Variant report

Variant	rs11942988
Chromosome Location	chr4:20252822-20252823
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	KAP1	chr4:20251918-20253159	U2OS	brain:	n/a	n/a
2	MAX	chr4:20252775-20254559	ECC-1	luminal epithelium:	n/a	chr4:20253386-20253396
3	SIN3A	chr4:20252815-20254790	H1-hESC	embryonic stem cell:	n/a	chr4:20254076-20254085 chr4:20254559-20254573
4	CTBP2	chr4:20252818-20254039	H1-hESC	embryonic stem cell:	n/a	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr4:20252458..20255013-chr4:20255238..20258452,3	MCF-7	breast:
2	chr4:20252097..20254985-chr4:20256141..20260392,5	MCF-7	breast:

Variant related genes	Relation type
SLIT2	TF binding region
ENSG00000145147	Chromatin interaction

Extended variants
information (count: 33 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:30)

rs_ID	r²[population]
rs10516347	0.89[AMR][1000 genomes];1.00[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs10516348	0.89[AMR][1000 genomes];1.00[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs10516354	1.00[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs16867613	0.89[AMR][1000 genomes];1.00[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs16867614	0.89[AMR][1000 genomes];0.87[ASN][1000 genomes]
rs16869447	0.83[AMR][1000 genomes];1.00[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs16869450	0.83[AMR][1000 genomes];0.87[ASN][1000 genomes]
rs16869454	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs16869455	0.80[AMR][1000 genomes];1.00[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs16869457	0.89[AMR][1000 genomes];1.00[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs16869461	1.00[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs16869465	0.84[AMR][1000 genomes];0.87[ASN][1000 genomes]
rs16869475	0.89[AMR][1000 genomes];1.00[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs16869481	0.89[AMR][1000 genomes];1.00[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs1951740	1.00[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2296014	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs56967065	0.89[AMR][1000 genomes];1.00[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs57013929	0.89[AMR][1000 genomes];1.00[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs61114792	0.89[AMR][1000 genomes];1.00[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs6832019	0.94[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs6833323	1.00[EUR][1000 genomes]
rs715214	0.84[AMR][1000 genomes];1.00[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs73803832	0.84[AMR][1000 genomes];1.00[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs7661055	0.84[AMR][1000 genomes];0.92[ASN][1000 genomes]
rs7668570	0.80[AMR][1000 genomes];0.92[ASN][1000 genomes]
rs7668724	0.89[AMR][1000 genomes];0.92[ASN][1000 genomes]
rs7668969	0.89[AMR][1000 genomes];1.00[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs7668991	0.89[AMR][1000 genomes];1.00[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs7673645	0.94[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs7674173	0.94[AMR][1000 genomes];1.00[EUR][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	nsv878736	chr4:20233035-20279858	Enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Weak transcription Bivalent Enhancer Bivalent/Poised TSS Active TSS Transcr. at gene 5' and 3' Strong transcription Genic enhancers	TF binding region CpG island Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
2	nsv878737	chr4:20233035-20282334	Enhancers Weak transcription Flanking Active TSS Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Strong transcription Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
3	esv3373550	chr4:20252479-20255027	Active TSS Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh Flanking Active TSS Weak transcription Enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region	1 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:75 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:20252200-20258200	Active TSS	NHDF-Ad	bronchial
2	chr4:20252400-20253000	Bivalent/Poised TSS	ES-WA7 Cell Line	embryonic stem cell
3	chr4:20252400-20253000	Enhancers	Placenta Amnion	Placenta Amnion
4	chr4:20252400-20253000	Bivalent Enhancer	Rectal Mucosa Donor 31	rectum
5	chr4:20252400-20255200	Bivalent/Poised TSS	iPS-15b Cell Line	embryonic stem cell
6	chr4:20252400-20256400	Active TSS	Brain Anterior Caudate	brain
7	chr4:20252400-20257000	Bivalent/Poised TSS	HUES64 Cell Line	embryonic stem cell
8	chr4:20252400-20257400	Bivalent/Poised TSS	ES-I3 Cell Line	embryonic stem cell
9	chr4:20252600-20253000	Flanking Active TSS	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
10	chr4:20252600-20253000	Flanking Active TSS	H9 Derived Neuron Cultured Cells	ES cell derived
11	chr4:20252600-20253000	Flanking Active TSS	Brain Hippocampus Middle	brain
12	chr4:20252600-20253200	Flanking Active TSS	Muscle Satellite Cultured Cells	--
13	chr4:20252600-20253200	Flanking Active TSS	Ganglion Eminence derived primary cultured neurospheres	brain
14	chr4:20252600-20253200	Flanking Active TSS	Foreskin Keratinocyte Primary Cells skin03	Skin
15	chr4:20252600-20254200	Bivalent/Poised TSS	ES-UCSF4 Cell Line	embryonic stem cell
16	chr4:20252600-20254400	Active TSS	Right Atrium	heart
17	chr4:20252600-20255000	Bivalent/Poised TSS	HUES48 Cell Line	embryonic stem cell
18	chr4:20252600-20255000	Bivalent/Poised TSS	HUES6 Cell Line	embryonic stem cell
19	chr4:20252600-20255000	Bivalent/Poised TSS	iPS-20b Cell Line	embryonic stem cell
20	chr4:20252600-20255600	Active TSS	Foreskin Fibroblast Primary Cells skin02	Skin
21	chr4:20252600-20257000	Bivalent/Poised TSS	H9 Cell Line	embryonic stem cell
22	chr4:20252600-20257200	Bivalent/Poised TSS	iPS-18 Cell Line	embryonic stem cell
23	chr4:20252600-20257400	Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
24	chr4:20252600-20257800	Active TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
25	chr4:20252800-20253000	Bivalent Enhancer	Primary hematopoietic stem cells G-CSF-mobilized Female	--
26	chr4:20252800-20253000	Bivalent Enhancer	Cortex derived primary cultured neurospheres	brain
27	chr4:20252800-20253000	Active TSS	Foreskin Melanocyte Primary Cells skin03	Skin
28	chr4:20252800-20253000	Bivalent Enhancer	Brain Germinal Matrix	brain
29	chr4:20252800-20253000	Flanking Active TSS	Fetal Adrenal Gland	Adrenal Gland
30	chr4:20252800-20253000	Enhancers	Pancreatic Islets	Pancreatic Islet
31	chr4:20252800-20253000	Flanking Active TSS	Fetal Lung	lung
32	chr4:20252800-20253000	Active TSS	Fetal Muscle Trunk	muscle
33	chr4:20252800-20253000	Flanking Active TSS	Fetal Stomach	stomach
34	chr4:20252800-20253000	Active TSS	Skeletal Muscle Male	skeletal muscle
35	chr4:20252800-20253000	Flanking Active TSS	Hela-S3	cervix
36	chr4:20252800-20253000	Bivalent Enhancer	HepG2	liver
37	chr4:20252800-20253200	Flanking Bivalent TSS/Enh	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
38	chr4:20252800-20253200	Active TSS	IMR90 fetal lung fibroblasts Cell Line	lung
39	chr4:20252800-20253200	Flanking Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
40	chr4:20252800-20253200	Flanking Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
41	chr4:20252800-20253200	Flanking Active TSS	Liver	Liver
42	chr4:20252800-20253200	Flanking Active TSS	Brain Angular Gyrus	brain
43	chr4:20252800-20253200	Flanking Active TSS	Brain Cingulate Gyrus	brain
44	chr4:20252800-20253200	Flanking Active TSS	Fetal Brain Male	brain
45	chr4:20252800-20253200	Flanking Active TSS	Fetal Brain Female	brain
46	chr4:20252800-20253200	Flanking Active TSS	Fetal Heart	heart
47	chr4:20252800-20253200	Bivalent Enhancer	A549	lung
48	chr4:20252800-20253200	Flanking Active TSS	HUVEC	blood vessel
49	chr4:20252800-20253200	Flanking Active TSS	NH-A	brain
50	chr4:20252800-20253200	Flanking Active TSS	NHEK	skin

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