Variant report

Variant	rs12608270
Chromosome Location	chr18:12462093-12462094
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr18:12455304..12456976-chr18:12462047..12463621,2	K562	blood:
2	chr18:12455476..12457390-chr18:12462003..12463621,2	K562	blood:
3	chr18:12461944..12463816-chr18:12474818..12476468,2	K562	blood:
4	chr18:12326777..12329132-chr18:12461073..12463843,2	K562	blood:

Extended variants
information (count: 23 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:14)

rs_ID	r²[population]
rs12455439	0.85[EUR][1000 genomes]
rs12455481	0.96[AFR][1000 genomes];0.99[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12457760	0.90[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12958049	0.89[AMR][1000 genomes];0.92[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12964631	0.85[EUR][1000 genomes]
rs17615158	0.89[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2016707	0.80[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2116004	0.90[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs36109961	0.90[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs58193967	0.91[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs59992891	0.85[EUR][1000 genomes]
rs7234589	0.85[AMR][1000 genomes];0.89[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs7234742	0.84[AMR][1000 genomes];0.91[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs8099288	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:9 , 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

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs12608270	RP11-861E21.2	cis	Thyroid	GTEx

Chromatin state (count:95 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr18:12420600-12477600	Weak transcription	Rectal Mucosa Donor 29	rectum
2	chr18:12433200-12464600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
3	chr18:12434200-12477000	Weak transcription	Esophagus	oesophagus
4	chr18:12439400-12468200	Weak transcription	K562	blood
5	chr18:12444000-12467400	Weak transcription	A549	lung
6	chr18:12444200-12463200	Weak transcription	ES-I3 Cell Line	embryonic stem cell
7	chr18:12444400-12465800	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
8	chr18:12444600-12477600	Weak transcription	Rectal Smooth Muscle	rectum
9	chr18:12446200-12479600	Weak transcription	iPS-15b Cell Line	embryonic stem cell
10	chr18:12448000-12463000	Weak transcription	Psoas Muscle	Psoas
11	chr18:12449600-12470600	Weak transcription	HUES64 Cell Line	embryonic stem cell
12	chr18:12449600-12477600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
13	chr18:12449800-12465400	Weak transcription	Monocytes-CD14+_RO01746	blood
14	chr18:12449800-12466800	Weak transcription	iPS-20b Cell Line	embryonic stem cell
15	chr18:12449800-12470600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
16	chr18:12449800-12477600	Weak transcription	H1 Cell Line	embryonic stem cell
17	chr18:12449800-12477600	Weak transcription	Spleen	Spleen
18	chr18:12449800-12477800	Weak transcription	H9 Cell Line	embryonic stem cell
19	chr18:12449800-12478000	Weak transcription	Gastric	stomach
20	chr18:12449800-12478000	Weak transcription	Sigmoid Colon	Sigmoid Colon
21	chr18:12449800-12479600	Weak transcription	iPS-18 Cell Line	embryonic stem cell
22	chr18:12450000-12478200	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
23	chr18:12452200-12464600	Weak transcription	Pancreas	Pancrea
24	chr18:12453400-12484400	Weak transcription	Hela-S3	cervix
25	chr18:12455800-12462400	Weak transcription	Ovary	ovary
26	chr18:12456200-12465000	Strong transcription	Osteobl	bone
27	chr18:12456800-12464600	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
28	chr18:12456800-12477400	Weak transcription	Fetal Kidney	kidney
29	chr18:12457800-12470400	Weak transcription	Fetal Brain Male	brain
30	chr18:12457800-12477600	Weak transcription	Brain Cingulate Gyrus	brain
31	chr18:12458000-12462400	Strong transcription	Cortex derived primary cultured neurospheres	brain
32	chr18:12458400-12465800	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
33	chr18:12458600-12463200	Strong transcription	Fetal Muscle Trunk	muscle
34	chr18:12458600-12465400	Strong transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
35	chr18:12458600-12465800	Strong transcription	Ganglion Eminence derived primary cultured neurospheres	brain
36	chr18:12458800-12465400	Strong transcription	Muscle Satellite Cultured Cells	--
37	chr18:12458800-12465600	Strong transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
38	chr18:12458800-12465600	Strong transcription	Adipose Nuclei	Adipose
39	chr18:12458800-12465800	Strong transcription	Stomach Smooth Muscle	stomach
40	chr18:12458800-12466400	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
41	chr18:12459200-12463400	Strong transcription	Fetal Lung	lung
42	chr18:12459200-12463600	Strong transcription	Fetal Brain Female	brain
43	chr18:12459200-12465400	Strong transcription	Fetal Stomach	stomach
44	chr18:12459200-12465400	Strong transcription	Skeletal Muscle Female	skeletal muscle
45	chr18:12459400-12465600	Strong transcription	Breast Myoepithelial Primary Cells	Breast
46	chr18:12459600-12477600	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
47	chr18:12459600-12478200	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
48	chr18:12460000-12464000	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
49	chr18:12460000-12464600	Weak transcription	Brain Anterior Caudate	brain
50	chr18:12460200-12462400	Weak transcription	NHLF	lung

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