Variant report

Variant	rs12460264
Chromosome Location	chr19:38829977-38829978
allele	G/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	GATA2	chr19:38829690-38830009	SH-SY5Y	brain:	n/a	n/a
2	NR2F2	chr19:38829592-38829995	K562	blood:	n/a	n/a
3	TEAD4	chr19:38829555-38830046	K562	blood:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr19:38824766..38830853-chr19:38863348..38868089,16	MCF-7	breast:
2	chr19:38826489..38830578-chr19:38835148..38838719,4	K562	blood:
3	chr19:38824024..38830842-chr19:38863522..38868048,10	MCF-7	breast:

Variant related genes	Relation type
CATSPERG	TF binding region
ENSG00000099341	Chromatin interaction
ENSG00000099338	Chromatin interaction

Extended variants
information (count: 27 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:24)

rs_ID	r²[population]
rs1060455	0.83[EUR][1000 genomes]
rs12460181	0.81[AMR][1000 genomes];0.83[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs12460599	0.81[AMR][1000 genomes];0.99[ASN][1000 genomes]
rs12461248	0.81[AMR][1000 genomes];0.83[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs12461700	0.84[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12462230	0.83[EUR][1000 genomes]
rs12463175	0.81[AMR][1000 genomes];0.95[ASN][1000 genomes]
rs2072350	0.87[AMR][1000 genomes];0.85[ASN][1000 genomes]
rs2074979	0.83[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs2074980	0.83[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs2286547	0.81[AMR][1000 genomes];0.83[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2286550	0.83[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2286551	0.83[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs2302226	0.89[ASN][1000 genomes]
rs35848839	0.81[AMR][1000 genomes];0.83[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs3745955	0.93[ASN][1000 genomes]
rs3745956	0.83[EUR][1000 genomes]
rs3745960	0.87[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs3745961	0.87[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs3745962	0.83[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs60577771	0.82[AFR][1000 genomes];0.81[AMR][1000 genomes];0.83[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs60759642	0.83[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs60915799	0.82[AFR][1000 genomes];0.84[AMR][1000 genomes];0.83[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs61379500	0.82[AFR][1000 genomes];0.84[AMR][1000 genomes];0.83[EUR][1000 genomes];0.99[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1063471	chr19:38734744-39148392	Weak transcription Enhancers Flanking Active TSS Bivalent/Poised TSS Genic enhancers Strong transcription Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	73 gene(s)	inside rSNPs	diseases
2	nsv833822	chr19:38760748-38945105	Strong transcription Weak transcription Enhancers Flanking Bivalent TSS/Enh Active TSS Genic enhancers Bivalent Enhancer Flanking Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	50 gene(s)	inside rSNPs	diseases
3	nsv911658	chr19:38785318-39002140	Genic enhancers Weak transcription Active TSS Strong transcription Flanking Active TSS Bivalent/Poised TSS Enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	55 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:83 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr19:38828000-38830600	Enhancers	Placenta	Placenta
2	chr19:38828000-38833400	Weak transcription	Aorta	Aorta
3	chr19:38828000-38834600	Weak transcription	Sigmoid Colon	Sigmoid Colon
4	chr19:38828000-38838400	Weak transcription	HSMMtube	muscle
5	chr19:38828200-38831600	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
6	chr19:38828200-38831800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
7	chr19:38828200-38831800	Weak transcription	Stomach Smooth Muscle	stomach
8	chr19:38828200-38833200	Weak transcription	Lung	lung
9	chr19:38828200-38833400	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
10	chr19:38828200-38833400	Weak transcription	Spleen	Spleen
11	chr19:38828200-38833800	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
12	chr19:38828200-38834000	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
13	chr19:38828200-38834000	Weak transcription	Brain Hippocampus Middle	brain
14	chr19:38828200-38834600	Weak transcription	Gastric	stomach
15	chr19:38828200-38834800	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
16	chr19:38828200-38836400	Weak transcription	Brain Cingulate Gyrus	brain
17	chr19:38828200-38836600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
18	chr19:38828200-38836800	Weak transcription	Cortex derived primary cultured neurospheres	brain
19	chr19:38828200-38837000	Weak transcription	Colon Smooth Muscle	Colon
20	chr19:38828200-38837400	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
21	chr19:38828200-38838000	Weak transcription	Monocytes-CD14+_RO01746	blood
22	chr19:38828200-38838200	Weak transcription	Rectal Smooth Muscle	rectum
23	chr19:38828200-38838400	Weak transcription	Colonic Mucosa	Colon
24	chr19:38828200-38838400	Weak transcription	Duodenum Smooth Muscle	Duodenum
25	chr19:38828200-38839000	Weak transcription	Brain Anterior Caudate	brain
26	chr19:38828200-38840400	Weak transcription	Left Ventricle	heart
27	chr19:38828200-38841400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
28	chr19:38828200-38842000	Weak transcription	Brain Angular Gyrus	brain
29	chr19:38828200-38842600	Weak transcription	Esophagus	oesophagus
30	chr19:38828200-38844800	Weak transcription	Brain Substantia Nigra	brain
31	chr19:38828200-38852000	Weak transcription	Right Atrium	heart
32	chr19:38828400-38830200	Enhancers	Breast Myoepithelial Primary Cells	Breast
33	chr19:38828400-38830800	Weak transcription	Fetal Thymus	thymus
34	chr19:38828400-38831400	Weak transcription	Duodenum Mucosa	Duodenum
35	chr19:38828400-38831600	Weak transcription	Rectal Mucosa Donor 29	rectum
36	chr19:38828400-38834200	Weak transcription	Fetal Brain Male	brain
37	chr19:38828400-38834600	Weak transcription	Fetal Muscle Leg	muscle
38	chr19:38828400-38834800	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
39	chr19:38828400-38835000	Weak transcription	iPS-20b Cell Line	embryonic stem cell
40	chr19:38828400-38835400	Weak transcription	Primary monocytes fromperipheralblood	blood
41	chr19:38828400-38836200	Weak transcription	Skeletal Muscle Female	skeletal muscle
42	chr19:38828400-38836800	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
43	chr19:38828400-38837200	Weak transcription	Primary B cells from peripheral blood	blood
44	chr19:38828400-38837800	Weak transcription	Rectal Mucosa Donor 31	rectum
45	chr19:38828400-38838200	Weak transcription	Adipose Nuclei	Adipose
46	chr19:38828400-38839200	Weak transcription	Skeletal Muscle Male	skeletal muscle
47	chr19:38828400-38839600	Weak transcription	Primary T cells from cord blood	blood
48	chr19:38828400-38839800	Weak transcription	Brain Inferior Temporal Lobe	brain
49	chr19:38828400-38839800	Weak transcription	Right Ventricle	heart
50	chr19:38828400-38840000	Weak transcription	iPS-15b Cell Line	embryonic stem cell

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