Variant report

Variant	rs12457760
Chromosome Location	chr18:12459134-12459135
allele	A/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr18:12451035..12453688-chr18:12457472..12459891,2	K562	blood:
2	chr18:12457149..12459237-chr18:12472773..12475117,2	K562	blood:

Variant related genes	Relation type
ENSG00000134278	Chromatin interaction

Extended variants
information (count: 31 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:22)

rs_ID	r²[population]
rs12455439	0.85[AFR][1000 genomes];0.84[EUR][1000 genomes]
rs12455481	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12457903	0.84[CEU][hapmap]
rs12608270	0.90[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12958049	0.98[AFR][1000 genomes];0.99[AMR][1000 genomes];0.94[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12964631	0.86[EUR][1000 genomes]
rs17615158	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];1.00[YRI][hapmap];0.95[AFR][1000 genomes];0.99[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1940974	0.81[CEU][hapmap]
rs2016707	0.85[AMR][1000 genomes];0.82[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2116004	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs36109961	0.88[AFR][1000 genomes];0.84[AMR][1000 genomes];0.92[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs4389196	0.81[CEU][hapmap]
rs58193967	0.86[AMR][1000 genomes];0.93[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs59992891	0.86[EUR][1000 genomes]
rs7234589	0.87[AFR][1000 genomes];0.94[AMR][1000 genomes];0.90[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs7234742	0.86[AFR][1000 genomes];0.94[AMR][1000 genomes];0.92[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7242395	0.80[CEU][hapmap]
rs8088786	0.84[CEU][hapmap]
rs8093571	0.84[CEU][hapmap]
rs8099288	0.90[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9959759	0.80[CEU][hapmap]
rs9964759	0.84[CEU][hapmap]

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
rs12457760	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	chr18:12442000-12459200	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
6	chr18:12444000-12460200	Weak transcription	Fetal Intestine Large	intestine
7	chr18:12444000-12467400	Weak transcription	A549	lung
8	chr18:12444200-12463200	Weak transcription	ES-I3 Cell Line	embryonic stem cell
9	chr18:12444400-12465800	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
10	chr18:12444600-12459400	Weak transcription	Pancreatic Islets	Pancreatic Islet
11	chr18:12444600-12477600	Weak transcription	Rectal Smooth Muscle	rectum
12	chr18:12445600-12459200	Weak transcription	Fetal Intestine Small	intestine
13	chr18:12445600-12460800	Weak transcription	Primary hematopoietic stem cells	blood
14	chr18:12446200-12479600	Weak transcription	iPS-15b Cell Line	embryonic stem cell
15	chr18:12447000-12460800	Weak transcription	Duodenum Mucosa	Duodenum
16	chr18:12447800-12459200	Weak transcription	Fetal Lung	lung
17	chr18:12447800-12461200	Weak transcription	Colon Smooth Muscle	Colon
18	chr18:12448000-12463000	Weak transcription	Psoas Muscle	Psoas
19	chr18:12449600-12459200	Weak transcription	NHLF	lung
20	chr18:12449600-12470600	Weak transcription	HUES64 Cell Line	embryonic stem cell
21	chr18:12449600-12477600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
22	chr18:12449800-12459200	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
23	chr18:12449800-12459400	Weak transcription	HUES6 Cell Line	embryonic stem cell
24	chr18:12449800-12461000	Weak transcription	HUES48 Cell Line	embryonic stem cell
25	chr18:12449800-12461000	Weak transcription	Duodenum Smooth Muscle	Duodenum
26	chr18:12449800-12465400	Weak transcription	Monocytes-CD14+_RO01746	blood
27	chr18:12449800-12466800	Weak transcription	iPS-20b Cell Line	embryonic stem cell
28	chr18:12449800-12470600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
29	chr18:12449800-12477600	Weak transcription	H1 Cell Line	embryonic stem cell
30	chr18:12449800-12477600	Weak transcription	Spleen	Spleen
31	chr18:12449800-12477800	Weak transcription	H9 Cell Line	embryonic stem cell
32	chr18:12449800-12478000	Weak transcription	Gastric	stomach
33	chr18:12449800-12478000	Weak transcription	Sigmoid Colon	Sigmoid Colon
34	chr18:12449800-12479600	Weak transcription	iPS-18 Cell Line	embryonic stem cell
35	chr18:12450000-12460800	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
36	chr18:12450000-12478200	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
37	chr18:12452200-12464600	Weak transcription	Pancreas	Pancrea
38	chr18:12452400-12459200	Weak transcription	Skeletal Muscle Female	skeletal muscle
39	chr18:12452600-12459200	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
40	chr18:12452600-12459200	Weak transcription	Aorta	Aorta
41	chr18:12452800-12459400	Weak transcription	HMEC	breast
42	chr18:12452800-12460400	Weak transcription	Brain Germinal Matrix	brain
43	chr18:12453200-12459400	Weak transcription	NH-A	brain
44	chr18:12453400-12460200	Strong transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
45	chr18:12453400-12484400	Weak transcription	Hela-S3	cervix
46	chr18:12454400-12459200	Weak transcription	Liver	Liver
47	chr18:12454600-12459200	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
48	chr18:12454800-12459200	Weak transcription	Fetal Stomach	stomach
49	chr18:12454800-12459400	Weak transcription	Breast Myoepithelial Primary Cells	Breast
50	chr18:12455800-12462400	Weak transcription	Ovary	ovary

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