Variant report

Variant	rs3760554
Chromosome Location	chr18:12430198-12430199
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	POLR2A	chr18:12430028-12431318	HepG2	liver:	n/a	n/a
2	POLR2A	chr18:12430061-12431062	GM12892	blood:	n/a	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr18:12428003..12430631-chr18:12490469..12492690,2	K562	blood:
2	chr18:12427958..12434396-chr18:12436312..12440619,6	K562	blood:

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

Extended variants
information (count: 22 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:10)

rs_ID	r²[population]
rs12457016	0.84[EUR][1000 genomes]
rs12605067	0.84[EUR][1000 genomes]
rs12605079	0.80[EUR][1000 genomes]
rs3760548	0.88[EUR][1000 genomes]
rs3760550	0.88[EUR][1000 genomes]
rs3760551	0.88[EUR][1000 genomes]
rs45476491	0.84[EUR][1000 genomes]
rs579225	0.84[EUR][1000 genomes]
rs7243034	0.84[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs72875382	0.84[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:12 , 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	nsv909404	chr18:12409955-12438402	Weak transcription Active TSS Enhancers Flanking Active TSS ZNF genes & repeats Strong transcription Bivalent Enhancer Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
11	nsv519557	chr18:12417905-12431506	Flanking Active TSS ZNF genes & repeats Weak transcription Strong transcription Enhancers Transcr. at gene 5' and 3' Active TSS Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region	8 gene(s)	inside rSNPs	diseases
12	esv3341464	chr18:12428452-12432250	Weak transcription ZNF genes & repeats Transcr. at gene 5' and 3' Strong transcription Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:98 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr18:12410400-12430400	Weak transcription	A549	lung
2	chr18:12418200-12430400	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
3	chr18:12420200-12434800	Weak transcription	Stomach Mucosa	stomach
4	chr18:12420600-12432400	Weak transcription	Left Ventricle	heart
5	chr18:12420600-12432600	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
6	chr18:12420600-12433600	Weak transcription	Duodenum Mucosa	Duodenum
7	chr18:12420600-12443600	Weak transcription	Sigmoid Colon	Sigmoid Colon
8	chr18:12420600-12477600	Weak transcription	Rectal Mucosa Donor 29	rectum
9	chr18:12421200-12432400	Weak transcription	Esophagus	oesophagus
10	chr18:12421200-12443400	Weak transcription	Skeletal Muscle Male	skeletal muscle
11	chr18:12421200-12447600	Weak transcription	Placenta Amnion	Placenta Amnion
12	chr18:12421200-12452800	Weak transcription	Colonic Mucosa	Colon
13	chr18:12421400-12430800	Weak transcription	Adipose Nuclei	Adipose
14	chr18:12421400-12431200	Weak transcription	Right Ventricle	heart
15	chr18:12421400-12433600	Weak transcription	Placenta	Placenta
16	chr18:12421400-12434600	Weak transcription	Colon Smooth Muscle	Colon
17	chr18:12421400-12444200	Weak transcription	Rectal Smooth Muscle	rectum
18	chr18:12421800-12430400	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
19	chr18:12421800-12434400	Weak transcription	iPS-15b Cell Line	embryonic stem cell
20	chr18:12421800-12442400	Weak transcription	GM12878-XiMat	blood
21	chr18:12422000-12431800	Weak transcription	Fetal Thymus	thymus
22	chr18:12422600-12430400	Weak transcription	K562	blood
23	chr18:12426600-12433200	Strong transcription	Brain Angular Gyrus	brain
24	chr18:12426600-12434200	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
25	chr18:12426600-12434600	Strong transcription	Brain Germinal Matrix	brain
26	chr18:12426600-12434600	Strong transcription	NHLF	lung
27	chr18:12426600-12434800	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
28	chr18:12426600-12435000	Strong transcription	Brain Dorsolateral Prefrontal Cortex	brain
29	chr18:12426600-12435400	Strong transcription	Fetal Muscle Trunk	muscle
30	chr18:12426600-12438600	Strong transcription	Foreskin Fibroblast Primary Cells skin02	Skin
31	chr18:12426800-12430200	Strong transcription	Duodenum Smooth Muscle	Duodenum
32	chr18:12426800-12431200	Strong transcription	Osteobl	bone
33	chr18:12426800-12431800	Strong transcription	Stomach Smooth Muscle	stomach
34	chr18:12426800-12433400	Strong transcription	HepG2	liver
35	chr18:12426800-12434400	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
36	chr18:12426800-12436400	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
37	chr18:12427000-12430200	Weak transcription	NHEK	skin
38	chr18:12427000-12430400	Strong transcription	Fetal Intestine Large	intestine
39	chr18:12427000-12435000	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
40	chr18:12427200-12430800	ZNF genes & repeats	iPS DF 19.11 Cell Line	embryonic stem cell
41	chr18:12427200-12430800	Strong transcription	Lung	lung
42	chr18:12427200-12432000	Weak transcription	HUVEC	blood vessel
43	chr18:12427200-12433000	Strong transcription	NHDF-Ad	bronchial
44	chr18:12427200-12434600	Strong transcription	Cortex derived primary cultured neurospheres	brain
45	chr18:12427400-12435000	Strong transcription	Brain Hippocampus Middle	brain
46	chr18:12427600-12430200	Weak transcription	H9 Cell Line	embryonic stem cell
47	chr18:12427600-12431000	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
48	chr18:12427600-12433400	Strong transcription	Brain Cingulate Gyrus	brain
49	chr18:12428000-12433000	Strong transcription	Muscle Satellite Cultured Cells	--
50	chr18:12428000-12433400	Strong transcription	HUES48 Cell Line	embryonic stem cell

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