21	chr18:12432000-12443800	Weak transcription	Skeletal Muscle Female	skeletal muscle
22	chr18:12432600-12447000	Weak transcription	HMEC	breast
23	chr18:12433000-12441400	Weak transcription	Brain Substantia Nigra	brain
24	chr18:12433000-12441600	Weak transcription	NHDF-Ad	bronchial
25	chr18:12433000-12442800	Weak transcription	Muscle Satellite Cultured Cells	--
26	chr18:12433000-12443200	Weak transcription	Primary hematopoietic stem cells	blood
27	chr18:12433000-12443600	Weak transcription	Fetal Brain Male	brain
28	chr18:12433000-12448800	Weak transcription	HUVEC	blood vessel
29	chr18:12433200-12441400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
30	chr18:12433200-12443400	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
31	chr18:12433200-12443400	Weak transcription	Duodenum Smooth Muscle	Duodenum
32	chr18:12433200-12443600	Weak transcription	Brain Angular Gyrus	brain
33	chr18:12433200-12444000	Weak transcription	Left Ventricle	heart
34	chr18:12433200-12444000	Weak transcription	Right Ventricle	heart
35	chr18:12433200-12449200	Weak transcription	H9 Cell Line	embryonic stem cell
36	chr18:12433200-12449200	Weak transcription	Gastric	stomach
37	chr18:12433200-12449200	Weak transcription	Spleen	Spleen
38	chr18:12433200-12450200	Weak transcription	Thymus	Thymus
39	chr18:12433200-12464600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
40	chr18:12433400-12443600	Weak transcription	Brain Cingulate Gyrus	brain
41	chr18:12433400-12458600	Weak transcription	HepG2	liver
42	chr18:12434200-12443600	Weak transcription	Fetal Intestine Large	intestine
43	chr18:12434200-12477000	Weak transcription	Esophagus	oesophagus
44	chr18:12434400-12441400	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
45	chr18:12434600-12443400	Weak transcription	Ovary	ovary
46	chr18:12434800-12441400	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
47	chr18:12434800-12443000	Weak transcription	Fetal Lung	lung
48	chr18:12434800-12443400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
49	chr18:12435000-12441400	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
50	chr18:12435000-12441400	Weak transcription	Fetal Muscle Leg	muscle

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