Variant report

Variant	rs479409
Chromosome Location	chr4:75057096-75057097
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	FOXA2	chr4:75056526-75057439	HepG2	liver:	n/a	n/a
2	MYBL2	chr4:75056627-75057210	HepG2	liver:	n/a	n/a
3	FOXA1	chr4:75056736-75057326	HepG2	liver:	n/a	chr4:75057037-75057052
4	CEBPZ	chr4:75056955-75057155	HepG2	liver:	n/a	n/a
5	NR2F2	chr4:75056814-75057234	HepG2	liver:	n/a	n/a
6	FOXA2	chr4:75056771-75057176	HepG2	liver:	n/a	n/a
7	SP1	chr4:75056800-75057217	HepG2	liver:	n/a	n/a
8	ARID3A	chr4:75056779-75057213	HepG2	liver:	n/a	n/a
9	FOSL2	chr4:75056718-75057108	HepG2	liver:	n/a	n/a
10	EP300	chr4:75056735-75057245	HepG2	liver:	n/a	n/a
11	FOXA1	chr4:75056673-75057225	HepG2	liver:	n/a	chr4:75057037-75057052
12	FOXA1	chr4:75056729-75057228	HepG2	liver:	n/a	chr4:75057037-75057052
13	BHLHE40	chr4:75056850-75057158	HepG2	liver:	n/a	n/a
14	FOXA1	chr4:75056623-75057262	HepG2	liver:	n/a	chr4:75057037-75057052
15	EP300	chr4:75056791-75057124	HepG2	liver:	n/a	n/a
16	HNF4A	chr4:75056848-75057122	HepG2	liver:	n/a	chr4:75057042-75057057 chr4:75057043-75057057 chr4:75057042-75057057 chr4:75057043-75057051 chr4:75057044-75057056 chr4:75057041-75057059 chr4:75057043-75057056 chr4:75057042-75057057 chr4:75057042-75057057 chr4:75057044-75057056 chr4:75057044-75057056 chr4:75057042-75057057
17	MBD4	chr4:75056667-75057215	HepG2	liver:	n/a	n/a
18	FOXA2	chr4:75056775-75057217	A549	lung:	n/a	n/a
19	EP300	chr4:75056938-75057107	HepG2	liver:	n/a	n/a
20	HNF4A	chr4:75056772-75057171	HepG2	liver:	n/a	chr4:75057042-75057057 chr4:75057043-75057057 chr4:75057042-75057057 chr4:75057043-75057051 chr4:75057044-75057056 chr4:75057041-75057059 chr4:75057043-75057056 chr4:75057042-75057057 chr4:75057042-75057057 chr4:75057044-75057056 chr4:75057044-75057056 chr4:75057042-75057057
21	NFIC	chr4:75056727-75057294	HepG2	liver:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr4:75055396..75057559-chr4:75092904..75094536,2	K562	blood:
2	chr4:75055610..75058145-chr4:75064035..75065745,2	K562	blood:
3	chr4:75023556..75025318-chr4:75054789..75057123,2	MCF-7	breast:
4	chr4:75055479..75057780-chr4:75061856..75063799,2	K562	blood:

Variant related genes	Relation type
MTHFD2L	TF binding region
ENSG00000163738	Chromatin interaction
ENSG00000269559	Chromatin interaction

Extended variants
information (count: 38 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:30)

rs_ID	r²[population]
rs10026869	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10028397	1.00[JPT][hapmap];0.81[EUR][1000 genomes]
rs10938111	0.81[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs12163831	1.00[CEU][hapmap];0.94[EUR][1000 genomes]
rs12646785	1.00[CEU][hapmap];0.91[CHB][hapmap];0.88[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs1265346	0.84[AFR][1000 genomes];0.97[AMR][1000 genomes];0.89[ASN][1000 genomes]
rs13116686	0.88[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs13136363	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.97[ASN][1000 genomes]
rs1440407	1.00[CEU][hapmap];0.91[CHB][hapmap];0.88[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs16850531	1.00[CEU][hapmap];0.94[EUR][1000 genomes]
rs16850541	0.94[EUR][1000 genomes]
rs2289443	1.00[CEU][hapmap]
rs28823933	0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4694183	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs510884	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.80[YRI][hapmap];0.86[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs518475	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[YRI][hapmap];0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs519014	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[YRI][hapmap];0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];0.94[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs533352	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs535753	1.00[JPT][hapmap];0.90[AMR][1000 genomes];0.87[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs537061	1.00[CEU][hapmap];0.91[CHB][hapmap];1.00[YRI][hapmap];0.89[AFR][1000 genomes];1.00[AMR][1000 genomes];0.94[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs538542	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs538775	1.00[CEU][hapmap];0.83[CHB][hapmap];0.83[EUR][1000 genomes]
rs547975	1.00[CEU][hapmap];0.92[CHB][hapmap];1.00[YRI][hapmap];0.85[AFR][1000 genomes];1.00[AMR][1000 genomes];0.94[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs551906	1.00[CEU][hapmap];0.91[CHB][hapmap];1.00[YRI][hapmap];0.88[AFR][1000 genomes];1.00[AMR][1000 genomes];0.94[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs564793	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.89[AFR][1000 genomes];1.00[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6446975	0.91[CHB][hapmap];0.86[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs6446976	1.00[CEU][hapmap];0.91[CHB][hapmap];0.88[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs6824352	1.00[CEU][hapmap];0.90[CHB][hapmap];1.00[JPT][hapmap];0.96[ASN][1000 genomes]
rs977597	0.88[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs977598	1.00[CEU][hapmap];0.92[CHB][hapmap];0.88[EUR][1000 genomes];0.92[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:8 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv525980	chr4:74731526-75382209	Strong transcription Weak transcription Enhancers Bivalent/Poised TSS Flanking Active TSS Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	40 gene(s)	inside rSNPs	diseases
2	nsv1004768	chr4:74774372-75109579	Weak transcription Enhancers Active TSS Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Strong transcription ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	25 gene(s)	inside rSNPs	diseases
3	nsv1006218	chr4:74782324-75105424	Enhancers Weak transcription Flanking Active TSS Active TSS Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh Strong transcription Transcr. at gene 5' and 3' ZNF genes & repeats Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	25 gene(s)	inside rSNPs	diseases
4	nsv594683	chr4:75013441-75106485	Enhancers Active TSS Weak transcription Strong transcription Flanking Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Genic enhancers Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	14 gene(s)	inside rSNPs	diseases
5	nsv1013260	chr4:75013441-75121643	Weak transcription Active TSS Enhancers Strong transcription Flanking Active TSS ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	14 gene(s)	inside rSNPs	diseases
6	nsv1002907	chr4:75013441-75131443	Weak transcription Enhancers Flanking Active TSS Active TSS Strong transcription ZNF genes & repeats Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	14 gene(s)	inside rSNPs	diseases
7	nsv1004706	chr4:75014770-75121643	Enhancers Weak transcription Genic enhancers Flanking Active TSS Strong transcription Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	14 gene(s)	inside rSNPs	diseases
8	nsv594684	chr4:75015750-75106485	Weak transcription Enhancers Strong transcription ZNF genes & repeats Flanking Active TSS Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	14 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:22 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:75024800-75080600	Weak transcription	Left Ventricle	heart
2	chr4:75025400-75067600	Weak transcription	Brain Inferior Temporal Lobe	brain
3	chr4:75025400-75073600	Weak transcription	Right Ventricle	heart
4	chr4:75025600-75067600	Weak transcription	Thymus	Thymus
5	chr4:75028200-75067600	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
6	chr4:75028800-75072800	Weak transcription	Liver	Liver
7	chr4:75034200-75071800	Weak transcription	HMEC	breast
8	chr4:75041200-75067000	Weak transcription	Primary T cells from cord blood	blood
9	chr4:75042600-75067400	Weak transcription	Fetal Thymus	thymus
10	chr4:75048400-75058800	Weak transcription	Breast Myoepithelial Primary Cells	Breast
11	chr4:75048600-75060800	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
12	chr4:75048600-75066600	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
13	chr4:75049400-75071400	Weak transcription	Primary hematopoietic stem cells	blood
14	chr4:75050200-75065400	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
15	chr4:75053200-75073400	Weak transcription	iPS-20b Cell Line	embryonic stem cell
16	chr4:75055200-75057800	Enhancers	HepG2	liver
17	chr4:75056200-75057600	Enhancers	Stomach Mucosa	stomach
18	chr4:75056600-75057600	Enhancers	Pancreas	Pancrea
19	chr4:75056600-75067000	Weak transcription	NHEK	skin
20	chr4:75056600-75067400	Weak transcription	Brain Hippocampus Middle	brain
21	chr4:75056800-75096600	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
22	chr4:75057000-75067600	Weak transcription	A549	lung

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