Variant report

Variant	rs4393551
Chromosome Location	chr15:99950772-99950773
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr15:99947884..99951610-chr15:100057572..100060447,3	MCF-7	breast:
2	chr15:99942972..99945321-chr15:99949749..99952573,2	K562	blood:
3	chr15:99948631..99950805-chr15:100153730..100155690,2	MCF-7	breast:
4	chr15:99949443..99953317-chr15:100104194..100106896,3	MCF-7	breast:
5	chr15:99943334..99944866-chr15:99950624..99952403,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000068305	Chromatin interaction

Extended variants
information (count: 30 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:15)

rs_ID	r²[population]
rs11247091	0.86[AFR][1000 genomes];0.88[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs11247092	1.00[ASW][hapmap];0.96[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.95[MEX][hapmap];0.97[TSI][hapmap];0.93[YRI][hapmap];0.84[AFR][1000 genomes];0.85[AMR][1000 genomes];0.93[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs13379749	0.91[AFR][1000 genomes];0.91[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs13380154	0.86[EUR][1000 genomes]
rs1985459	0.85[EUR][1000 genomes]
rs28379050	0.86[EUR][1000 genomes]
rs28414217	0.83[AMR][1000 genomes];0.91[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs4288976	0.86[AFR][1000 genomes];0.90[AMR][1000 genomes];0.94[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4408522	0.86[EUR][1000 genomes]
rs56149147	0.93[AFR][1000 genomes];0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs60800535	0.81[EUR][1000 genomes]
rs74035717	0.98[AFR][1000 genomes];0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs74035721	0.86[EUR][1000 genomes]
rs74035722	0.86[EUR][1000 genomes]
rs8033835	0.91[AFR][1000 genomes];0.90[AMR][1000 genomes];0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:15 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1055008	chr15:99477144-100019861	Enhancers Weak transcription Strong transcription Flanking Active TSS Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh Active TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	46 gene(s)	inside rSNPs	diseases
2	nsv904543	chr15:99513231-99991506	Weak transcription Flanking Active TSS Enhancers Strong transcription Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	45 gene(s)	inside rSNPs	diseases
3	nsv533926	chr15:99519820-99997114	Enhancers Active TSS Weak transcription Bivalent Enhancer Flanking Active TSS Strong transcription Bivalent/Poised TSS Flanking Bivalent TSS/Enh Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	45 gene(s)	inside rSNPs	diseases
4	nsv915926	chr15:99519820-100138705	Active TSS Enhancers Weak transcription Flanking Bivalent TSS/Enh Strong transcription Flanking Active TSS Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	55 gene(s)	inside rSNPs	diseases
5	nsv817289	chr15:99621061-100138705	Weak transcription Flanking Active TSS Enhancers ZNF genes & repeats Strong transcription Bivalent/Poised TSS Active TSS Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	44 gene(s)	inside rSNPs	diseases
6	nsv431411	chr15:99621061-100143999	Enhancers Flanking Active TSS Weak transcription Active TSS Bivalent/Poised TSS Strong transcription Genic enhancers ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	44 gene(s)	inside rSNPs	diseases
7	nsv904546	chr15:99696046-100166300	Flanking Active TSS Weak transcription Enhancers Bivalent Enhancer Strong transcription Active TSS ZNF genes & repeats Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	41 gene(s)	inside rSNPs	diseases
8	nsv1036346	chr15:99752391-100365458	Flanking Bivalent TSS/Enh Flanking Active TSS Strong transcription Enhancers Weak transcription Active TSS Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	47 gene(s)	inside rSNPs	diseases
9	nsv542520	chr15:99752391-100365458	Enhancers Flanking Active TSS Weak transcription Active TSS Strong transcription Genic enhancers ZNF genes & repeats 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	47 gene(s)	inside rSNPs	diseases
10	nsv1051560	chr15:99837102-100124483	Enhancers Flanking Active TSS Weak transcription Active TSS ZNF genes & repeats Strong transcription Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	19 gene(s)	inside rSNPs	diseases
11	nsv817201	chr15:99839238-100537341	Weak transcription Strong transcription Flanking Active TSS Enhancers Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Genic enhancers Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	36 gene(s)	inside rSNPs	diseases
12	nsv904547	chr15:99940221-99979159	Enhancers Weak transcription Flanking Active TSS Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
13	nsv904548	chr15:99940221-99979418	Enhancers Weak transcription Flanking Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Active TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
14	nsv904549	chr15:99940221-99991506	Enhancers Weak transcription Flanking Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
15	nsv519800	chr15:99950772-99987109	Enhancers Flanking Active TSS Bivalent Enhancer Weak transcription Flanking Bivalent TSS/Enh Active TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs4393551	NR2F2	cis	parietal	SCAN

Chromatin state (count:33 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:99944800-99972400	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
2	chr15:99945000-99954600	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
3	chr15:99947400-99951200	Enhancers	Breast Myoepithelial Primary Cells	Breast
4	chr15:99948000-99951000	Enhancers	Fetal Stomach	stomach
5	chr15:99948200-99951000	Enhancers	Fetal Muscle Trunk	muscle
6	chr15:99948200-99951000	Enhancers	Right Atrium	heart
7	chr15:99948200-99951000	Enhancers	HSMMtube	muscle
8	chr15:99948600-99950800	Weak transcription	Thymus	Thymus
9	chr15:99949000-99952400	Weak transcription	Hela-S3	cervix
10	chr15:99949400-99950800	Weak transcription	Primary T cells from cord blood	blood
11	chr15:99949400-99951400	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
12	chr15:99949400-99954400	Weak transcription	HMEC	breast
13	chr15:99949600-99950800	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
14	chr15:99949600-99950800	Weak transcription	Cortex derived primary cultured neurospheres	brain
15	chr15:99949600-99950800	Weak transcription	Fetal Heart	heart
16	chr15:99949600-99950800	Weak transcription	Spleen	Spleen
17	chr15:99949600-99951200	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
18	chr15:99949600-99954800	Weak transcription	Placenta Amnion	Placenta Amnion
19	chr15:99949600-99956400	Weak transcription	HepG2	liver
20	chr15:99949800-99954600	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
21	chr15:99950000-99952600	Weak transcription	Right Ventricle	heart
22	chr15:99950000-99954600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
23	chr15:99950000-99954600	Weak transcription	Esophagus	oesophagus
24	chr15:99950000-99964800	Weak transcription	Adipose Nuclei	Adipose
25	chr15:99950200-99950800	Weak transcription	Brain Substantia Nigra	brain
26	chr15:99950200-99954200	Weak transcription	Rectal Smooth Muscle	rectum
27	chr15:99950200-99954600	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
28	chr15:99950200-99955000	Weak transcription	Left Ventricle	heart
29	chr15:99950200-99956600	Weak transcription	Lung	lung
30	chr15:99950200-99956800	Weak transcription	Skeletal Muscle Male	skeletal muscle
31	chr15:99950600-99950800	Enhancers	Aorta	Aorta
32	chr15:99950600-99951600	Enhancers	Brain Dorsolateral Prefrontal Cortex	brain
33	chr15:99950600-99951600	Enhancers	Fetal Thymus	thymus

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