Variant report

Variant	rs3888463
Chromosome Location	chr22:27598602-27598603
allele	A/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	JUND	chr22:27598521-27599103	HCT-116	colon:	n/a	n/a
2	FOS	chr22:27598596-27599077	MCF10A-Er-Src	breast:	n/a	n/a
3	TEAD4	chr22:27598470-27599145	SK-N-SH	brain:	n/a	chr22:27598835-27598844
4	JUND	chr22:27598518-27599199	SK-N-SH	brain:	n/a	n/a
5	TEAD4	chr22:27598523-27599137	HCT-116	colon:	n/a	chr22:27598835-27598844
6	MYC	chr22:27598462-27599077	MCF10A-Er-Src	breast:	n/a	n/a
7	TEAD4	chr22:27598588-27599051	H1-hESC	embryonic stem cell:	n/a	chr22:27598835-27598844
8	TEAD4	chr22:27598597-27599115	ECC-1	luminal epithelium:	n/a	chr22:27598835-27598844
9	TEAD4	chr22:27598548-27599107	A549	lung:	n/a	chr22:27598835-27598844
10	TEAD4	chr22:27598593-27599110	ECC-1	luminal epithelium:	n/a	chr22:27598835-27598844
11	TCF12	chr22:27598496-27599199	SK-N-SH	brain:	n/a	n/a
12	TCF12	chr22:27598457-27599231	A549	lung:	n/a	n/a
13	TEAD4	chr22:27598482-27599137	A549	lung:	n/a	chr22:27598835-27598844
14	FOSL2	chr22:27598583-27599020	A549	lung:	n/a	n/a
15	FOSL2	chr22:27598556-27599170	MCF-7	breast:	n/a	n/a
16	EP300	chr22:27598539-27599133	A549	lung:	n/a	n/a
17	EP300	chr22:27598414-27599192	SK-N-SH	brain:	n/a	n/a
18	FOSL2	chr22:27598494-27599140	A549	lung:	n/a	n/a
19	FOSL1	chr22:27598547-27599136	HCT-116	colon:	n/a	n/a
20	MAX	chr22:27598475-27599295	A549	lung:	n/a	n/a
21	TEAD4	chr22:27598551-27599095	SK-N-SH	brain:	n/a	chr22:27598835-27598844
22	FOSL2	chr22:27598593-27599064	SK-N-SH	brain:	n/a	n/a
23	RAD21	chr22:27598457-27599112	IMR90	lung:	n/a	n/a
24	FOSL2	chr22:27598563-27599117	MCF-7	breast:	n/a	n/a
25	JUND	chr22:27598541-27599135	SK-N-SH	brain:	n/a	n/a
26	JUND	chr22:27598544-27599136	MCF-7	breast:	n/a	n/a
27	FOSL1	chr22:27598565-27599176	HCT-116	colon:	n/a	n/a
28	SP1	chr22:27598568-27599100	H1-hESC	embryonic stem cell:	n/a	chr22:27598687-27598701 chr22:27598945-27598957 chr22:27598723-27598732
29	FOSL2	chr22:27598562-27599089	SK-N-SH	brain:	n/a	n/a
30	SP1	chr22:27598561-27599204	A549	lung:	n/a	chr22:27598687-27598701 chr22:27598945-27598957 chr22:27598723-27598732
31	FOS	chr22:27598390-27599213	MCF10A-Er-Src	breast:	n/a	n/a
32	FOS	chr22:27598468-27599183	MCF10A-Er-Src	breast:	n/a	n/a
33	MAX	chr22:27598389-27599364	A549	lung:	n/a	n/a
34	SP1	chr22:27598600-27599060	H1-hESC	embryonic stem cell:	n/a	chr22:27598687-27598701 chr22:27598945-27598957 chr22:27598723-27598732
35	CEBPB	chr22:27598575-27599238	A549	lung:	n/a	n/a
36	JUND	chr22:27598529-27599117	HCT-116	colon:	n/a	n/a
37	JUND	chr22:27598310-27599365	SK-N-SH	brain:	n/a	n/a
38	EP300	chr22:27598502-27599269	A549	lung:	n/a	n/a
39	SP1	chr22:27598478-27599176	A549	lung:	n/a	chr22:27598687-27598701 chr22:27598945-27598957 chr22:27598723-27598732
40	GATA3	chr22:27598399-27599319	A549	lung:	n/a	n/a
41	TCF12	chr22:27598557-27599095	SK-N-SH	brain:	n/a	n/a
42	MAZ	chr22:27598303-27599181	IMR90	lung:	n/a	n/a
43	GATA3	chr22:27598527-27599204	SK-N-SH	brain:	n/a	n/a
44	JUND	chr22:27598538-27599145	T-47D	breast:	n/a	n/a
45	PBX3	chr22:27598581-27599223	SK-N-SH	brain:	n/a	n/a
46	JUND	chr22:27598583-27599100	A549	lung:	n/a	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr22:27591652..27595199-chr22:27596302..27600048,3	MCF-7	breast:

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-CRYBA4-6	chr22:27596085-27601088	NONHSAT084576

Variant related genes	Relation type
ENSG00000238195	TF binding region

Extended variants
information (count: 16 )
Associated
traits (count: 0)

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

rs_ID	r²[population]
rs11090478	0.90[AMR][1000 genomes];0.84[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs2342399	0.90[AMR][1000 genomes];0.84[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs2342400	0.90[AMR][1000 genomes];0.84[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs2342401	0.87[AMR][1000 genomes];0.94[ASN][1000 genomes]
rs551334	0.86[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs565638	0.95[AMR][1000 genomes];0.95[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs8135373	0.90[AMR][1000 genomes];0.84[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs9306437	0.90[AMR][1000 genomes];0.84[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs9613397	0.86[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs9613399	0.83[AMR][1000 genomes];0.80[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs9941926	0.83[AMR][1000 genomes];0.94[ASN][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	nsv917333	chr22:26931825-27692024	Enhancers Weak transcription Genic enhancers Flanking Active TSS Strong transcription Active TSS Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	142 gene(s)	inside rSNPs	diseases
2	esv34168	chr22:27289097-27678031	Weak transcription Enhancers Bivalent Enhancer Flanking Active TSS Active TSS ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3' Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	14 gene(s)	inside rSNPs	diseases
3	esv3413125	chr22:27404463-28121577	Enhancers Weak transcription Bivalent Enhancer Flanking Active TSS Active TSS Strong transcription Bivalent/Poised TSS ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	31 gene(s)	inside rSNPs	diseases
4	nsv459860	chr22:27527005-28181436	Strong transcription Enhancers Weak transcription Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS Flanking Active TSS Active TSS Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	27 gene(s)	inside rSNPs	diseases
5	nsv588872	chr22:27527005-28181436	Weak transcription Enhancers Strong transcription Flanking Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Genic enhancers ZNF genes & repeats Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	27 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:67 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr22:27588600-27598800	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
2	chr22:27588800-27599000	Weak transcription	Aorta	Aorta
3	chr22:27593600-27599000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
4	chr22:27593600-27608800	Weak transcription	Right Atrium	heart
5	chr22:27595000-27599000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
6	chr22:27596400-27599400	Enhancers	Fetal Brain Male	brain
7	chr22:27597200-27598800	Enhancers	Fetal Brain Female	brain
8	chr22:27597200-27599400	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
9	chr22:27597200-27599600	Enhancers	Cortex derived primary cultured neurospheres	brain
10	chr22:27597400-27598800	Enhancers	HUES6 Cell Line	embryonic stem cell
11	chr22:27597400-27599400	Enhancers	H1 Cell Line	embryonic stem cell
12	chr22:27597400-27599600	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
13	chr22:27597400-27600000	Enhancers	ES-I3 Cell Line	embryonic stem cell
14	chr22:27597400-27600000	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
15	chr22:27597600-27598800	Enhancers	HUES48 Cell Line	embryonic stem cell
16	chr22:27597600-27599000	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
17	chr22:27597600-27599000	Enhancers	Osteobl	bone
18	chr22:27597600-27599600	Enhancers	iPS-18 Cell Line	embryonic stem cell
19	chr22:27597600-27599800	Enhancers	NH-A	brain
20	chr22:27597600-27600200	Enhancers	Fetal Intestine Small	intestine
21	chr22:27597800-27599000	Weak transcription	H9 Cell Line	embryonic stem cell
22	chr22:27597800-27599000	Enhancers	Adipose Nuclei	Adipose
23	chr22:27597800-27599800	Enhancers	ES-WA7 Cell Line	embryonic stem cell
24	chr22:27597800-27600000	Enhancers	Fetal Stomach	stomach
25	chr22:27597800-27600000	Enhancers	HMEC	breast
26	chr22:27598000-27599200	Enhancers	Colon Smooth Muscle	Colon
27	chr22:27598000-27599600	Enhancers	HSMM	muscle
28	chr22:27598000-27599600	Enhancers	HUVEC	blood vessel
29	chr22:27598000-27599800	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
30	chr22:27598000-27599800	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
31	chr22:27598000-27599800	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
32	chr22:27598000-27599800	Enhancers	Fetal Muscle Leg	muscle
33	chr22:27598000-27599800	Enhancers	NHLF	lung
34	chr22:27598000-27600000	Enhancers	Fetal Intestine Large	intestine
35	chr22:27598200-27598800	Weak transcription	Fetal Lung	lung
36	chr22:27598200-27599200	Weak transcription	Placenta Amnion	Placenta Amnion
37	chr22:27598200-27599400	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
38	chr22:27598200-27599600	Enhancers	Rectal Smooth Muscle	rectum
39	chr22:27598400-27598800	Weak transcription	iPS-15b Cell Line	embryonic stem cell
40	chr22:27598400-27598800	Weak transcription	HSMMtube	muscle
41	chr22:27598400-27599200	Flanking Active TSS	H9 Derived Neuron Cultured Cells	ES cell derived
42	chr22:27598400-27599200	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
43	chr22:27598400-27599200	Flanking Active TSS	A549	lung
44	chr22:27598400-27599400	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
45	chr22:27598400-27599600	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
46	chr22:27598400-27599800	Bivalent Enhancer	Fetal Muscle Trunk	muscle
47	chr22:27598400-27607800	Weak transcription	Duodenum Smooth Muscle	Duodenum
48	chr22:27598600-27598800	Enhancers	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
49	chr22:27598600-27598800	Flanking Active TSS	HUES64 Cell Line	embryonic stem cell
50	chr22:27598600-27598800	Flanking Active TSS	iPS-20b Cell Line	embryonic stem cell

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