Variant report

Variant	rs1652670
Chromosome Location	chr18:12431210-12431211
allele	C/T
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	NFATC1	chr18:12430449-12431222	GM12878	blood:	n/a	n/a
2	POLR2A	chr18:12430028-12431318	HepG2	liver:	n/a	n/a
3	NFATC1	chr18:12430240-12431249	GM12878	blood:	n/a	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr18:12418687..12420720-chr18:12430201..12431737,2	MCF-7	breast:
2	chr18:12427958..12434396-chr18:12436312..12440619,6	K562	blood:

Variant related genes	Relation type
ENSG00000256786	TF binding region
ENSG00000267108	TF binding region
ENSG00000141391	Chromatin interaction
ENSG00000267199	Chromatin interaction

Extended variants
information (count: 23 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:11)

rs_ID	r²[population]
rs1573330	0.84[AMR][1000 genomes]
rs1785326	0.87[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs3906620	0.85[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4483914	0.86[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs500300	0.81[EUR][1000 genomes]
rs503307	0.87[AMR][1000 genomes];0.83[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs529538	0.99[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs558090	0.84[AMR][1000 genomes]
rs573390	0.81[EUR][1000 genomes]
rs62095752	0.96[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs8089169	0.80[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	chr18:12420200-12434800	Weak transcription	Stomach Mucosa	stomach
2	chr18:12420600-12432400	Weak transcription	Left Ventricle	heart
3	chr18:12420600-12432600	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
4	chr18:12420600-12433600	Weak transcription	Duodenum Mucosa	Duodenum
5	chr18:12420600-12443600	Weak transcription	Sigmoid Colon	Sigmoid Colon
6	chr18:12420600-12477600	Weak transcription	Rectal Mucosa Donor 29	rectum
7	chr18:12421200-12432400	Weak transcription	Esophagus	oesophagus
8	chr18:12421200-12443400	Weak transcription	Skeletal Muscle Male	skeletal muscle
9	chr18:12421200-12447600	Weak transcription	Placenta Amnion	Placenta Amnion
10	chr18:12421200-12452800	Weak transcription	Colonic Mucosa	Colon
11	chr18:12421400-12433600	Weak transcription	Placenta	Placenta
12	chr18:12421400-12434600	Weak transcription	Colon Smooth Muscle	Colon
13	chr18:12421400-12444200	Weak transcription	Rectal Smooth Muscle	rectum
14	chr18:12421800-12434400	Weak transcription	iPS-15b Cell Line	embryonic stem cell
15	chr18:12421800-12442400	Weak transcription	GM12878-XiMat	blood
16	chr18:12422000-12431800	Weak transcription	Fetal Thymus	thymus
17	chr18:12426600-12433200	Strong transcription	Brain Angular Gyrus	brain
18	chr18:12426600-12434200	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
19	chr18:12426600-12434600	Strong transcription	Brain Germinal Matrix	brain
20	chr18:12426600-12434600	Strong transcription	NHLF	lung
21	chr18:12426600-12434800	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
22	chr18:12426600-12435000	Strong transcription	Brain Dorsolateral Prefrontal Cortex	brain
23	chr18:12426600-12435400	Strong transcription	Fetal Muscle Trunk	muscle
24	chr18:12426600-12438600	Strong transcription	Foreskin Fibroblast Primary Cells skin02	Skin
25	chr18:12426800-12431800	Strong transcription	Stomach Smooth Muscle	stomach
26	chr18:12426800-12433400	Strong transcription	HepG2	liver
27	chr18:12426800-12434400	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
28	chr18:12426800-12436400	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
29	chr18:12427000-12435000	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
30	chr18:12427200-12432000	Weak transcription	HUVEC	blood vessel
31	chr18:12427200-12433000	Strong transcription	NHDF-Ad	bronchial
32	chr18:12427200-12434600	Strong transcription	Cortex derived primary cultured neurospheres	brain
33	chr18:12427400-12435000	Strong transcription	Brain Hippocampus Middle	brain
34	chr18:12427600-12433400	Strong transcription	Brain Cingulate Gyrus	brain
35	chr18:12428000-12433000	Strong transcription	Muscle Satellite Cultured Cells	--
36	chr18:12428000-12433400	Strong transcription	HUES48 Cell Line	embryonic stem cell
37	chr18:12428000-12435600	Strong transcription	Fetal Brain Female	brain
38	chr18:12428200-12432000	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
39	chr18:12428200-12432000	Weak transcription	HMEC	breast
40	chr18:12428200-12434600	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
41	chr18:12428200-12435600	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
42	chr18:12428200-12440200	Strong transcription	Primary hematopoietic stem cells short term culture	blood
43	chr18:12428200-12440600	Strong transcription	Breast Myoepithelial Primary Cells	Breast
44	chr18:12428400-12433800	Strong transcription	Foreskin Fibroblast Primary Cells skin01	Skin
45	chr18:12428400-12435000	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
46	chr18:12428400-12435000	Strong transcription	Fetal Muscle Leg	muscle
47	chr18:12428400-12435400	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
48	chr18:12428400-12437400	Strong transcription	Fetal Intestine Small	intestine
49	chr18:12428400-12439600	Weak transcription	Primary B cells from cord blood	blood
50	chr18:12428400-12443400	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived

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