Variant report

Variant	rs12949049
Chromosome Location	chr17:19653310-19653311
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	BCL3	chr17:19647775-19653407	A549	lung:	n/a	chr17:19652977-19652986 chr17:19650882-19650891 chr17:19650661-19650670 chr17:19652047-19652060
2	MAX	chr17:19648056-19653846	A549	lung:	n/a	chr17:19651879-19651888 chr17:19648221-19648230 chr17:19648968-19648984

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr11:67370569..67373136-chr17:19651754..19653561,2	MCF-7	breast:
2	chr17:19649191..19653636-chr17:19654131..19659903,8	MCF-7	breast:

Variant related genes	Relation type
ALDH3A1	TF binding region
ENSG00000255119	Chromatin interaction
ENSG00000230607	Chromatin interaction

Extended variants
information (count: 14 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:5)

rs_ID	r²[population]
rs1006556	0.90[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs12939864	0.80[AMR][1000 genomes];0.84[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2072327	1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2228100	0.99[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs4646785	0.92[AMR][1000 genomes];0.88[EUR][1000 genomes];0.99[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	nsv1062853	chr17:19547912-20206601	Enhancers Weak transcription Flanking Active TSS Flanking Bivalent TSS/Enh Genic enhancers Strong transcription ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	63 gene(s)	inside rSNPs	diseases
2	nsv1063892	chr17:19564634-19808485	Weak transcription Enhancers Strong transcription Flanking Active TSS Genic enhancers Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	28 gene(s)	inside rSNPs	diseases
3	nsv907866	chr17:19582533-19697976	Weak transcription Genic enhancers Enhancers Strong transcription Bivalent/Poised TSS ZNF genes & repeats Active TSS Flanking Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	21 gene(s)	inside rSNPs	diseases
4	esv1807724	chr17:19597423-19656009	Weak transcription Enhancers Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Flanking Active TSS Strong transcription Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	16 gene(s)	inside rSNPs	diseases
5	nsv907867	chr17:19603060-19697976	Weak transcription Enhancers Flanking Active TSS Bivalent Enhancer Strong transcription Flanking Bivalent TSS/Enh ZNF genes & repeats Active TSS Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	21 gene(s)	inside rSNPs	diseases
6	esv1793043	chr17:19604821-19670329	Bivalent/Poised TSS Bivalent Enhancer Enhancers Weak transcription Flanking Active TSS Flanking Bivalent TSS/Enh Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Strong transcription Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	19 gene(s)	inside rSNPs	diseases
7	nsv457704	chr17:19620477-19663747	Active TSS Enhancers Flanking Active TSS Weak transcription Bivalent Enhancer Genic enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS Strong transcription Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	18 gene(s)	inside rSNPs	diseases
8	nsv470582	chr17:19620477-19663747	Enhancers Bivalent Enhancer Flanking Active TSS Weak transcription Active TSS ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh Strong transcription Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	18 gene(s)	inside rSNPs	diseases
9	nsv574580	chr17:19620477-19663747	Weak transcription Bivalent Enhancer Flanking Active TSS Active TSS Enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS Strong transcription Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	18 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:48 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr17:19648800-19654200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
2	chr17:19648800-19654200	Weak transcription	HUVEC	blood vessel
3	chr17:19648800-19656200	Weak transcription	Aorta	Aorta
4	chr17:19648800-19657000	Weak transcription	Spleen	Spleen
5	chr17:19649000-19656400	Weak transcription	Right Atrium	heart
6	chr17:19649200-19656200	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
7	chr17:19650200-19656800	Enhancers	Breast Myoepithelial Primary Cells	Breast
8	chr17:19650600-19657000	Enhancers	HMEC	breast
9	chr17:19650600-19657600	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
10	chr17:19651000-19656200	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
11	chr17:19651200-19653400	Enhancers	iPS DF 19.11 Cell Line	embryonic stem cell
12	chr17:19651200-19654400	Enhancers	NHEK	skin
13	chr17:19651600-19654800	Enhancers	Esophagus	oesophagus
14	chr17:19651800-19653400	Enhancers	Stomach Mucosa	stomach
15	chr17:19652000-19653400	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
16	chr17:19652000-19655400	Weak transcription	HSMMtube	muscle
17	chr17:19652000-19655800	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
18	chr17:19652200-19653600	Enhancers	HepG2	liver
19	chr17:19652200-19654200	Weak transcription	Lung	lung
20	chr17:19652200-19654200	Weak transcription	HSMM	muscle
21	chr17:19652200-19655800	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
22	chr17:19652200-19655800	Weak transcription	Brain Angular Gyrus	brain
23	chr17:19652200-19656000	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
24	chr17:19652200-19656000	Weak transcription	Cortex derived primary cultured neurospheres	brain
25	chr17:19652200-19656000	Weak transcription	Osteobl	bone
26	chr17:19652400-19655400	Weak transcription	Muscle Satellite Cultured Cells	--
27	chr17:19652400-19655400	Weak transcription	Brain Substantia Nigra	brain
28	chr17:19652400-19655600	Weak transcription	Adipose Nuclei	Adipose
29	chr17:19652400-19655600	Weak transcription	Brain Inferior Temporal Lobe	brain
30	chr17:19652400-19655800	Weak transcription	Brain Anterior Caudate	brain
31	chr17:19652400-19655800	Weak transcription	Brain Cingulate Gyrus	brain
32	chr17:19652400-19655800	Weak transcription	Skeletal Muscle Female	skeletal muscle
33	chr17:19652400-19656200	Weak transcription	Rectal Mucosa Donor 29	rectum
34	chr17:19652400-19656400	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
35	chr17:19652400-19656600	Weak transcription	Pancreas	Pancrea
36	chr17:19652600-19653400	Enhancers	A549	lung
37	chr17:19652600-19654200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
38	chr17:19652600-19655400	Weak transcription	Duodenum Mucosa	Duodenum
39	chr17:19652600-19655400	Weak transcription	Stomach Smooth Muscle	stomach
40	chr17:19652600-19655400	Enhancers	Hela-S3	cervix
41	chr17:19652600-19655400	Weak transcription	NHDF-Ad	bronchial
42	chr17:19652600-19655600	Weak transcription	Brain Hippocampus Middle	brain
43	chr17:19652600-19655800	Weak transcription	Colonic Mucosa	Colon
44	chr17:19652600-19656000	Weak transcription	Rectal Mucosa Donor 31	rectum
45	chr17:19652600-19656200	Weak transcription	HUES6 Cell Line	embryonic stem cell
46	chr17:19652600-19656600	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
47	chr17:19652800-19654800	Enhancers	GM12878-XiMat	blood
48	chr17:19653000-19654200	Weak transcription	Gastric	stomach

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