Variant report

Variant	rs7203999
Chromosome Location	chr16:31017554-31017555
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr16:31014981..31017878-chr16:31019821..31021502,2	MCF-7	breast:
2	chr16:31015311..31017608-chr16:31032189..31035035,2	MCF-7	breast:
3	chr16:31007063..31009126-chr16:31016617..31018445,2	MCF-7	breast:
4	chr16:31017113..31020249-chr16:31190318..31192799,3	K562	blood:
5	chr16:31016193..31017724-chr16:31190060..31191679,2	MCF-7	breast:
6	chr16:31015384..31017554-chr16:31043816..31046429,2	MCF-7	breast:
7	chr16:31012830..31015179-chr16:31017421..31020382,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000089280	Chromatin interaction
ENSG00000103496	Chromatin interaction
ENSG00000099365	Chromatin interaction

Extended variants
information (count: 109 )
Associated
traits (count: 21 )

rSNPs within LD-proxies of this variant (count:96)

rs_ID	r²[population]
rs1046276	0.83[CEU][hapmap];1.00[GIH][hapmap];0.89[JPT][hapmap];0.80[TSI][hapmap]
rs1060506	0.82[CHD][hapmap];0.89[JPT][hapmap];0.82[MEX][hapmap]
rs10782001	0.83[CEU][hapmap];1.00[JPT][hapmap];0.81[EUR][1000 genomes]
rs10782002	0.83[CEU][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.85[TSI][hapmap];0.81[EUR][1000 genomes]
rs10871454	1.00[CHB][hapmap];0.82[CHD][hapmap];0.89[JPT][hapmap]
rs11076	0.82[CEU][hapmap];1.00[JPT][hapmap];0.80[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs11150600	0.83[CEU][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.88[TSI][hapmap];0.81[EUR][1000 genomes]
rs11150601	1.00[CEU][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.88[TSI][hapmap];0.87[EUR][1000 genomes]
rs11150604	1.00[CHB][hapmap];0.82[CHD][hapmap];0.89[JPT][hapmap]
rs11640534	0.83[CEU][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.88[TSI][hapmap]
rs11640961	1.00[JPT][hapmap]
rs11649653	0.89[JPT][hapmap]
rs11862744	0.91[CEU][hapmap];1.00[CHB][hapmap];0.82[CHD][hapmap];0.88[GIH][hapmap];0.89[JPT][hapmap];1.00[MEX][hapmap];0.97[TSI][hapmap]
rs11864839	1.00[CHB][hapmap];0.82[JPT][hapmap]
rs11865038	0.83[CEU][hapmap];0.88[GIH][hapmap];0.89[JPT][hapmap];0.91[MEX][hapmap]
rs11865499	0.82[CHD][hapmap];0.89[JPT][hapmap];0.82[MEX][hapmap]
rs12445568	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[GIH][hapmap];0.95[MEX][hapmap];0.95[TSI][hapmap];0.86[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs12445650	0.91[CEU][hapmap];1.00[CHB][hapmap];0.88[JPT][hapmap]
rs12447930	0.93[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs12597511	0.82[CHD][hapmap];0.89[JPT][hapmap]
rs12599631	0.81[EUR][1000 genomes]
rs12716978	0.84[EUR][1000 genomes]
rs12920772	0.87[EUR][1000 genomes]
rs12924903	0.83[CEU][hapmap];1.00[GIH][hapmap];0.89[JPT][hapmap]
rs12928852	0.83[CEU][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.87[TSI][hapmap];0.81[EUR][1000 genomes]
rs12930545	1.00[GIH][hapmap];0.88[TSI][hapmap];0.81[EUR][1000 genomes]
rs12931046	0.96[CEU][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.82[TSI][hapmap];0.80[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs13708	1.00[CEU][hapmap];1.00[JPT][hapmap];0.80[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs14235	0.82[CHD][hapmap];0.89[JPT][hapmap]
rs1458201	0.84[GIH][hapmap]
rs1458202	0.83[CEU][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.88[TSI][hapmap];0.81[EUR][1000 genomes]
rs1549293	0.82[CHD][hapmap];0.89[JPT][hapmap]
rs1870293	1.00[CEU][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.82[TSI][hapmap];0.81[EUR][1000 genomes]
rs1978487	0.82[CHD][hapmap];0.89[JPT][hapmap]
rs2032915	0.82[CHD][hapmap];0.89[JPT][hapmap]
rs2054213	1.00[CEU][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.88[TSI][hapmap];0.85[EUR][1000 genomes]
rs2199036	0.83[AMR][1000 genomes];0.95[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2303222	0.82[CHD][hapmap];0.89[JPT][hapmap]
rs2303223	0.89[JPT][hapmap]
rs2305880	1.00[CEU][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.90[TSI][hapmap];0.80[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs2305884	1.00[CEU][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];0.88[TSI][hapmap];0.84[EUR][1000 genomes]
rs2359612	0.82[CHD][hapmap];0.89[JPT][hapmap]
rs28360557	0.80[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs2855475	0.89[JPT][hapmap]
rs34454770	0.82[EUR][1000 genomes]
rs35468353	0.91[CEU][hapmap];1.00[CHB][hapmap];0.82[CHD][hapmap];0.88[GIH][hapmap];0.89[JPT][hapmap];1.00[MEX][hapmap];0.97[TSI][hapmap]
rs35675346	0.84[GIH][hapmap];0.89[JPT][hapmap]
rs3751855	0.87[CEU][hapmap];0.89[JPT][hapmap]
rs3813020	0.82[CEU][hapmap];1.00[GIH][hapmap];0.90[JPT][hapmap];0.85[TSI][hapmap];0.81[EUR][1000 genomes]
rs4468641	0.83[CEU][hapmap];0.82[CHD][hapmap];0.88[GIH][hapmap];0.89[JPT][hapmap];0.91[MEX][hapmap];0.86[TSI][hapmap]
rs4502227	0.81[EUR][1000 genomes]
rs4527034	0.82[CHD][hapmap];0.89[JPT][hapmap]
rs4889514	0.81[EUR][1000 genomes]
rs4889525	0.92[CEU][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.88[TSI][hapmap];0.81[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs4889571	0.81[EUR][1000 genomes]
rs4889599	1.00[CEU][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.88[TSI][hapmap];0.84[EUR][1000 genomes]
rs4889603	1.00[JPT][hapmap]
rs4889604	0.96[CEU][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.82[TSI][hapmap];0.80[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs4889606	1.00[CHB][hapmap];0.89[CHD][hapmap];1.00[JPT][hapmap];0.96[ASN][1000 genomes]
rs4889609	0.91[CEU][hapmap];0.97[GIH][hapmap];0.89[JPT][hapmap];1.00[MEX][hapmap];0.95[TSI][hapmap]
rs61239537	0.93[EUR][1000 genomes]
rs62055866	0.82[EUR][1000 genomes]
rs6565217	0.83[CEU][hapmap];0.82[CHD][hapmap];0.88[GIH][hapmap];0.89[JPT][hapmap];0.86[MEX][hapmap];0.81[TSI][hapmap]
rs6950	1.00[CEU][hapmap];1.00[JPT][hapmap];0.80[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs7184567	0.91[CEU][hapmap];0.92[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs7196726	0.83[CEU][hapmap];0.89[JPT][hapmap]
rs7197717	0.83[CEU][hapmap];0.82[CHD][hapmap];0.88[GIH][hapmap];0.89[JPT][hapmap];0.91[MEX][hapmap];0.86[TSI][hapmap]
rs7199949	0.87[CEU][hapmap];0.89[JPT][hapmap]
rs7200879	0.84[GIH][hapmap];0.89[JPT][hapmap]
rs7204459	0.96[CEU][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.82[TSI][hapmap];0.80[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs7206511	0.83[CEU][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.88[TSI][hapmap];0.81[EUR][1000 genomes]
rs72800847	0.92[EUR][1000 genomes]
rs7294	0.83[CEU][hapmap];0.82[CHD][hapmap];0.85[GIH][hapmap];0.89[JPT][hapmap];0.80[TSI][hapmap]
rs729482	1.00[CEU][hapmap];0.97[GIH][hapmap];0.89[JPT][hapmap];0.87[MEX][hapmap];0.87[TSI][hapmap];0.94[EUR][1000 genomes]
rs732172	0.91[CEU][hapmap];1.00[CHB][hapmap];0.82[CHD][hapmap];0.85[GIH][hapmap];0.89[JPT][hapmap];0.87[MEX][hapmap];0.87[TSI][hapmap]
rs749670	0.88[JPT][hapmap]
rs749671	0.82[CHD][hapmap];0.89[JPT][hapmap]
rs749767	0.82[CHD][hapmap];0.89[JPT][hapmap]
rs750952	0.83[CEU][hapmap];0.82[CHD][hapmap];0.85[GIH][hapmap];0.89[JPT][hapmap];0.80[TSI][hapmap]
rs8050588	0.83[CEU][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.88[TSI][hapmap];0.80[EUR][1000 genomes]
rs8050894	0.89[JPT][hapmap]
rs8052245	0.80[EUR][1000 genomes]
rs8056842	0.91[CEU][hapmap];1.00[CHB][hapmap];0.89[JPT][hapmap]
rs8060857	0.96[CEU][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.82[MEX][hapmap];0.88[TSI][hapmap];0.80[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs8062719	1.00[CEU][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.82[TSI][hapmap];0.86[EUR][1000 genomes]
rs881929	0.82[CHD][hapmap];0.89[JPT][hapmap]
rs889548	0.89[JPT][hapmap]
rs889555	0.89[JPT][hapmap]
rs897986	1.00[CEU][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.88[TSI][hapmap];0.87[EUR][1000 genomes]
rs9319588	0.83[CEU][hapmap];0.81[EUR][1000 genomes]
rs9923231	0.82[CHD][hapmap];0.89[JPT][hapmap]
rs9926533	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.96[ASN][1000 genomes]
rs9934438	0.90[CHD][hapmap];0.89[JPT][hapmap]
rs9936329	0.82[CHD][hapmap];0.89[JPT][hapmap]
rs9938550	0.96[CEU][hapmap];1.00[GIH][hapmap];0.81[JPT][hapmap];0.90[TSI][hapmap];0.80[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs9939417	1.00[CHB][hapmap];0.82[CHD][hapmap];0.89[JPT][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	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	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
10	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
11	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
12	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
13	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:21)

SNP	Gene	Cis/trans	Tissue	Source
rs7203999	MYST1	Cis_1M	lymphoblastoid	RTeQTL
rs7203999	ZNF48	cis	cerebellum	SCAN
rs7203999	STX4	Cis_1M	lymphoblastoid	RTeQTL
rs7203999	VKORC1	cis	cerebellum	SCAN
rs7203999	STX1B	cis	Thyroid	GTEx
rs7203999	TAOK2	cis	parietal	SCAN
rs7203999	KAT8	cis	Skin Sun Exposed Lower leg	GTEx
rs7203999	ZNF785	cis	lymphoblastoid	seeQTL
rs7203999	RABEP2	cis	cerebellum	SCAN
rs7203999	YPEL3	cis	parietal	SCAN
rs7203999	MYST1	cis	cerebellum	SCAN
rs7203999	STX4	cis	lymphoblastoid	seeQTL
rs7203999	NCRNA00095	cis	cerebellum	SCAN
rs7203999	RP11-196G11.2	cis	Muscle Skeletal	GTEx
rs7203999	MYST1	cis	parietal	SCAN
rs7203999	HSD3B7	cis	Esophagus Mucosa	GTEx
rs7203999	MYST1	cis	lymphoblastoid	seeQTL
rs7203999	RP11-196G11.2	cis	Esophagus Muscularis	GTEx
rs7203999	ZNF747	cis	parietal	SCAN
rs7203999	RP11-196G11.2	cis	lung	GTEx
rs7203999	HSD3B7	cis	Muscle Skeletal	GTEx

Chromatin state (count:39 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr16:31009000-31020400	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
2	chr16:31009200-31020400	Weak transcription	Brain Angular Gyrus	brain
3	chr16:31009200-31034400	Weak transcription	Right Atrium	heart
4	chr16:31009400-31020600	Weak transcription	H9 Cell Line	embryonic stem cell
5	chr16:31009800-31021000	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
6	chr16:31010200-31020800	Weak transcription	HUES48 Cell Line	embryonic stem cell
7	chr16:31010600-31017600	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
8	chr16:31011200-31018600	Weak transcription	HUES6 Cell Line	embryonic stem cell
9	chr16:31011200-31019800	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
10	chr16:31012600-31020400	Weak transcription	Brain Germinal Matrix	brain
11	chr16:31013200-31018800	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
12	chr16:31013800-31017600	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
13	chr16:31013800-31021000	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
14	chr16:31014200-31019200	Weak transcription	HMEC	breast
15	chr16:31014200-31019600	Weak transcription	Cortex derived primary cultured neurospheres	brain
16	chr16:31014400-31018600	Weak transcription	NH-A	brain
17	chr16:31014400-31019200	Weak transcription	ES-I3 Cell Line	embryonic stem cell
18	chr16:31014600-31019000	Weak transcription	Brain Cingulate Gyrus	brain
19	chr16:31015400-31020600	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
20	chr16:31015800-31020600	Weak transcription	Breast Myoepithelial Primary Cells	Breast
21	chr16:31016800-31021000	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
22	chr16:31017000-31017600	Active TSS	Brain Dorsolateral Prefrontal Cortex	brain
23	chr16:31017000-31017800	Flanking Bivalent TSS/Enh	HepG2	liver
24	chr16:31017000-31017800	Enhancers	K562	blood
25	chr16:31017000-31018000	Enhancers	Osteobl	bone
26	chr16:31017000-31018600	Strong transcription	Fetal Brain Female	brain
27	chr16:31017000-31021000	Enhancers	NHLF	lung
28	chr16:31017200-31017600	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
29	chr16:31017200-31017600	Bivalent Enhancer	Fetal Muscle Trunk	muscle
30	chr16:31017200-31017800	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
31	chr16:31017200-31018000	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
32	chr16:31017200-31018000	Enhancers	Fetal Brain Male	brain
33	chr16:31017200-31018200	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
34	chr16:31017400-31017600	Enhancers	H1 Cell Line	embryonic stem cell
35	chr16:31017400-31017600	Bivalent Enhancer	Fetal Lung	lung
36	chr16:31017400-31017600	Enhancers	Placenta Amnion	Placenta Amnion
37	chr16:31017400-31018000	Enhancers	A549	lung
38	chr16:31017400-31018200	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
39	chr16:31017400-31018400	Strong transcription	Brain Inferior Temporal Lobe	brain

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