Variant report

Variant	rs1106934
Chromosome Location	chr15:42072623-42072624
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	chr15:42061280..42063508-chr15:42070993..42072761,2	K562	blood:
2	chr15:42064976..42070217-chr15:42070811..42075517,5	K562	blood:

Variant related genes	Relation type
ENSG00000137802	Chromatin interaction

Extended variants
information (count: 65 )
Associated
traits (count: 5 )

rSNPs within LD-proxies of this variant (count:55)

rs_ID	r²[population]
rs1043627	0.93[CEU][hapmap];1.00[CHB][hapmap];0.91[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.89[TSI][hapmap];0.91[ASN][1000 genomes]
rs11070346	0.87[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs11070349	0.95[CHB][hapmap];0.88[CHD][hapmap];0.94[JPT][hapmap];0.90[ASN][1000 genomes]
rs11547012	0.95[CHB][hapmap];0.94[JPT][hapmap];0.84[ASN][1000 genomes]
rs11630242	0.88[ASN][1000 genomes]
rs11853665	0.88[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs11858843	1.00[CHB][hapmap];0.93[JPT][hapmap];0.91[ASN][1000 genomes]
rs1197659	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.94[JPT][hapmap];0.94[MEX][hapmap];1.00[TSI][hapmap];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1197662	0.80[CHB][hapmap];0.86[JPT][hapmap]
rs1197668	0.95[CHB][hapmap];0.94[JPT][hapmap]
rs1197687	0.93[CEU][hapmap];1.00[CHB][hapmap];0.94[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.94[MEX][hapmap];0.94[TSI][hapmap];0.88[AMR][1000 genomes];0.92[ASN][1000 genomes]
rs1197688	0.93[CEU][hapmap];0.95[CHB][hapmap];0.91[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.94[MEX][hapmap];0.94[TSI][hapmap];0.88[AMR][1000 genomes];0.90[ASN][1000 genomes]
rs1197689	0.95[CHB][hapmap];0.94[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.83[MEX][hapmap];0.89[TSI][hapmap];0.91[AMR][1000 genomes];0.93[ASN][1000 genomes]
rs1197690	0.93[CEU][hapmap];0.90[CHB][hapmap];0.94[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.94[TSI][hapmap];0.93[AMR][1000 genomes];0.86[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1197770	0.85[AMR][1000 genomes];0.98[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs1197773	0.93[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[AMR][1000 genomes];0.91[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1206842	0.85[CEU][hapmap];1.00[CHB][hapmap];0.91[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.94[MEX][hapmap];1.00[TSI][hapmap];0.90[AMR][1000 genomes];0.93[ASN][1000 genomes]
rs1209333	0.91[AMR][1000 genomes];0.88[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12439771	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.94[JPT][hapmap];0.94[MEX][hapmap];0.94[TSI][hapmap];0.88[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs12440605	1.00[CHB][hapmap];0.88[CHD][hapmap];0.94[JPT][hapmap];0.91[ASN][1000 genomes]
rs12591285	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.94[JPT][hapmap];0.89[MEX][hapmap];0.94[TSI][hapmap];0.90[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12595271	1.00[CEU][hapmap];1.00[CHB][hapmap];0.94[JPT][hapmap];1.00[YRI][hapmap];0.90[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs12901742	1.00[CEU][hapmap];0.90[CHB][hapmap];0.94[JPT][hapmap];0.88[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs16971915	0.82[ASW][hapmap];1.00[CEU][hapmap];0.90[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.88[JPT][hapmap];0.94[MEX][hapmap];0.94[TSI][hapmap]
rs1726915	0.93[AMR][1000 genomes];0.83[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1918312	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.95[GIH][hapmap];0.94[JPT][hapmap];0.94[MEX][hapmap];0.94[TSI][hapmap];0.87[YRI][hapmap];0.89[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs1918313	1.00[CEU][hapmap];0.95[CHB][hapmap];0.94[CHD][hapmap];1.00[GIH][hapmap];0.94[JPT][hapmap];0.94[MEX][hapmap];0.94[TSI][hapmap];0.87[YRI][hapmap];0.90[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2077361	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.94[JPT][hapmap];0.94[MEX][hapmap];0.94[TSI][hapmap];1.00[YRI][hapmap];0.88[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2077543	0.94[CHB][hapmap];0.93[JPT][hapmap];0.83[ASN][1000 genomes]
rs2241523	0.95[CHB][hapmap];0.94[JPT][hapmap];0.84[ASN][1000 genomes]
rs2412639	0.80[ASN][1000 genomes]
rs2412640	1.00[CHB][hapmap];0.88[CHD][hapmap];0.94[JPT][hapmap];0.88[ASN][1000 genomes]
rs2577949	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.95[GIH][hapmap];0.94[JPT][hapmap];0.94[MEX][hapmap];0.88[MKK][hapmap];0.94[TSI][hapmap];1.00[YRI][hapmap];0.88[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs28671571	0.90[ASN][1000 genomes]
rs2925340	0.93[AMR][1000 genomes];0.81[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs34769385	0.84[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs35033220	0.88[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs35359048	0.90[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs3816533	0.86[CEU][hapmap];0.95[CHB][hapmap];0.91[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];0.89[MEX][hapmap];1.00[TSI][hapmap];0.83[AMR][1000 genomes];0.88[ASN][1000 genomes]
rs4072386	1.00[CEU][hapmap];0.95[CHB][hapmap];0.88[JPT][hapmap]
rs4923906	1.00[CEU][hapmap];0.88[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs4923907	0.82[ASW][hapmap];1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.94[JPT][hapmap];0.94[MEX][hapmap];0.94[TSI][hapmap];0.88[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs4923913	0.93[AMR][1000 genomes];0.83[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4923917	0.95[CHB][hapmap];0.88[CHD][hapmap];0.94[JPT][hapmap];0.86[ASN][1000 genomes]
rs4924573	1.00[CEU][hapmap];1.00[CHB][hapmap];0.94[JPT][hapmap];0.87[YRI][hapmap];0.90[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs57814590	0.85[ASN][1000 genomes]
rs7166139	0.95[CHB][hapmap];0.85[CHD][hapmap];0.94[JPT][hapmap];0.84[ASN][1000 genomes]
rs7168489	0.88[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs7173779	0.92[CEU][hapmap];1.00[CHB][hapmap];0.94[JPT][hapmap];1.00[YRI][hapmap]
rs7174099	0.95[CHB][hapmap];0.94[JPT][hapmap];0.90[ASN][1000 genomes]
rs7175346	0.94[CHB][hapmap];0.94[JPT][hapmap];0.90[ASN][1000 genomes]
rs7177495	0.93[CEU][hapmap];0.90[CHB][hapmap];0.94[JPT][hapmap];1.00[YRI][hapmap];0.84[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs883329	0.82[AMR][1000 genomes];0.81[ASN][1000 genomes]
rs890504	0.84[ASN][1000 genomes]
rs9806709	0.86[EUR][1000 genomes];0.88[ASN][1000 genomes]

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	nsv1049514	chr15:41958482-42081210	Weak transcription Strong transcription Active TSS Enhancers Flanking Active TSS ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	17 gene(s)	inside rSNPs	diseases
2	nsv931223	chr15:41989960-42781757	Enhancers Weak transcription Strong transcription Flanking Active TSS Genic enhancers Bivalent Enhancer Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	81 gene(s)	inside rSNPs	diseases
3	nsv1036086	chr15:42004962-42091451	Strong transcription Weak transcription Flanking Active TSS Active TSS Enhancers Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	15 gene(s)	inside rSNPs	diseases
4	nsv1054671	chr15:42016097-42098896	Flanking Active TSS Enhancers Weak transcription Strong transcription Genic enhancers Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	18 gene(s)	inside rSNPs	diseases
5	nsv1038894	chr15:42038152-42077452	Flanking Active TSS Weak transcription Strong transcription Active TSS Transcr. at gene 5' and 3' Enhancers Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	14 gene(s)	inside rSNPs	diseases
6	esv2757597	chr15:42047173-42122617	Enhancers Weak transcription Strong transcription Transcr. at gene 5' and 3' Flanking Active TSS Genic enhancers Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	25 gene(s)	inside rSNPs	diseases
7	esv2760027	chr15:42047173-42122617	Flanking Active TSS Weak transcription Enhancers Genic enhancers Strong transcription Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	25 gene(s)	inside rSNPs	diseases
8	nsv904113	chr15:42050390-42118971	Genic enhancers Strong transcription Enhancers Flanking Active TSS Weak transcription Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	19 gene(s)	inside rSNPs	diseases
9	nsv904114	chr15:42050390-42119900	Strong transcription Weak transcription Genic enhancers Enhancers Transcr. at gene 5' and 3' Flanking Active TSS Active TSS ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	19 gene(s)	inside rSNPs	diseases
10	nsv427958	chr15:42051317-42301283	Strong transcription Weak transcription Enhancers Active TSS Bivalent Enhancer Genic enhancers Flanking Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	45 gene(s)	inside rSNPs	diseases

mRNA abundance (count:5)

SNP	Gene	Cis/trans	Tissue	Source
rs1106934	ZFYVE19	cis	parietal	SCAN
rs1106934	JMJD7-PLA2G4B	cis	cerebellum	SCAN
rs1106934	NUSAP1	cis	cerebellum	SCAN
rs1106934	EHD4	cis	multi-tissue	Pritchard
rs1106934	VPS18	cis	parietal	SCAN

Chromatin state (count:114 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:42067600-42083000	Weak transcription	Fetal Muscle Trunk	muscle
2	chr15:42068000-42075200	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
3	chr15:42068000-42078800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
4	chr15:42068200-42073600	Enhancers	HepG2	liver
5	chr15:42068200-42082600	Weak transcription	Placenta Amnion	Placenta Amnion
6	chr15:42068400-42072800	Enhancers	Primary T helper naive cells fromperipheralblood	blood
7	chr15:42068400-42073000	Enhancers	Brain Hippocampus Middle	brain
8	chr15:42068400-42073800	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
9	chr15:42068400-42074600	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
10	chr15:42068400-42075200	Weak transcription	Pancreas	Pancrea
11	chr15:42068400-42081800	Weak transcription	Rectal Mucosa Donor 31	rectum
12	chr15:42068600-42073000	Weak transcription	Placenta	Placenta
13	chr15:42068600-42073200	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
14	chr15:42068600-42073800	Weak transcription	Primary monocytes fromperipheralblood	blood
15	chr15:42068600-42073800	Enhancers	Fetal Adrenal Gland	Adrenal Gland
16	chr15:42068600-42081600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
17	chr15:42068800-42072800	Enhancers	Brain Anterior Caudate	brain
18	chr15:42068800-42073200	Enhancers	Colon Smooth Muscle	Colon
19	chr15:42068800-42074400	Weak transcription	Primary B cells from cord blood	blood
20	chr15:42068800-42074400	Weak transcription	Primary B cells from peripheral blood	blood
21	chr15:42069200-42075200	Weak transcription	K562	blood
22	chr15:42069400-42075200	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
23	chr15:42069600-42073200	Enhancers	ES-I3 Cell Line	embryonic stem cell
24	chr15:42069800-42075200	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
25	chr15:42069800-42075200	Weak transcription	Gastric	stomach
26	chr15:42069800-42081800	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
27	chr15:42070000-42081600	Weak transcription	Aorta	Aorta
28	chr15:42070000-42082600	Weak transcription	Primary T cells fromperipheralblood	blood
29	chr15:42070200-42073200	Enhancers	NHLF	lung
30	chr15:42070200-42109800	Weak transcription	Fetal Brain Male	brain
31	chr15:42070600-42072800	Enhancers	HUES6 Cell Line	embryonic stem cell
32	chr15:42070800-42075000	Weak transcription	Dnd41	blood
33	chr15:42071000-42073200	Enhancers	Brain Substantia Nigra	brain
34	chr15:42071000-42074800	Weak transcription	HUES48 Cell Line	embryonic stem cell
35	chr15:42071000-42082400	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
36	chr15:42071000-42082800	Weak transcription	Primary T helper naive cells from peripheral blood	blood
37	chr15:42071000-42092800	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
38	chr15:42071200-42074000	Enhancers	HUVEC	blood vessel
39	chr15:42071200-42074400	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
40	chr15:42071200-42074600	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
41	chr15:42071200-42092000	Weak transcription	Brain Germinal Matrix	brain
42	chr15:42071600-42072800	Enhancers	Left Ventricle	heart
43	chr15:42071600-42072800	Enhancers	Ovary	ovary
44	chr15:42071600-42073000	Genic enhancers	NHEK	skin
45	chr15:42071600-42073200	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
46	chr15:42071600-42073200	Enhancers	Brain Angular Gyrus	brain
47	chr15:42071600-42073200	Enhancers	Brain Inferior Temporal Lobe	brain
48	chr15:42071600-42073400	Enhancers	Fetal Thymus	thymus
49	chr15:42071800-42072800	Genic enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
50	chr15:42071800-42072800	Flanking Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links