Variant report

Variant	rs4776576
Chromosome Location	chr15:72098672-72098673
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	GATA3	chr15:72098623-72099259	A549	lung:	n/a	chr15:72098800-72098809
2	EBF1	chr15:72098669-72099211	GM12878	blood:	n/a	chr15:72098870-72098881 chr15:72098871-72098881 chr15:72098872-72098881 chr15:72098838-72098849
3	FOSL2	chr15:72098625-72099216	SK-N-SH	brain:	n/a	chr15:72098687-72098698
4	TEAD4	chr15:72098661-72099181	SK-N-SH	brain:	n/a	n/a
5	NFIC	chr15:72098551-72099308	SK-N-SH	brain:	n/a	chr15:72099116-72099133 chr15:72099116-72099132
6	GATA3	chr15:72098552-72099284	SK-N-SH	brain:	n/a	chr15:72098800-72098809
7	FOSL2	chr15:72098629-72099057	A549	lung:	n/a	chr15:72098687-72098698
8	TCF12	chr15:72098573-72099177	A549	lung:	n/a	chr15:72098792-72098802
9	EP300	chr15:72098647-72099097	SK-N-SH_RA	brain:	n/a	n/a
10	GATA3	chr15:72098642-72099203	SK-N-SH	brain:	n/a	chr15:72098800-72098809
11	TCF12	chr15:72098631-72099352	SK-N-SH	brain:	n/a	chr15:72098792-72098802

No.	Distal block	Cell Line	Cell type
1	chr15:72095402..72097708-chr15:72097755..72100613,2	MCF-7	breast:
2	chr15:72097461..72102477-chr15:72104726..72109263,4	MCF-7	breast:
3	chr15:72093317..72095057-chr15:72097968..72100782,2	MCF-7	breast:

Variant related genes	Relation type
NR2E3	TF binding region

Extended variants
information (count: 18 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:14)

rs_ID	r²[population]
rs11072329	0.83[ASN][1000 genomes]
rs11072331	1.00[CEU][hapmap];0.83[ASN][1000 genomes]
rs12101574	1.00[CEU][hapmap];0.92[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs16956225	0.81[AFR][1000 genomes]
rs16956228	0.81[AFR][1000 genomes]
rs2245596	1.00[CHB][hapmap]
rs2625536	1.00[CHB][hapmap]
rs2723340	0.84[JPT][hapmap];0.85[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs6494968	1.00[CEU][hapmap];0.83[ASN][1000 genomes]
rs6494969	1.00[CHB][hapmap];0.84[JPT][hapmap];0.81[AMR][1000 genomes];0.83[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs7164847	0.83[ASN][1000 genomes]
rs7174353	0.82[AMR][1000 genomes];0.93[ASN][1000 genomes]
rs73432487	0.81[AFR][1000 genomes]
rs7495064	1.00[CEU][hapmap];0.83[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv904334	chr15:71737376-72177659	Strong transcription Active TSS Enhancers Weak transcription Flanking Bivalent TSS/Enh Genic enhancers ZNF genes & repeats Flanking Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	13 gene(s)	inside rSNPs	diseases
2	nsv1036938	chr15:71948106-72272855	Weak transcription Strong transcription Flanking Active TSS ZNF genes & repeats Enhancers Genic enhancers Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	11 gene(s)	inside rSNPs	diseases
3	esv3331306	chr15:72049818-72427559	Strong transcription ZNF genes & repeats Active TSS Weak transcription Enhancers Flanking Active TSS Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	34 gene(s)	inside rSNPs	diseases
4	esv3433206	chr15:72049838-72427529	Enhancers Strong transcription Weak transcription Flanking Active TSS ZNF genes & repeats Active TSS Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	34 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:57 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:72076000-72099000	Weak transcription	Right Atrium	heart
2	chr15:72084800-72098800	Weak transcription	Pancreas	Pancrea
3	chr15:72093600-72098800	Weak transcription	HUES6 Cell Line	embryonic stem cell
4	chr15:72093600-72098800	Weak transcription	HUES64 Cell Line	embryonic stem cell
5	chr15:72093600-72098800	Weak transcription	iPS-20b Cell Line	embryonic stem cell
6	chr15:72093600-72098800	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
7	chr15:72093600-72100200	Weak transcription	Fetal Kidney	kidney
8	chr15:72094000-72099000	Weak transcription	H9 Cell Line	embryonic stem cell
9	chr15:72094200-72098800	Weak transcription	iPS-15b Cell Line	embryonic stem cell
10	chr15:72094200-72098800	Weak transcription	Hela-S3	cervix
11	chr15:72095400-72098800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
12	chr15:72096000-72100600	Enhancers	Fetal Muscle Trunk	muscle
13	chr15:72096000-72105600	Enhancers	Fetal Muscle Leg	muscle
14	chr15:72096200-72100400	Enhancers	Fetal Heart	heart
15	chr15:72096200-72103400	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
16	chr15:72097000-72098800	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
17	chr15:72097200-72100600	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
18	chr15:72097400-72098800	Weak transcription	iPS-18 Cell Line	embryonic stem cell
19	chr15:72097400-72098800	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
20	chr15:72097400-72099000	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
21	chr15:72097400-72099400	Weak transcription	Primary hematopoietic stem cells short term culture	blood
22	chr15:72097600-72098800	Weak transcription	HSMM	muscle
23	chr15:72097600-72099000	Weak transcription	HSMMtube	muscle
24	chr15:72097600-72099400	Weak transcription	Breast Myoepithelial Primary Cells	Breast
25	chr15:72097800-72098800	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
26	chr15:72097800-72098800	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
27	chr15:72097800-72098800	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
28	chr15:72097800-72099000	Weak transcription	Placenta Amnion	Placenta Amnion
29	chr15:72098000-72099000	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
30	chr15:72098400-72099400	Enhancers	HUES48 Cell Line	embryonic stem cell
31	chr15:72098400-72100600	Enhancers	Fetal Lung	lung
32	chr15:72098400-72100600	Enhancers	A549	lung
33	chr15:72098400-72100800	Enhancers	Placenta	Placenta
34	chr15:72098600-72099000	Enhancers	ES-I3 Cell Line	embryonic stem cell
35	chr15:72098600-72099000	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
36	chr15:72098600-72099000	Enhancers	Fetal Intestine Small	intestine
37	chr15:72098600-72099200	Enhancers	Fetal Intestine Large	intestine
38	chr15:72098600-72099200	Enhancers	NHEK	skin
39	chr15:72098600-72099400	Enhancers	Foreskin Fibroblast Primary Cells skin02	Skin
40	chr15:72098600-72099400	Enhancers	Fetal Adrenal Gland	Adrenal Gland
41	chr15:72098600-72100200	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
42	chr15:72098600-72100400	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
43	chr15:72098600-72100400	Enhancers	Cortex derived primary cultured neurospheres	brain
44	chr15:72098600-72100400	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
45	chr15:72098600-72100400	Enhancers	Fetal Stomach	stomach
46	chr15:72098600-72100400	Enhancers	Left Ventricle	heart
47	chr15:72098600-72100400	Enhancers	HMEC	breast
48	chr15:72098600-72100400	Enhancers	HUVEC	blood vessel
49	chr15:72098600-72100600	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
50	chr15:72098600-72100600	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links