Variant report

Variant	rs4889606
Chromosome Location	chr16:31011183-31011184
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	MAX	chr16:31010241-31011193	HepG2	liver:	n/a	n/a

No data

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

No.	Distal block	Cell Line	Cell type
1	chr16:31004363..31015645-chr16:31042809..31047717,18	MCF-7	breast:
2	chr16:31007054..31011428-chr16:31011544..31016044,11	MCF-7	breast:
3	chr16:30960482..30963722-chr16:31009124..31011668,3	K562	blood:
4	chr16:31006807..31011358-chr16:31082999..31086095,12	MCF-7	breast:
5	chr16:31010991..31014838-chr16:31020635..31023865,5	MCF-7	breast:

No data

Variant related genes	Relation type
STX1B	TF binding region
ENSG00000103496	Chromatin interaction
ENSG00000167394	Chromatin interaction
ENSG00000099365	Chromatin interaction
ENSG00000167395	Chromatin interaction

Extended variants
information (count: 97 )
Associated
traits (count: 14 )

rSNPs within LD-proxies of this variant (count:83)

rs_ID	r²[population]
rs1046276	0.89[JPT][hapmap]
rs1060506	0.89[JPT][hapmap]
rs10782001	1.00[JPT][hapmap]
rs10782002	1.00[JPT][hapmap]
rs10871454	0.96[CEU][hapmap];1.00[CHB][hapmap];0.84[GIH][hapmap];0.89[JPT][hapmap];1.00[MEX][hapmap];0.98[TSI][hapmap]
rs11076	1.00[JPT][hapmap]
rs11150600	1.00[JPT][hapmap]
rs11150601	1.00[JPT][hapmap]
rs11150604	0.96[CEU][hapmap];1.00[CHB][hapmap];0.97[GIH][hapmap];0.89[JPT][hapmap];1.00[MEX][hapmap];0.98[TSI][hapmap]
rs11640534	1.00[JPT][hapmap]
rs11640961	0.91[CEU][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.83[MEX][hapmap];0.88[TSI][hapmap];0.82[AMR][1000 genomes]
rs11649653	0.97[GIH][hapmap];0.89[JPT][hapmap]
rs11862744	1.00[CHB][hapmap];0.89[JPT][hapmap]
rs11864839	1.00[CHB][hapmap];0.82[JPT][hapmap]
rs11865038	0.89[JPT][hapmap]
rs11865499	0.89[JPT][hapmap]
rs12445568	1.00[CHB][hapmap];0.82[ASN][1000 genomes]
rs12445650	1.00[CHB][hapmap];0.88[JPT][hapmap]
rs12597511	0.92[CEU][hapmap];0.89[JPT][hapmap];0.87[MEX][hapmap];0.83[TSI][hapmap]
rs12716979	0.99[AFR][1000 genomes];0.98[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs12924903	0.89[JPT][hapmap]
rs12928852	1.00[JPT][hapmap]
rs12931046	1.00[JPT][hapmap]
rs12934418	0.80[EUR][1000 genomes]
rs13708	1.00[JPT][hapmap]
rs14235	0.96[CEU][hapmap];0.81[GIH][hapmap];0.89[JPT][hapmap];0.91[MEX][hapmap];0.87[TSI][hapmap]
rs1458202	1.00[JPT][hapmap]
rs1549293	0.96[CEU][hapmap];0.81[GIH][hapmap];0.89[JPT][hapmap];0.92[MEX][hapmap];0.87[TSI][hapmap]
rs1870293	1.00[JPT][hapmap]
rs1978487	0.96[CEU][hapmap];0.89[JPT][hapmap]
rs2032915	0.96[CEU][hapmap];0.81[GIH][hapmap];0.89[JPT][hapmap];0.92[MEX][hapmap];0.87[TSI][hapmap]
rs2054213	1.00[JPT][hapmap]
rs2199036	0.95[ASN][1000 genomes]
rs2303222	0.96[CEU][hapmap];0.81[GIH][hapmap];0.89[JPT][hapmap];0.83[MEX][hapmap];0.87[TSI][hapmap]
rs2303223	0.96[CEU][hapmap];0.89[JPT][hapmap]
rs2305880	1.00[JPT][hapmap]
rs2305884	1.00[JPT][hapmap]
rs2359612	0.96[CEU][hapmap];0.84[GIH][hapmap];0.89[JPT][hapmap];0.96[MEX][hapmap];0.95[TSI][hapmap]
rs2855475	0.83[CEU][hapmap];0.89[JPT][hapmap];0.84[TSI][hapmap]
rs35468353	1.00[CHB][hapmap];0.89[JPT][hapmap]
rs35675346	0.89[JPT][hapmap]
rs3751855	0.89[JPT][hapmap]
rs3813020	0.90[JPT][hapmap]
rs4468641	0.89[JPT][hapmap]
rs4527034	0.96[CEU][hapmap];0.81[GIH][hapmap];0.89[JPT][hapmap];0.87[TSI][hapmap]
rs4889525	1.00[JPT][hapmap]
rs4889599	1.00[JPT][hapmap]
rs4889603	0.88[CEU][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.87[MEX][hapmap];0.80[TSI][hapmap];0.82[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs4889604	1.00[JPT][hapmap]
rs4889609	0.89[JPT][hapmap]
rs6565217	0.89[JPT][hapmap]
rs6950	1.00[JPT][hapmap]
rs7196726	0.89[JPT][hapmap]
rs7197717	0.89[JPT][hapmap]
rs7199949	0.89[JPT][hapmap]
rs7200879	0.89[JPT][hapmap]
rs7203999	1.00[CHB][hapmap];0.89[CHD][hapmap];1.00[JPT][hapmap];0.96[ASN][1000 genomes]
rs7204459	1.00[JPT][hapmap]
rs7206511	1.00[JPT][hapmap]
rs7294	0.89[JPT][hapmap]
rs729482	0.89[JPT][hapmap]
rs732172	1.00[CHB][hapmap];0.89[JPT][hapmap]
rs749670	0.96[CEU][hapmap];0.88[JPT][hapmap]
rs749671	0.92[CEU][hapmap];0.84[GIH][hapmap];0.89[JPT][hapmap];0.87[MEX][hapmap];0.87[TSI][hapmap]
rs749767	0.96[CEU][hapmap];0.89[JPT][hapmap]
rs750952	0.89[JPT][hapmap]
rs8046707	1.00[GIH][hapmap]
rs8050588	1.00[JPT][hapmap]
rs8050894	0.96[CEU][hapmap];0.89[JPT][hapmap]
rs8056842	1.00[CHB][hapmap];0.89[JPT][hapmap]
rs8060857	1.00[JPT][hapmap]
rs8062719	1.00[JPT][hapmap]
rs881929	0.96[CEU][hapmap];0.84[GIH][hapmap];0.89[JPT][hapmap];1.00[MEX][hapmap];0.95[TSI][hapmap]
rs889548	0.96[CEU][hapmap];0.81[GIH][hapmap];0.89[JPT][hapmap];0.92[MEX][hapmap];0.87[TSI][hapmap]
rs889555	0.89[JPT][hapmap]
rs897986	1.00[JPT][hapmap]
rs9923231	0.96[CEU][hapmap];0.84[GIH][hapmap];0.89[JPT][hapmap];0.96[MEX][hapmap];0.95[TSI][hapmap]
rs9925964	0.95[CEU][hapmap]
rs9926533	1.00[CEU][hapmap];1.00[CHB][hapmap];0.89[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.95[TSI][hapmap];0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9934438	0.96[CEU][hapmap];0.81[CHD][hapmap];0.84[GIH][hapmap];0.89[JPT][hapmap];0.96[MEX][hapmap];0.95[TSI][hapmap]
rs9936329	0.96[CEU][hapmap];0.81[GIH][hapmap];0.89[JPT][hapmap];0.92[MEX][hapmap];0.87[TSI][hapmap]
rs9938550	0.81[JPT][hapmap]
rs9939417	0.96[CEU][hapmap];1.00[CHB][hapmap];0.84[GIH][hapmap];0.89[JPT][hapmap];1.00[MEX][hapmap];0.95[TSI][hapmap]

Variant overlapped rSNPs/rCNVs (count:14 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1062456	chr16:30442166-31253997	Weak transcription Flanking Active TSS Enhancers Strong transcription Active TSS Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	437 gene(s)	inside rSNPs	diseases
2	nsv542898	chr16:30442166-31253997	Enhancers Active TSS Strong transcription Flanking Active TSS Weak transcription Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	437 gene(s)	inside rSNPs	diseases
3	nsv1064134	chr16:30640293-31087327	Genic enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Active TSS Strong transcription Weak transcription Enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	238 gene(s)	inside rSNPs	diseases
4	nsv905729	chr16:30642867-31247924	Active TSS Bivalent/Poised TSS Flanking Active TSS Enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Strong transcription Genic enhancers Weak transcription Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	387 gene(s)	inside rSNPs	diseases
5	nsv431451	chr16:30682399-31340999	Transcr. at gene 5' and 3' Genic enhancers Weak transcription Flanking Active TSS Strong transcription Active TSS Enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	350 gene(s)	inside rSNPs	diseases
6	nsv833191	chr16:30864242-31048051	Flanking Active TSS Weak transcription Enhancers Strong transcription Active TSS Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	115 gene(s)	inside rSNPs	diseases
7	nsv905734	chr16:30877544-31191482	Active TSS Strong transcription Weak transcription Enhancers ZNF genes & repeats Flanking Active TSS Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	271 gene(s)	inside rSNPs	diseases
8	nsv905735	chr16:30890538-31247924	Strong transcription Genic enhancers Active TSS Weak transcription Flanking Active TSS Bivalent Enhancer Enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	264 gene(s)	inside rSNPs	diseases
9	nsv905737	chr16:30900235-31014179	Enhancers Flanking Active TSS Weak transcription Transcr. at gene 5' and 3' Genic enhancers Active TSS Strong transcription Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	95 gene(s)	inside rSNPs	diseases
10	nsv457483	chr16:30903679-31191482	Active TSS Flanking Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Genic enhancers Strong transcription Enhancers ZNF genes & repeats Weak transcription Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	253 gene(s)	inside rSNPs	diseases
11	nsv571820	chr16:30903679-31191482	Enhancers Genic enhancers Bivalent/Poised TSS Weak transcription Active TSS Flanking Active TSS Bivalent Enhancer Strong transcription Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	253 gene(s)	inside rSNPs	diseases
12	esv1797877	chr16:30948643-31188432	Flanking Active TSS Enhancers Weak transcription Strong transcription Active TSS Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	114 gene(s)	inside rSNPs	diseases
13	nsv833193	chr16:30960796-31133604	Enhancers Active TSS Weak transcription Flanking Active TSS Genic enhancers Flanking Bivalent TSS/Enh Strong transcription Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	109 gene(s)	inside rSNPs	diseases
14	nsv916994	chr16:30971725-31078117	Active TSS Strong transcription Enhancers Weak transcription Genic enhancers Flanking Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	45 gene(s)	inside rSNPs	diseases

mRNA abundance (count:14)

SNP	Gene	Cis/trans	Tissue	Source
rs4889606	ZNF668	cis	multi-tissue	Pritchard
rs4889606	BCKDK	cis	multi-tissue	Pritchard
rs4889606	MYST1	cis	cerebellum	SCAN
rs4889606	AHSP	cis	parietal	SCAN
rs4889606	VKORC1	cis	Liver	GTEx
rs4889606	RP11-196G11.2	cis	Muscle Skeletal	GTEx
rs4889606	C16orf93	cis	parietal	SCAN
rs4889606	YPEL3	cis	cerebellum	SCAN
rs4889606	ZNF668	cis	cerebellum	SCAN
rs4889606	KAT8	cis	Skin Sun Exposed Lower leg	GTEx
rs4889606	MYST1	cis	parietal	SCAN
rs4889606	NCRNA00095	cis	cerebellum	SCAN
rs4889606	HSD3B7	cis	Whole Blood	GTEx
rs4889606	STX1B	cis	cerebellum	SCAN

Chromatin state (count:66 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr16:30997600-31013600	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
2	chr16:31009000-31013200	Weak transcription	Brain Inferior Temporal Lobe	brain
3	chr16:31009000-31013800	Enhancers	Liver	Liver
4	chr16:31009000-31020400	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
5	chr16:31009200-31011200	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
6	chr16:31009200-31011200	Enhancers	Fetal Intestine Large	intestine
7	chr16:31009200-31011200	Enhancers	Fetal Intestine Small	intestine
8	chr16:31009200-31011200	Enhancers	Placenta Amnion	Placenta Amnion
9	chr16:31009200-31012200	Weak transcription	Duodenum Mucosa	Duodenum
10	chr16:31009200-31013200	Weak transcription	Fetal Heart	heart
11	chr16:31009200-31013200	Weak transcription	Left Ventricle	heart
12	chr16:31009200-31013200	Weak transcription	Right Ventricle	heart
13	chr16:31009200-31013600	Weak transcription	Cortex derived primary cultured neurospheres	brain
14	chr16:31009200-31013600	Weak transcription	Brain Anterior Caudate	brain
15	chr16:31009200-31013600	Weak transcription	Brain Cingulate Gyrus	brain
16	chr16:31009200-31013800	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
17	chr16:31009200-31020400	Weak transcription	Brain Angular Gyrus	brain
18	chr16:31009200-31034400	Weak transcription	Right Atrium	heart
19	chr16:31009400-31012000	Enhancers	Adipose Nuclei	Adipose
20	chr16:31009400-31015000	Enhancers	Placenta	Placenta
21	chr16:31009400-31020600	Weak transcription	H9 Cell Line	embryonic stem cell
22	chr16:31009600-31011200	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
23	chr16:31009600-31011200	Enhancers	NHDF-Ad	bronchial
24	chr16:31009600-31013000	Enhancers	NHEK	skin
25	chr16:31009600-31013200	Weak transcription	Pancreas	Pancrea
26	chr16:31009800-31011200	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
27	chr16:31009800-31011200	Enhancers	Foreskin Fibroblast Primary Cells skin02	Skin
28	chr16:31009800-31011200	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
29	chr16:31009800-31011600	Weak transcription	Colonic Mucosa	Colon
30	chr16:31009800-31012200	Weak transcription	Esophagus	oesophagus
31	chr16:31009800-31013200	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
32	chr16:31009800-31013400	Weak transcription	Fetal Stomach	stomach
33	chr16:31009800-31013800	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
34	chr16:31009800-31014200	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
35	chr16:31009800-31021000	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
36	chr16:31010000-31011200	Enhancers	Muscle Satellite Cultured Cells	--
37	chr16:31010000-31011200	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
38	chr16:31010000-31011200	Enhancers	Fetal Muscle Leg	muscle
39	chr16:31010000-31011200	Flanking Active TSS	HepG2	liver
40	chr16:31010000-31013200	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
41	chr16:31010200-31011200	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
42	chr16:31010200-31011200	Enhancers	A549	lung
43	chr16:31010200-31011200	Enhancers	Hela-S3	cervix
44	chr16:31010200-31011200	Enhancers	HSMM	muscle
45	chr16:31010200-31011200	Enhancers	NH-A	brain
46	chr16:31010200-31011200	Enhancers	Osteobl	bone
47	chr16:31010200-31011400	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
48	chr16:31010200-31013400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
49	chr16:31010200-31020800	Weak transcription	HUES48 Cell Line	embryonic stem cell
50	chr16:31010400-31011200	Genic enhancers	Brain Germinal Matrix	brain

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