Variant report

Variant	rs12443084
Chromosome Location	chr15:44040965-44040966
allele	G/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	HCFC1	chr15:44040527-44041060	Hela-S3	cervix:	n/a	n/a
2	HCFC1	chr15:44040602-44040967	K562	blood:	n/a	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr15:44040936..44043692-chr15:44068997..44071077,2	K562	blood:
2	chr15:44038791..44041212-chr15:44089540..44091517,2	MCF-7	breast:

Variant related genes	Relation type
CATSPER2P1	TF binding region
ENSG00000184716	Chromatin interaction
ENSG00000128886	Chromatin interaction
ENSG00000140264	Chromatin interaction

Extended variants
information (count: 45 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:32)

rs_ID	r²[population]
rs10163069	1.00[ASW][hapmap];1.00[CEU][hapmap];0.84[GIH][hapmap];0.98[LWK][hapmap];0.93[MKK][hapmap];0.90[TSI][hapmap];0.85[YRI][hapmap];0.82[AFR][1000 genomes];0.89[EUR][1000 genomes]
rs11070411	1.00[CEU][hapmap];1.00[GIH][hapmap];0.85[LWK][hapmap];1.00[MEX][hapmap];0.82[MKK][hapmap];1.00[TSI][hapmap];0.88[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]
rs2729494	1.00[CEU][hapmap];0.81[EUR][1000 genomes]
rs28410121	1.00[CEU][hapmap];1.00[GIH][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.88[EUR][1000 genomes]
rs2930529	0.84[EUR][1000 genomes]
rs2930530	0.81[ASW][hapmap];1.00[CEU][hapmap];1.00[GIH][hapmap];0.95[LWK][hapmap];1.00[MEX][hapmap];0.90[MKK][hapmap];0.90[TSI][hapmap];0.96[YRI][hapmap];0.84[EUR][1000 genomes]
rs2930531	1.00[CEU][hapmap];0.96[GIH][hapmap];0.81[LWK][hapmap];1.00[MEX][hapmap];0.90[TSI][hapmap];0.81[EUR][1000 genomes]
rs3102448	0.80[EUR][1000 genomes]
rs3110081	0.82[EUR][1000 genomes]
rs3844075	1.00[YRI][hapmap]
rs3862143	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]
rs3986209	0.89[EUR][1000 genomes]
rs4644832	1.00[CEU][hapmap];0.86[EUR][1000 genomes]
rs4923964	1.00[CEU][hapmap];0.88[EUR][1000 genomes]
rs4923965	1.00[CEU][hapmap];0.86[EUR][1000 genomes]
rs495880	0.94[CEU][hapmap];1.00[GIH][hapmap];0.81[LWK][hapmap];1.00[MEX][hapmap];0.90[TSI][hapmap];0.84[EUR][1000 genomes]
rs514311	0.94[CEU][hapmap]
rs528764	1.00[CEU][hapmap];0.81[EUR][1000 genomes]
rs541871	0.94[CEU][hapmap]
rs62018940	0.86[EUR][1000 genomes]
rs62018944	0.84[EUR][1000 genomes]
rs6493090	1.00[CEU][hapmap];1.00[GIH][hapmap];0.85[LWK][hapmap];1.00[MEX][hapmap];0.96[TSI][hapmap];0.84[EUR][1000 genomes]
rs654276	0.94[CEU][hapmap];0.83[GIH][hapmap];0.85[MEX][hapmap]
rs678084	1.00[CEU][hapmap];1.00[GIH][hapmap];1.00[MEX][hapmap];0.90[TSI][hapmap];0.81[EUR][1000 genomes]
rs7174241	0.84[GIH][hapmap]
rs7174260	1.00[CEU][hapmap];0.87[EUR][1000 genomes]
rs7178230	0.89[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:13 , 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	esv2757598	chr15:43831923-44058634	Enhancers Weak transcription Flanking Active TSS Active TSS Strong transcription ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	31 gene(s)	inside rSNPs	diseases
7	nsv904150	chr15:43836478-44040965	Flanking Active TSS Enhancers Weak transcription Active TSS Strong transcription ZNF genes & repeats Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	31 gene(s)	inside rSNPs	diseases
8	nsv904158	chr15:43852043-44053617	Strong transcription Flanking Active TSS Active TSS Enhancers Weak transcription ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	31 gene(s)	inside rSNPs	diseases
9	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
10	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
11	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
12	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
13	esv33661	chr15:44016519-44064420	Weak transcription Enhancers Strong transcription Flanking Active TSS Active TSS Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	19 gene(s)	inside rSNPs	diseases

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs12443084	TUBGCP4	cis	parietal	SCAN
rs12443084	WDR76	cis	parietal	SCAN
rs12443084	ZSCAN29	cis	multi-tissue	Pritchard
rs12443084	MAPKBP1	cis	parietal	SCAN

Chromatin state (count:127 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:44037800-44041000	Active TSS	HUES6 Cell Line	embryonic stem cell
2	chr15:44037800-44041000	Active TSS	Brain Dorsolateral Prefrontal Cortex	brain
3	chr15:44037800-44041200	Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
4	chr15:44037800-44041800	Active TSS	Breast Myoepithelial Primary Cells	Breast
5	chr15:44037800-44042000	Active TSS	Colonic Mucosa	Colon
6	chr15:44037800-44042200	Active TSS	Foreskin Keratinocyte Primary Cells skin02	Skin
7	chr15:44038000-44041000	Active TSS	HUES48 Cell Line	embryonic stem cell
8	chr15:44038000-44041000	Active TSS	HUES64 Cell Line	embryonic stem cell
9	chr15:44038000-44041000	Active TSS	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
10	chr15:44038000-44041800	Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
11	chr15:44038000-44042000	Active TSS	NHLF	lung
12	chr15:44038200-44041400	Active TSS	Foreskin Keratinocyte Primary Cells skin03	Skin
13	chr15:44038200-44041600	Active TSS	GM12878-XiMat	blood
14	chr15:44038800-44041000	Active TSS	Right Atrium	heart
15	chr15:44039200-44049400	Weak transcription	Spleen	Spleen
16	chr15:44039600-44041400	Weak transcription	Fetal Muscle Trunk	muscle
17	chr15:44039600-44041800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
18	chr15:44039600-44041800	Weak transcription	Gastric	stomach
19	chr15:44039600-44041800	Weak transcription	Lung	lung
20	chr15:44039600-44052000	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
21	chr15:44039600-44055400	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
22	chr15:44039800-44041200	Enhancers	Colon Smooth Muscle	Colon
23	chr15:44039800-44041800	Enhancers	Primary B cells from peripheral blood	blood
24	chr15:44039800-44042200	Enhancers	Primary monocytes fromperipheralblood	blood
25	chr15:44039800-44048800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
26	chr15:44040000-44041000	Flanking Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
27	chr15:44040000-44041000	Flanking Active TSS	Primary T cells from cord blood	blood
28	chr15:44040000-44041000	Flanking Active TSS	Dnd41	blood
29	chr15:44040000-44041200	Flanking Active TSS	Primary T helper cells PMA-I stimulated	--
30	chr15:44040000-44041200	Flanking Active TSS	Liver	Liver
31	chr15:44040000-44041800	Enhancers	Primary T cells fromperipheralblood	blood
32	chr15:44040000-44041800	Enhancers	Brain Cingulate Gyrus	brain
33	chr15:44040200-44041000	Enhancers	Rectal Mucosa Donor 31	rectum
34	chr15:44040200-44041000	Flanking Active TSS	Hela-S3	cervix
35	chr15:44040200-44041000	Flanking Active TSS	HepG2	liver
36	chr15:44040200-44041000	Flanking Active TSS	HUVEC	blood vessel
37	chr15:44040200-44041200	Enhancers	Fetal Heart	heart
38	chr15:44040200-44041400	Weak transcription	Aorta	Aorta
39	chr15:44040200-44041600	Weak transcription	Skeletal Muscle Male	skeletal muscle
40	chr15:44040200-44041800	Weak transcription	Primary neutrophils fromperipheralblood	blood
41	chr15:44040200-44041800	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
42	chr15:44040200-44041800	Weak transcription	Fetal Lung	lung
43	chr15:44040200-44041800	Weak transcription	Right Ventricle	heart
44	chr15:44040200-44042000	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
45	chr15:44040200-44043600	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
46	chr15:44040200-44048200	Weak transcription	Fetal Kidney	kidney
47	chr15:44040200-44049200	Weak transcription	Esophagus	oesophagus
48	chr15:44040200-44056000	Weak transcription	ES-I3 Cell Line	embryonic stem cell
49	chr15:44040200-44062000	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
50	chr15:44040400-44041000	Flanking Active TSS	Primary T helper 17 cells PMA-I stimulated	--

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