Variant report

Variant	rs4975709
Chromosome Location	chr5:1877280-1877281
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr5:1706531..1709352-chr5:1876772..1878582,2	K562	blood:
2	chr5:1800060..1803631-chr5:1877148..1879062,3	MCF-7	breast:

Variant related genes	Relation type
ENSG00000145494	Chromatin interaction
ENSG00000171421	Chromatin interaction
ENSG00000263746	Chromatin interaction

Extended variants
information (count: 32 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:18)

rs_ID	r²[population]
rs10475118	0.86[AMR][1000 genomes];0.91[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs10475119	0.87[AMR][1000 genomes];0.92[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs11957344	0.80[AMR][1000 genomes];0.84[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs11960636	0.81[AMR][1000 genomes];0.87[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2232373	0.85[AMR][1000 genomes];0.89[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2232374	0.82[AMR][1000 genomes];0.87[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2279588	0.87[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2307118	0.87[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs3797063	0.91[CEU][hapmap];0.94[CHB][hapmap];0.94[JPT][hapmap];0.84[AMR][1000 genomes];0.86[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs4975707	0.83[JPT][hapmap]
rs4975744	0.83[JPT][hapmap]
rs4975752	0.91[CEU][hapmap];0.94[CHB][hapmap];1.00[CHD][hapmap];0.91[GIH][hapmap];0.94[JPT][hapmap];0.86[MEX][hapmap];0.86[MKK][hapmap];0.97[TSI][hapmap];0.86[AMR][1000 genomes];0.92[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs4975753	0.91[CEU][hapmap];0.94[CHB][hapmap];0.97[CHD][hapmap];0.97[GIH][hapmap];0.94[JPT][hapmap];0.86[MEX][hapmap];0.87[MKK][hapmap];0.97[TSI][hapmap];0.86[AMR][1000 genomes];0.91[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs4975756	0.81[AMR][1000 genomes];0.89[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs4975757	0.81[AMR][1000 genomes];0.87[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs6886669	0.83[JPT][hapmap]
rs9312959	0.90[AMR][1000 genomes];0.96[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs931508	0.83[JPT][hapmap]

Variant overlapped rSNPs/rCNVs (count:14 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv933805	chr5:1450724-1941619	Enhancers Bivalent Enhancer Bivalent/Poised TSS Flanking Active TSS Strong transcription Active TSS Weak transcription Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	96 gene(s)	inside rSNPs	diseases
2	nsv817407	chr5:1495354-2191460	Weak transcription Strong transcription Enhancers Flanking Active TSS Bivalent/Poised TSS Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA	107 gene(s)	inside rSNPs	diseases
3	nsv869236	chr5:1719263-2259100	Flanking Active TSS Active TSS Bivalent/Poised TSS Bivalent Enhancer Enhancers Weak transcription ZNF genes & repeats Genic enhancers Strong transcription Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	66 gene(s)	inside rSNPs	diseases
4	nsv596891	chr5:1822326-1880891	Bivalent Enhancer Weak transcription Bivalent/Poised TSS Strong transcription Active TSS Enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Genic enhancers Flanking Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
5	nsv880647	chr5:1822326-1880891	Bivalent Enhancer Flanking Bivalent TSS/Enh Enhancers ZNF genes & repeats Bivalent/Poised TSS Weak transcription Strong transcription Flanking Active TSS Active TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
6	nsv881619	chr5:1822326-1886471	Flanking Bivalent TSS/Enh Enhancers Bivalent Enhancer ZNF genes & repeats Active TSS Flanking Active TSS Strong transcription Bivalent/Poised TSS Weak transcription Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	13 gene(s)	inside rSNPs	diseases
7	nsv881557	chr5:1822326-1932463	Weak transcription Enhancers Bivalent Enhancer Flanking Active TSS Bivalent/Poised TSS Genic enhancers Strong transcription Flanking Bivalent TSS/Enh Active TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	16 gene(s)	inside rSNPs	diseases
8	nsv596892	chr5:1832240-1892759	Enhancers Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Active TSS Weak transcription Flanking Active TSS ZNF genes & repeats Strong transcription Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	13 gene(s)	inside rSNPs	diseases
9	nsv1019713	chr5:1833072-1884738	Bivalent Enhancer Weak transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS Enhancers Genic enhancers Active TSS Flanking Active TSS ZNF genes & repeats Strong transcription Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	13 gene(s)	inside rSNPs	diseases
10	nsv596893	chr5:1839498-1892759	Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS Active TSS Enhancers Weak transcription Genic enhancers Flanking Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	13 gene(s)	inside rSNPs	diseases
11	nsv1018082	chr5:1849721-1884738	Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS Enhancers ZNF genes & repeats Weak transcription Active TSS Flanking Active TSS Transcr. at gene 5' and 3' Genic enhancers Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	12 gene(s)	inside rSNPs	diseases
12	nsv881470	chr5:1850563-1892759	Bivalent/Poised TSS Flanking Active TSS Weak transcription Bivalent Enhancer Enhancers Flanking Bivalent TSS/Enh Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Strong transcription Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	12 gene(s)	inside rSNPs	diseases
13	nsv881188	chr5:1852284-1892759	Flanking Bivalent TSS/Enh Weak transcription Bivalent Enhancer Bivalent/Poised TSS Enhancers Active TSS Flanking Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Strong transcription Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	12 gene(s)	inside rSNPs	diseases
14	nsv822961	chr5:1877184-1877830	Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Weak transcription Strong transcription Enhancers	Chromatin interactive region	3 gene(s)	inside rSNPs	diseases

Variant related diseases (count:1)

Disease	PMID	Source
Cardiovascular disease risk factors	21779381	GWAS catalog

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs4975709	IRX4	cis	parietal	SCAN
rs4975709	NKD2	cis	cerebellum	SCAN

Chromatin state (count:25 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:1874400-1877400	Bivalent Enhancer	Primary B cells from peripheral blood	blood
2	chr5:1874800-1877400	Bivalent/Poised TSS	ES-I3 Cell Line	embryonic stem cell
3	chr5:1875200-1877400	Bivalent/Poised TSS	iPS-15b Cell Line	embryonic stem cell
4	chr5:1875800-1877400	Bivalent Enhancer	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
5	chr5:1876400-1877400	Bivalent Enhancer	Fetal Muscle Leg	muscle
6	chr5:1876600-1877800	Weak transcription	Right Ventricle	heart
7	chr5:1876600-1878400	ZNF genes & repeats	Foreskin Keratinocyte Primary Cells skin03	Skin
8	chr5:1876600-1882400	Weak transcription	Right Atrium	heart
9	chr5:1876800-1878800	Bivalent Enhancer	Foreskin Melanocyte Primary Cells skin03	Skin
10	chr5:1877000-1878000	Bivalent Enhancer	HUES48 Cell Line	embryonic stem cell
11	chr5:1877000-1880800	Strong transcription	NHEK	skin
12	chr5:1877200-1877400	Bivalent/Poised TSS	ES-WA7 Cell Line	embryonic stem cell
13	chr5:1877200-1877400	Flanking Bivalent TSS/Enh	HUES6 Cell Line	embryonic stem cell
14	chr5:1877200-1877400	Bivalent/Poised TSS	iPS-18 Cell Line	embryonic stem cell
15	chr5:1877200-1877600	Bivalent Enhancer	H9 Cell Line	embryonic stem cell
16	chr5:1877200-1877600	Bivalent Enhancer	HUES64 Cell Line	embryonic stem cell
17	chr5:1877200-1877800	Bivalent Enhancer	iPS-20b Cell Line	embryonic stem cell
18	chr5:1877200-1877800	Bivalent Enhancer	Primary T helper naive cells fromperipheralblood	blood
19	chr5:1877200-1877800	Bivalent Enhancer	Fetal Heart	heart
20	chr5:1877200-1878400	Bivalent Enhancer	iPS DF 19.11 Cell Line	embryonic stem cell
21	chr5:1877200-1880600	Strong transcription	Breast Myoepithelial Primary Cells	Breast
22	chr5:1877200-1881200	Strong transcription	HMEC	breast
23	chr5:1877200-1881600	Bivalent Enhancer	ES-UCSF4 Cell Line	embryonic stem cell
24	chr5:1877200-1881600	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
25	chr5:1877200-1881600	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin

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