Variant report

Variant	rs3864130
Chromosome Location	chr4:646409-646410
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr4:644054..646414-chr4:656838..659721,2	MCF-7	breast:
2	chr4:644162..647846-chr4:649268..652076,4	MCF-7	breast:

Variant related genes	Relation type
ENSG00000242686	Chromatin interaction
ENSG00000133256	Chromatin interaction

Extended variants
information (count: 53 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:37)

rs_ID	r²[population]
rs10023472	0.81[MKK][hapmap]
rs10027549	1.00[ASN][1000 genomes]
rs10027866	0.82[TSI][hapmap];0.84[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs10030136	1.00[ASN][1000 genomes]
rs1135375	0.93[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13119162	0.81[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs28374488	0.87[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs28438498	0.82[TSI][hapmap];0.84[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs28470912	1.00[CHD][hapmap];0.80[MEX][hapmap];1.00[ASN][1000 genomes]
rs28483373	1.00[ASN][1000 genomes]
rs28488910	1.00[ASN][1000 genomes]
rs28525003	1.00[ASN][1000 genomes]
rs28568555	0.80[AMR][1000 genomes];0.84[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28569875	0.81[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs28573204	1.00[ASN][1000 genomes]
rs28583078	1.00[CHD][hapmap];0.88[TSI][hapmap];0.81[AMR][1000 genomes];0.84[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28586910	0.88[EUR][1000 genomes]
rs28588872	0.87[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs28600205	0.81[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs28630797	0.86[AMR][1000 genomes];0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28742266	1.00[ASN][1000 genomes]
rs28742899	1.00[CHD][hapmap];0.84[GIH][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.88[AMR][1000 genomes];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3864131	1.00[ASN][1000 genomes]
rs3891250	1.00[CHD][hapmap];0.91[MEX][hapmap];0.88[TSI][hapmap];0.84[AMR][1000 genomes];0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3934459	0.89[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs4463020	1.00[CHD][hapmap];0.80[MEX][hapmap];1.00[ASN][1000 genomes]
rs4505760	0.82[TSI][hapmap];0.89[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs4518182	1.00[ASN][1000 genomes]
rs58227539	1.00[ASN][1000 genomes]
rs60316402	0.82[AMR][1000 genomes];0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs67030464	0.83[EUR][1000 genomes]
rs71602496	0.80[AMR][1000 genomes];0.84[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73056602	1.00[ASN][1000 genomes]
rs73058406	1.00[ASN][1000 genomes]
rs7436737	1.00[CHD][hapmap];1.00[ASN][1000 genomes]
rs9991613	1.00[CHD][hapmap];0.91[MEX][hapmap];1.00[ASN][1000 genomes]
rs9992641	0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:16 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1011715	chr4:43860-823487	Active TSS Weak transcription Bivalent Enhancer Bivalent/Poised TSS Strong transcription Enhancers Flanking Active TSS ZNF genes & repeats Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	76 gene(s)	inside rSNPs	diseases
2	esv2830422	chr4:72247-681939	Flanking Active TSS Enhancers Strong transcription Weak transcription ZNF genes & repeats Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	54 gene(s)	inside rSNPs	diseases
3	nsv931097	chr4:72447-683874	Strong transcription Active TSS Enhancers Genic enhancers Flanking Active TSS ZNF genes & repeats Weak transcription Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	54 gene(s)	inside rSNPs	diseases
4	nsv532702	chr4:72447-755236	Active TSS ZNF genes & repeats Strong transcription Weak transcription Flanking Active TSS Enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	60 gene(s)	inside rSNPs	diseases
5	nsv1005224	chr4:507005-900281	Enhancers Flanking Active TSS ZNF genes & repeats Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer Strong transcription Weak transcription Active TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	41 gene(s)	inside rSNPs	diseases
6	nsv536976	chr4:507005-900281	Weak transcription Enhancers Active TSS ZNF genes & repeats Bivalent Enhancer Flanking Active TSS Strong transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	41 gene(s)	inside rSNPs	diseases
7	nsv878245	chr4:509178-694613	Active TSS Flanking Active TSS Enhancers Strong transcription Weak transcription Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	22 gene(s)	inside rSNPs	diseases
8	nsv822425	chr4:540105-1413799	Weak transcription Flanking Bivalent TSS/Enh Active TSS Flanking Active TSS Enhancers ZNF genes & repeats Strong transcription Bivalent Enhancer Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	108 gene(s)	inside rSNPs	diseases
9	nsv878246	chr4:592507-696848	Flanking Active TSS Weak transcription Active TSS Strong transcription Enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	20 gene(s)	inside rSNPs	diseases
10	esv2757916	chr4:603208-931354	Weak transcription Strong transcription Genic enhancers Enhancers Bivalent Enhancer Bivalent/Poised TSS Flanking Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Active TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	40 gene(s)	inside rSNPs	diseases
11	esv2759217	chr4:603208-931354	Weak transcription Enhancers Strong transcription Active TSS Genic enhancers ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh Flanking Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	40 gene(s)	inside rSNPs	diseases
12	nsv878247	chr4:607202-925149	Bivalent Enhancer Flanking Active TSS Strong transcription Bivalent/Poised TSS Enhancers Active TSS Flanking Bivalent TSS/Enh Genic enhancers Weak transcription Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	38 gene(s)	inside rSNPs	diseases
13	nsv530490	chr4:614355-1399150	Bivalent Enhancer Enhancers Flanking Active TSS Weak transcription Genic enhancers ZNF genes & repeats Strong transcription Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	104 gene(s)	inside rSNPs	diseases
14	nsv593206	chr4:625962-735150	Weak transcription Flanking Active TSS Strong transcription Enhancers Genic enhancers Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	22 gene(s)	inside rSNPs	diseases
15	nsv4194	chr4:635316-657212	Weak transcription Enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Active TSS Bivalent Enhancer Strong transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS Active TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
16	nsv878248	chr4:645300-685993	Weak transcription Transcr. at gene 5' and 3' Flanking Active TSS Enhancers Active TSS Genic enhancers Bivalent Enhancer Strong transcription Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	18 gene(s)	inside rSNPs	diseases

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs3864130	ZNF141	cis	cerebellum	SCAN
rs3864130	MYOZ3	trans	parietal	SCAN
rs3864130	POLN	cis	parietal	SCAN
rs3864130	ZNF721	cis	parietal	SCAN

Chromatin state (count:18 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:631400-657000	Weak transcription	Right Atrium	heart
2	chr4:640400-648400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
3	chr4:641800-657000	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
4	chr4:642200-652800	Weak transcription	iPS-15b Cell Line	embryonic stem cell
5	chr4:642400-654600	ZNF genes & repeats	Foreskin Melanocyte Primary Cells skin01	Skin
6	chr4:642800-657000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
7	chr4:643000-657000	Weak transcription	HUES6 Cell Line	embryonic stem cell
8	chr4:643200-648200	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
9	chr4:645000-648200	Weak transcription	Esophagus	oesophagus
10	chr4:645200-646600	Active TSS	Brain Substantia Nigra	brain
11	chr4:645600-647000	Flanking Active TSS	Brain Anterior Caudate	brain
12	chr4:645800-646600	Active TSS	Brain Angular Gyrus	brain
13	chr4:645800-646800	Active TSS	Brain Cingulate Gyrus	brain
14	chr4:645800-649400	Weak transcription	Pancreas	Pancrea
15	chr4:645800-656800	Weak transcription	Gastric	stomach
16	chr4:646000-648400	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
17	chr4:646400-646800	Enhancers	Brain Inferior Temporal Lobe	brain
18	chr4:646400-647200	Enhancers	Brain Hippocampus Middle	brain

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