Variant report

Variant	rs3862143
Chromosome Location	chr15:44071480-44071481
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:1)
CpG islands
(count:0)
Chromatin interactive
region (count:5)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:1 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	RUNX3	chr15:44071184-44071561	GM12878	blood:	n/a	n/a

No data

(count:5 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr15:44066200..44071612-chr15:44082403..44086035,7	K562	blood:
2	chr15:44067716..44069540-chr15:44069766..44073252,3	MCF-7	breast:
3	chr15:44065408..44074556-chr15:44080543..44088380,28	MCF-7	breast:
4	chr15:44062113..44074982-chr15:44088756..44097846,29	MCF-7	breast:
5	chr15:44065227..44073214-chr15:44081584..44094479,46	MCF-7	breast:

No data

Variant related genes	Relation type
ELL3	TF binding region
ENSG00000242028	Chromatin interaction
ENSG00000128886	Chromatin interaction
ENSG00000184716	Chromatin interaction
ENSG00000140264	Chromatin interaction
ENSG00000221792	Chromatin interaction

Extended variants
information (count: 44 )
Associated
traits (count: 6 )

rSNPs within LD-proxies of this variant (count:34)

rs_ID	r²[population]
rs10163069	1.00[CEU][hapmap];0.84[GIH][hapmap];0.84[LWK][hapmap];0.90[TSI][hapmap];0.92[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs11070411	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[GIH][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.93[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs12443084	1.00[CEU][hapmap];1.00[GIH][hapmap];0.85[LWK][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.87[EUR][1000 genomes]
rs17727853	1.00[CEU][hapmap]
rs17795279	1.00[CEU][hapmap];1.00[MEX][hapmap];0.96[TSI][hapmap]
rs2412821	1.00[CEU][hapmap];0.82[EUR][1000 genomes]
rs2729494	1.00[CEU][hapmap];0.96[YRI][hapmap];0.88[EUR][1000 genomes]
rs28410121	1.00[CEU][hapmap];1.00[GIH][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.85[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs2918943	0.96[YRI][hapmap]
rs2918947	0.81[EUR][1000 genomes]
rs2930529	0.92[EUR][1000 genomes]
rs2930530	1.00[CEU][hapmap];1.00[GIH][hapmap];1.00[MEX][hapmap];0.84[MKK][hapmap];0.93[TSI][hapmap];0.81[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs2930531	1.00[CEU][hapmap];0.96[GIH][hapmap];0.95[LWK][hapmap];1.00[MEX][hapmap];0.96[MKK][hapmap];0.93[TSI][hapmap];0.96[YRI][hapmap];0.81[AFR][1000 genomes];0.88[EUR][1000 genomes]
rs3102448	0.86[EUR][1000 genomes]
rs3110081	0.84[EUR][1000 genomes]
rs35822148	0.87[EUR][1000 genomes]
rs3986209	0.97[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs4644832	1.00[CEU][hapmap];1.00[YRI][hapmap];0.95[AFR][1000 genomes];0.92[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs4923964	1.00[CEU][hapmap];0.90[EUR][1000 genomes]
rs4923965	1.00[CEU][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];0.89[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs495880	0.94[CEU][hapmap];1.00[GIH][hapmap];0.95[LWK][hapmap];1.00[MEX][hapmap];0.96[MKK][hapmap];0.93[TSI][hapmap];0.96[YRI][hapmap];0.87[EUR][1000 genomes]
rs514311	0.94[CEU][hapmap];0.95[YRI][hapmap];0.82[EUR][1000 genomes]
rs528764	1.00[CEU][hapmap];0.95[YRI][hapmap];0.88[EUR][1000 genomes]
rs541871	0.94[CEU][hapmap];0.96[YRI][hapmap];0.82[EUR][1000 genomes]
rs62018940	0.93[AFR][1000 genomes];0.89[EUR][1000 genomes]
rs62018944	0.87[EUR][1000 genomes]
rs6493090	0.93[ASW][hapmap];1.00[CEU][hapmap];1.00[GIH][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.94[MKK][hapmap];0.96[TSI][hapmap];1.00[YRI][hapmap];0.93[AFR][1000 genomes];0.87[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs654276	0.94[CEU][hapmap];0.83[GIH][hapmap];0.85[MEX][hapmap];0.82[TSI][hapmap];0.83[YRI][hapmap];0.89[EUR][1000 genomes]
rs678084	1.00[CEU][hapmap];1.00[GIH][hapmap];0.93[LWK][hapmap];1.00[MEX][hapmap];0.94[MKK][hapmap];0.93[TSI][hapmap];0.96[YRI][hapmap];0.81[AFR][1000 genomes];0.88[EUR][1000 genomes]
rs7174241	0.84[GIH][hapmap]
rs7174260	1.00[CEU][hapmap];0.81[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs7178230	1.00[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs8030536	1.00[CEU][hapmap];1.00[MEX][hapmap];0.96[TSI][hapmap]
rs8038068	1.00[CEU][hapmap];1.00[MEX][hapmap];0.96[TSI][hapmap]

Variant overlapped rSNPs/rCNVs (count:10 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv1846172	chr15:43632138-44116986	Bivalent Enhancer Weak transcription Genic enhancers Strong transcription Active TSS Enhancers Flanking Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	101 gene(s)	inside rSNPs	diseases
2	esv1846701	chr15:43759774-44116986	Strong transcription Weak transcription Active TSS Flanking Active TSS Enhancers Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	90 gene(s)	inside rSNPs	diseases
3	esv2758379	chr15:43823158-44148641	Strong transcription Enhancers Weak transcription Transcr. at gene 5' and 3' Flanking Active TSS Active TSS Bivalent/Poised TSS Genic enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	84 gene(s)	inside rSNPs	diseases
4	esv2760028	chr15:43823158-44148641	Genic enhancers Enhancers Active TSS Transcr. at gene 5' and 3' Weak transcription Strong transcription Flanking Active TSS ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	84 gene(s)	inside rSNPs	diseases
5	nsv427960	chr15:43823158-44148641	Flanking Active TSS Active TSS Strong transcription Weak transcription Transcr. at gene 5' and 3' ZNF genes & repeats Enhancers Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	84 gene(s)	inside rSNPs	diseases
6	nsv1037786	chr15:43888926-44318587	Weak transcription Flanking Active TSS Strong transcription Transcr. at gene 5' and 3' Enhancers Active TSS Genic enhancers Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	90 gene(s)	inside rSNPs	diseases
7	nsv542370	chr15:43888926-44318587	Weak transcription Genic enhancers Flanking Active TSS Active TSS Enhancers Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	90 gene(s)	inside rSNPs	diseases
8	nsv431387	chr15:43929378-44862930	Weak transcription Strong transcription Active TSS ZNF genes & repeats Enhancers Flanking Active TSS Bivalent/Poised TSS Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	158 gene(s)	inside rSNPs	diseases
9	nsv931051	chr15:43988761-44833518	Strong transcription Enhancers Weak transcription Active TSS Flanking Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Genic enhancers Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	154 gene(s)	inside rSNPs	diseases
10	nsv1036318	chr15:44053617-44160773	Flanking Active TSS Strong transcription Genic enhancers Enhancers Weak transcription Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	68 gene(s)	inside rSNPs	diseases

mRNA abundance (count:6)

SNP	Gene	Cis/trans	Tissue	Source
rs3862143	TUBGCP4	cis	parietal	SCAN
rs3862143	WDR76	cis	parietal	SCAN
rs3862143	ZSCAN29	cis	lymphoblastoid	seeQTL
rs3862143	MAPKBP1	cis	parietal	SCAN
rs3862143	TGM5	cis	lymphoblastoid	seeQTL
rs3862143	ZSCAN29	cis	multi-tissue	Pritchard

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:44068800-44073200	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
2	chr15:44070000-44072800	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
3	chr15:44070200-44071600	Enhancers	Primary T helper cells fromperipheralblood	blood
4	chr15:44070200-44072800	Weak transcription	K562	blood
5	chr15:44070200-44083800	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
6	chr15:44070200-44083800	Weak transcription	Cortex derived primary cultured neurospheres	brain
7	chr15:44070200-44083800	Weak transcription	Rectal Smooth Muscle	rectum
8	chr15:44070200-44083800	Weak transcription	NHDF-Ad	bronchial
9	chr15:44070200-44083800	Weak transcription	NHEK	skin
10	chr15:44070600-44071600	Enhancers	Dnd41	blood
11	chr15:44070600-44083600	Weak transcription	Primary hematopoietic stem cells short term culture	blood
12	chr15:44070600-44083800	Weak transcription	Rectal Mucosa Donor 29	rectum
13	chr15:44070800-44071600	Enhancers	Hela-S3	cervix
14	chr15:44070800-44071800	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
15	chr15:44070800-44072800	Weak transcription	Fetal Intestine Large	intestine
16	chr15:44070800-44074800	Weak transcription	Primary B cells from peripheral blood	blood
17	chr15:44070800-44083600	Weak transcription	Primary T cells fromperipheralblood	blood
18	chr15:44071200-44071600	Enhancers	GM12878-XiMat	blood

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