Variant report

Variant	rs3194383
Chromosome Location	chr4:54966667-54966668
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	POLR2A	chr4:54966147-54967131	H1-neurons	neurons:	n/a	n/a
2	CTBP2	chr4:54964983-54968272	H1-hESC	embryonic stem cell:	n/a	n/a
3	CTCF	chr4:54966560-54966710	AG04449	skin:	n/a	n/a
4	SUZ12	chr4:54964026-54970669	NT2-D1	testis:	n/a	n/a
5	SUZ12	chr4:54965302-54968257	H1-hESC	embryonic stem cell:	n/a	n/a
6	CTCF	chr4:54966540-54966690	SK-N-SH_RA	brain:	n/a	n/a
7	CEBPB	chr4:54966450-54966770	IMR90	lung:	n/a	n/a
8	BACH1	chr4:54966415-54966709	H1-hESC	embryonic stem cell:	n/a	n/a
9	CTCF	chr4:54966600-54966750	SK-N-SH_RA	brain:	n/a	n/a
10	POLR2A	chr4:54965847-54968503	H1-neurons	neurons:	n/a	n/a
11	CREB1	chr4:54966254-54966770	H1-hESC	embryonic stem cell:	n/a	n/a
12	CTCF	chr4:54966560-54966710	HMEC	breast:	n/a	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr4:54966084..54968498-chr4:54968560..54970883,2	MCF-7	breast:

Variant related genes	Relation type
GSX2	TF binding region
ENSG00000221219	Chromatin interaction

Extended variants
information (count: 17 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:12)

rs_ID	r²[population]
rs1132998	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs1158401	0.90[AFR][1000 genomes];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs1158402	0.90[AFR][1000 genomes];0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2278141	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2278142	1.00[CEU][hapmap];0.82[JPT][hapmap];0.96[YRI][hapmap];0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4293842	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4498189	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4565140	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6554150	1.00[ASW][hapmap];1.00[CEU][hapmap];0.84[CHB][hapmap];0.83[CHD][hapmap];0.94[GIH][hapmap];0.86[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.91[MKK][hapmap];0.98[TSI][hapmap];1.00[YRI][hapmap];0.94[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs7654979	0.88[ASW][hapmap];1.00[CEU][hapmap];0.92[GIH][hapmap];0.94[LWK][hapmap];0.96[MKK][hapmap];0.98[TSI][hapmap];0.96[YRI][hapmap];0.92[AFR][1000 genomes];0.94[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs7655181	0.94[ASW][hapmap];1.00[CEU][hapmap];0.92[GIH][hapmap];0.94[LWK][hapmap];0.93[MEX][hapmap];0.96[MKK][hapmap];0.98[TSI][hapmap];0.96[YRI][hapmap];0.92[AFR][1000 genomes];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs7676331	0.92[AFR][1000 genomes];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:5 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv879018	chr4:54714753-55030375	Active TSS Enhancers Weak transcription Flanking Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS Strong transcription ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	17 gene(s)	inside rSNPs	diseases
2	nsv1003167	chr4:54732051-55081905	Enhancers Flanking Active TSS Strong transcription Active TSS Weak transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	17 gene(s)	inside rSNPs	diseases
3	nsv537096	chr4:54732051-55081905	Bivalent Enhancer Weak transcription Enhancers Flanking Active TSS Strong transcription Flanking Bivalent TSS/Enh Active TSS 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	17 gene(s)	inside rSNPs	diseases
4	nsv594202	chr4:54943432-55011123	Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' Weak transcription	TF binding region CpG island Chromatin interactive region	5 gene(s)	inside rSNPs	diseases
5	nsv594203	chr4:54960005-55030375	Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Enhancers Bivalent/Poised TSS Active TSS Weak transcription Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region	5 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:114 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:54964800-54967800	Bivalent Enhancer	Primary T helper memory cells from peripheral blood 1	blood
2	chr4:54965200-54968000	Bivalent Enhancer	Placenta	Placenta
3	chr4:54965200-54968200	Bivalent Enhancer	Primary Natural Killer cells fromperipheralblood	blood
4	chr4:54965200-54968200	Bivalent Enhancer	Lung	lung
5	chr4:54965400-54966800	Flanking Bivalent TSS/Enh	H1 Cell Line	embryonic stem cell
6	chr4:54965400-54966800	Flanking Bivalent TSS/Enh	Monocytes-CD14+_RO01746	blood
7	chr4:54965400-54967000	Bivalent/Poised TSS	Brain Inferior Temporal Lobe	brain
8	chr4:54965400-54968000	Flanking Bivalent TSS/Enh	Primary T helper naive cells fromperipheralblood	blood
9	chr4:54965400-54968200	Bivalent Enhancer	Fetal Intestine Small	intestine
10	chr4:54965400-54968200	Bivalent Enhancer	Fetal Thymus	thymus
11	chr4:54965600-54966800	Bivalent/Poised TSS	ES-I3 Cell Line	embryonic stem cell
12	chr4:54965600-54966800	Flanking Bivalent TSS/Enh	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
13	chr4:54965600-54967000	Bivalent/Poised TSS	H9 Cell Line	embryonic stem cell
14	chr4:54965600-54967000	Flanking Bivalent TSS/Enh	iPS DF 19.11 Cell Line	embryonic stem cell
15	chr4:54965600-54967200	Flanking Bivalent TSS/Enh	ES-UCSF4 Cell Line	embryonic stem cell
16	chr4:54965600-54967200	Flanking Bivalent TSS/Enh	Foreskin Melanocyte Primary Cells skin01	Skin
17	chr4:54965600-54967200	Bivalent/Poised TSS	Brain Dorsolateral Prefrontal Cortex	brain
18	chr4:54965600-54967400	Flanking Bivalent TSS/Enh	Stomach Smooth Muscle	stomach
19	chr4:54965600-54967600	Bivalent/Poised TSS	HUES48 Cell Line	embryonic stem cell
20	chr4:54965600-54967600	Flanking Bivalent TSS/Enh	Adipose Nuclei	Adipose
21	chr4:54965600-54967600	Flanking Bivalent TSS/Enh	Brain Hippocampus Middle	brain
22	chr4:54965600-54968000	Bivalent Enhancer	Fetal Brain Male	brain
23	chr4:54965600-54968000	Bivalent Enhancer	Fetal Heart	heart
24	chr4:54965600-54968200	Flanking Bivalent TSS/Enh	Foreskin Fibroblast Primary Cells skin01	Skin
25	chr4:54965600-54968200	Bivalent Enhancer	Esophagus	oesophagus
26	chr4:54965600-54968400	Bivalent Enhancer	Primary T killer naive cells fromperipheralblood	blood
27	chr4:54965800-54966800	Flanking Bivalent TSS/Enh	Primary T cells effector/memory enriched fromperipheralblood	blood
28	chr4:54965800-54966800	Flanking Bivalent TSS/Enh	Fetal Brain Female	brain
29	chr4:54965800-54966800	Flanking Bivalent TSS/Enh	Osteobl	bone
30	chr4:54965800-54967000	Bivalent Enhancer	Left Ventricle	heart
31	chr4:54965800-54967000	Bivalent Enhancer	Sigmoid Colon	Sigmoid Colon
32	chr4:54965800-54967200	Bivalent/Poised TSS	iPS-15b Cell Line	embryonic stem cell
33	chr4:54965800-54967200	Bivalent/Poised TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
34	chr4:54965800-54967200	Bivalent Enhancer	Stomach Mucosa	stomach
35	chr4:54965800-54967400	Flanking Bivalent TSS/Enh	Foreskin Keratinocyte Primary Cells skin02	Skin
36	chr4:54965800-54967400	Bivalent Enhancer	Placenta Amnion	Placenta Amnion
37	chr4:54965800-54967800	Bivalent Enhancer	Primary monocytes fromperipheralblood	blood
38	chr4:54965800-54968000	Flanking Active TSS	Cortex derived primary cultured neurospheres	brain
39	chr4:54965800-54968000	Enhancers	Gastric	stomach
40	chr4:54965800-54968200	Flanking Bivalent TSS/Enh	Foreskin Fibroblast Primary Cells skin02	Skin
41	chr4:54965800-54968200	Enhancers	Pancreas	Pancrea
42	chr4:54966000-54966800	Bivalent/Poised TSS	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
43	chr4:54966000-54966800	Bivalent/Poised TSS	HUES64 Cell Line	embryonic stem cell
44	chr4:54966000-54967000	Bivalent Enhancer	Primary B cells from cord blood	blood
45	chr4:54966000-54967000	Bivalent/Poised TSS	Brain Angular Gyrus	brain
46	chr4:54966000-54967200	Bivalent Enhancer	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
47	chr4:54966000-54967200	Bivalent/Poised TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
48	chr4:54966000-54967200	Bivalent/Poised TSS	HUES6 Cell Line	embryonic stem cell
49	chr4:54966000-54967200	Bivalent/Poised TSS	iPS-18 Cell Line	embryonic stem cell
50	chr4:54966000-54967200	Bivalent/Poised TSS	iPS DF 6.9 Cell Line	embryonic stem cell

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