Variant report

Variant	rs1570892
Chromosome Location	chr13:67803436-67803437
allele	A/C
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	chr13:67803398-67803504	MCF10A-Er-Src	breast:	n/a	n/a
2	GATA2	chr13:67803222-67805671	SH-SY5Y	brain:	n/a	chr13:67803716-67803725 chr13:67803716-67803723 chr13:67805544-67805554 chr13:67803716-67803723 chr13:67803717-67803734 chr13:67803712-67803728 chr13:67803464-67803475 chr13:67803709-67803730 chr13:67803712-67803728 chr13:67803716-67803725 chr13:67803716-67803723 chr13:67803715-67803725
3	KAP1	chr13:67802968-67805980	HEK293	kidney:	n/a	n/a
4	MAZ	chr13:67803411-67805761	IMR90	lung:	n/a	n/a

Variant related genes	Relation type
PCDH9	TF binding region

Extended variants
information (count: 13 )
Associated
traits (count: 0)

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

rs_ID	r²[population]
rs1325675	0.88[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs4242930	0.88[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs4354805	0.88[EUR][1000 genomes]
rs4614602	0.80[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs7318837	0.88[ASW][hapmap];0.83[MKK][hapmap]
rs8000556	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.84[AFR][1000 genomes];0.94[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs8000565	0.88[ASW][hapmap]
rs9317652	0.88[ASW][hapmap];0.82[LWK][hapmap];0.86[MKK][hapmap]
rs9317653	0.88[ASW][hapmap];0.85[LWK][hapmap];0.83[MKK][hapmap]
rs9317657	0.88[ASW][hapmap];0.85[LWK][hapmap];0.84[MKK][hapmap]
rs994245	0.88[AMR][1000 genomes];0.95[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:2 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1035741	chr13:67212973-68077950	Enhancers Flanking Active TSS Active TSS Bivalent/Poised TSS Weak transcription Strong transcription Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
2	nsv541817	chr13:67212973-68077950	Weak transcription Enhancers Flanking Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer Active TSS Genic enhancers Bivalent/Poised TSS Strong transcription Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:100 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr13:67795400-67805600	Active TSS	Brain Substantia Nigra	brain
2	chr13:67796200-67806000	Active TSS	Brain Inferior Temporal Lobe	brain
3	chr13:67796200-67806200	Active TSS	Brain Angular Gyrus	brain
4	chr13:67797200-67806000	Active TSS	Right Ventricle	heart
5	chr13:67797600-67806200	Active TSS	Fetal Kidney	kidney
6	chr13:67799800-67805800	Active TSS	Brain Anterior Caudate	brain
7	chr13:67799800-67805800	Active TSS	Brain Dorsolateral Prefrontal Cortex	brain
8	chr13:67800200-67803600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
9	chr13:67800200-67805600	Active TSS	Fetal Brain Female	brain
10	chr13:67800200-67806000	Active TSS	Left Ventricle	heart
11	chr13:67800400-67806000	Active TSS	Brain Hippocampus Middle	brain
12	chr13:67800600-67803800	Active TSS	Stomach Smooth Muscle	stomach
13	chr13:67800800-67804200	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Female	--
14	chr13:67800800-67806600	Active TSS	Brain Cingulate Gyrus	brain
15	chr13:67801200-67810000	Active TSS	Right Atrium	heart
16	chr13:67801600-67803600	Active TSS	Fetal Adrenal Gland	Adrenal Gland
17	chr13:67801600-67808400	Active TSS	Pancreatic Islets	Pancreatic Islet
18	chr13:67802000-67805200	Bivalent/Poised TSS	Brain Germinal Matrix	brain
19	chr13:67802000-67806000	Active TSS	Foreskin Fibroblast Primary Cells skin02	Skin
20	chr13:67802000-67806200	Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
21	chr13:67802000-67806400	Active TSS	Ganglion Eminence derived primary cultured neurospheres	brain
22	chr13:67802200-67803600	Active TSS	NH-A	brain
23	chr13:67802200-67804000	Flanking Active TSS	Primary B cells from cord blood	blood
24	chr13:67802200-67805600	Active TSS	Lung	lung
25	chr13:67802400-67803600	Active TSS	Fetal Muscle Leg	muscle
26	chr13:67802400-67803600	Active TSS	Rectal Smooth Muscle	rectum
27	chr13:67802400-67804000	Bivalent/Poised TSS	Fetal Intestine Large	intestine
28	chr13:67802400-67804000	Flanking Active TSS	Dnd41	blood
29	chr13:67802400-67804400	Bivalent/Poised TSS	HUES6 Cell Line	embryonic stem cell
30	chr13:67802400-67804600	Active TSS	Colonic Mucosa	Colon
31	chr13:67802400-67806000	Active TSS	Aorta	Aorta
32	chr13:67802400-67806000	Active TSS	Fetal Stomach	stomach
33	chr13:67802400-67809400	Active TSS	A549	lung
34	chr13:67802600-67803600	Active TSS	Duodenum Smooth Muscle	Duodenum
35	chr13:67802600-67804200	Bivalent/Poised TSS	ES-I3 Cell Line	embryonic stem cell
36	chr13:67802600-67804400	Bivalent/Poised TSS	iPS-20b Cell Line	embryonic stem cell
37	chr13:67802600-67805200	Active TSS	Thymus	Thymus
38	chr13:67802600-67805800	Active TSS	Placenta Amnion	Placenta Amnion
39	chr13:67802600-67806000	Active TSS	HSMM	muscle
40	chr13:67802600-67806000	Active TSS	HSMMtube	muscle
41	chr13:67802800-67803600	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
42	chr13:67802800-67803600	Active TSS	Skeletal Muscle Female	skeletal muscle
43	chr13:67802800-67803800	Flanking Bivalent TSS/Enh	HUES48 Cell Line	embryonic stem cell
44	chr13:67802800-67803800	Bivalent/Poised TSS	Fetal Intestine Small	intestine
45	chr13:67802800-67804000	Flanking Active TSS	HUVEC	blood vessel
46	chr13:67802800-67804200	Bivalent/Poised TSS	Rectal Mucosa Donor 29	rectum
47	chr13:67802800-67805800	Active TSS	Muscle Satellite Cultured Cells	--
48	chr13:67802800-67806000	Active TSS	Fetal Muscle Trunk	muscle
49	chr13:67802800-67806200	Active TSS	IMR90 fetal lung fibroblasts Cell Line	lung
50	chr13:67803000-67803600	Bivalent/Poised TSS	H1 Cell Line	embryonic stem cell

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