Variant report

Variant	rs4628748
Chromosome Location	chr12:86725548-86725549
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 158 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:146)

rs_ID	r²[population]
rs10431399	0.88[CEU][hapmap];0.95[JPT][hapmap]
rs10735250	0.95[JPT][hapmap]
rs10745407	0.96[CEU][hapmap];0.94[CHB][hapmap];0.89[JPT][hapmap]
rs10745408	0.82[ASW][hapmap];0.96[CEU][hapmap];0.94[CHB][hapmap];0.88[GIH][hapmap];0.89[JPT][hapmap];0.82[MEX][hapmap];1.00[TSI][hapmap];0.86[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs10745416	0.94[JPT][hapmap]
rs10776955	0.96[CEU][hapmap];0.94[CHB][hapmap];0.92[GIH][hapmap];0.89[JPT][hapmap];0.86[MEX][hapmap];1.00[TSI][hapmap];0.83[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs10776957	0.86[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs10776959	0.91[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs10776961	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];0.96[LWK][hapmap];1.00[MEX][hapmap];0.93[MKK][hapmap];1.00[TSI][hapmap];0.96[YRI][hapmap];0.99[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10776966	1.00[CEU][hapmap];0.97[TSI][hapmap];0.98[EUR][1000 genomes]
rs10776968	0.87[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs10776969	1.00[CEU][hapmap];0.95[JPT][hapmap]
rs10776971	0.87[CEU][hapmap];0.90[CHD][hapmap];0.89[JPT][hapmap];0.86[MKK][hapmap];0.92[TSI][hapmap]
rs10776976	0.82[AMR][1000 genomes]
rs10776977	0.94[JPT][hapmap];0.82[AMR][1000 genomes]
rs10858408	0.96[CEU][hapmap];0.94[CHB][hapmap];0.89[JPT][hapmap]
rs10858409	0.80[ASN][1000 genomes]
rs10858412	0.83[ASW][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap]
rs10858415	0.80[CHD][hapmap];0.84[JPT][hapmap]
rs10858419	0.90[AMR][1000 genomes];0.99[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs10858425	0.88[CEU][hapmap];0.93[CHD][hapmap];0.97[GIH][hapmap];0.95[JPT][hapmap];0.95[MEX][hapmap];0.93[MKK][hapmap];0.93[TSI][hapmap]
rs10858427	0.88[CEU][hapmap];0.95[JPT][hapmap]
rs10858428	0.88[CEU][hapmap];0.89[CHB][hapmap];0.81[JPT][hapmap]
rs11103912	0.80[EUR][1000 genomes]
rs11103930	0.80[CHD][hapmap];0.84[JPT][hapmap]
rs11830208	0.84[JPT][hapmap]
rs12303046	0.80[CHD][hapmap];0.84[JPT][hapmap];0.83[ASN][1000 genomes]
rs12306280	0.97[ASN][1000 genomes]
rs12309874	0.83[ASN][1000 genomes]
rs12317113	0.88[CEU][hapmap];0.93[CHD][hapmap];0.97[GIH][hapmap];0.95[JPT][hapmap];0.95[MEX][hapmap];0.88[MKK][hapmap];0.93[TSI][hapmap]
rs12578669	0.88[CEU][hapmap];0.95[JPT][hapmap];0.83[YRI][hapmap]
rs12582690	0.94[CHB][hapmap];1.00[JPT][hapmap];0.91[ASN][1000 genomes]
rs1463749	0.92[CEU][hapmap];0.98[TSI][hapmap];0.93[EUR][1000 genomes]
rs1493415	0.90[CEU][hapmap];0.94[CHB][hapmap];0.87[JPT][hapmap];0.94[EUR][1000 genomes]
rs1493416	0.93[EUR][1000 genomes]
rs1532262	0.88[CEU][hapmap];0.86[EUR][1000 genomes]
rs1552839	0.88[CEU][hapmap];0.86[EUR][1000 genomes]
rs1602848	0.86[EUR][1000 genomes]
rs1602850	0.93[EUR][1000 genomes]
rs1689340	0.87[CEU][hapmap]
rs1689357	0.87[EUR][1000 genomes]
rs1698787	0.92[CEU][hapmap];0.83[CHB][hapmap];0.89[JPT][hapmap];0.87[EUR][1000 genomes]
rs1922742	0.94[JPT][hapmap];0.86[AMR][1000 genomes]
rs1922749	0.92[CEU][hapmap];0.95[JPT][hapmap]
rs1948448	0.94[EUR][1000 genomes]
rs1955399	0.89[JPT][hapmap]
rs2091818	0.84[CEU][hapmap];0.93[CHD][hapmap];0.94[GIH][hapmap];0.94[JPT][hapmap];0.85[MKK][hapmap];0.90[TSI][hapmap]
rs2131565	0.91[CEU][hapmap];0.86[EUR][1000 genomes]
rs2220782	0.84[CHB][hapmap];0.89[JPT][hapmap]
rs2405923	0.91[CEU][hapmap]
rs2405925	1.00[CEU][hapmap];0.90[CHB][hapmap];1.00[JPT][hapmap]
rs2405928	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs2405930	1.00[CHB][hapmap];1.00[JPT][hapmap];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2405931	0.84[JPT][hapmap];0.83[ASN][1000 genomes]
rs2405933	0.84[EUR][1000 genomes]
rs2406115	0.94[ASW][hapmap];0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];0.93[LWK][hapmap];0.91[MEX][hapmap];0.81[MKK][hapmap];1.00[TSI][hapmap];0.82[YRI][hapmap];0.84[AFR][1000 genomes];0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2406116	0.96[CEU][hapmap];0.94[CHB][hapmap];0.92[GIH][hapmap];0.89[JPT][hapmap];0.86[MEX][hapmap];1.00[TSI][hapmap];0.85[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs2406117	0.88[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs2406118	0.83[ASW][hapmap];0.96[CEU][hapmap];0.94[CHB][hapmap];0.92[GIH][hapmap];0.89[JPT][hapmap];0.86[MEX][hapmap];1.00[TSI][hapmap];0.87[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs2406119	0.83[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs2406122	0.96[CEU][hapmap];0.94[CHB][hapmap];0.89[GIH][hapmap];0.89[JPT][hapmap];0.86[MEX][hapmap];1.00[TSI][hapmap];0.83[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs2406123	0.96[CEU][hapmap];0.94[CHB][hapmap];0.89[JPT][hapmap];0.82[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs2406127	0.96[CEU][hapmap];0.94[CHB][hapmap];0.89[JPT][hapmap]
rs2406128	0.94[CHB][hapmap];0.89[JPT][hapmap]
rs2452806	0.92[CEU][hapmap];0.93[EUR][1000 genomes]
rs2452807	0.92[CEU][hapmap];0.94[CHB][hapmap];0.89[JPT][hapmap];0.94[EUR][1000 genomes]
rs2452811	0.88[CEU][hapmap];0.86[EUR][1000 genomes]
rs2452815	0.88[CEU][hapmap];0.87[EUR][1000 genomes]
rs2465143	0.92[CEU][hapmap];0.94[CHB][hapmap];0.84[JPT][hapmap];0.80[MEX][hapmap];0.94[EUR][1000 genomes]
rs2465144	0.92[CEU][hapmap];0.94[CHB][hapmap];0.89[JPT][hapmap];0.94[EUR][1000 genomes]
rs2465146	0.93[EUR][1000 genomes]
rs2465147	0.95[EUR][1000 genomes]
rs2465149	0.88[CEU][hapmap]
rs2471560	0.83[ASW][hapmap];0.88[CEU][hapmap];0.83[GIH][hapmap];0.89[JPT][hapmap];0.82[MEX][hapmap];0.85[TSI][hapmap];0.85[EUR][1000 genomes]
rs2471564	0.88[CEU][hapmap]
rs2471568	0.92[CEU][hapmap];0.94[CHB][hapmap];0.89[JPT][hapmap];0.93[EUR][1000 genomes]
rs2471569	0.92[CEU][hapmap];0.89[CHB][hapmap];0.89[JPT][hapmap];0.94[EUR][1000 genomes]
rs2471570	0.93[EUR][1000 genomes]
rs2897275	0.84[JPT][hapmap];0.83[ASN][1000 genomes]
rs2897277	0.80[CHD][hapmap];0.84[JPT][hapmap];0.83[ASN][1000 genomes]
rs2897278	0.92[CEU][hapmap];0.84[CHB][hapmap];0.80[CHD][hapmap];0.89[GIH][hapmap];0.84[JPT][hapmap];0.86[MEX][hapmap];1.00[TSI][hapmap];0.92[AMR][1000 genomes];0.98[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs2897280	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs4265650	0.95[CEU][hapmap];0.94[CHB][hapmap];0.94[JPT][hapmap];0.90[AMR][1000 genomes];0.98[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs4334094	0.86[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs4503614	0.83[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs4526834	0.84[JPT][hapmap];0.83[ASN][1000 genomes]
rs4842483	0.95[CEU][hapmap];0.97[TSI][hapmap];0.98[EUR][1000 genomes]
rs56293486	0.81[ASN][1000 genomes]
rs57002922	0.81[ASN][1000 genomes]
rs60555693	0.83[ASN][1000 genomes]
rs61014498	0.81[ASN][1000 genomes]
rs6538024	0.80[JPT][hapmap]
rs6538025	0.88[CEU][hapmap];0.83[GIH][hapmap];0.89[JPT][hapmap];0.82[MEX][hapmap];0.85[TSI][hapmap]
rs6538028	0.87[CEU][hapmap]
rs6538029	0.96[CEU][hapmap];0.94[CHB][hapmap];0.89[JPT][hapmap]
rs6538031	0.92[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs6538032	0.93[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs6538033	0.83[ASW][hapmap];0.96[CEU][hapmap];1.00[CHB][hapmap];0.94[GIH][hapmap];1.00[JPT][hapmap];0.90[TSI][hapmap]
rs6538042	0.93[CHD][hapmap];0.95[JPT][hapmap];0.91[MEX][hapmap];0.90[MKK][hapmap]
rs7134946	0.84[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs7135177	0.83[ASW][hapmap];0.96[CEU][hapmap];0.94[CHB][hapmap];0.91[GIH][hapmap];0.89[JPT][hapmap];0.82[MEX][hapmap];0.97[TSI][hapmap];0.87[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs7135733	0.87[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs7135741	0.88[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs7137308	0.92[CEU][hapmap];0.98[TSI][hapmap];0.93[EUR][1000 genomes]
rs7139324	0.94[JPT][hapmap]
rs7299319	0.89[ASW][hapmap];1.00[CEU][hapmap];0.84[CHB][hapmap];0.97[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];0.95[MEX][hapmap];0.89[MKK][hapmap];0.97[TSI][hapmap]
rs7303796	0.95[JPT][hapmap];0.82[AMR][1000 genomes]
rs7310186	0.90[AMR][1000 genomes];0.98[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs7953196	0.95[CEU][hapmap];0.94[CHB][hapmap];0.89[JPT][hapmap]
rs7957560	0.96[CEU][hapmap];0.94[CHB][hapmap];0.94[JPT][hapmap]
rs7963659	0.90[CHD][hapmap];0.95[JPT][hapmap]
rs7964553	0.96[CEU][hapmap];0.94[CHB][hapmap];0.89[JPT][hapmap]
rs7972484	0.96[CEU][hapmap];0.94[CHB][hapmap];0.94[JPT][hapmap];0.90[AMR][1000 genomes];0.99[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs7973773	0.96[CEU][hapmap];0.94[CHB][hapmap];0.89[JPT][hapmap]
rs7977689	0.89[JPT][hapmap]
rs7980126	0.80[CHD][hapmap];0.84[JPT][hapmap]
rs839104	0.92[CEU][hapmap];0.83[GIH][hapmap];0.89[JPT][hapmap];0.82[MEX][hapmap];0.85[TSI][hapmap]
rs839105	0.88[ASW][hapmap];0.82[CEU][hapmap];0.83[GIH][hapmap];0.84[JPT][hapmap];0.82[MEX][hapmap];0.85[TSI][hapmap]
rs839137	0.83[CHB][hapmap]
rs839148	0.88[CEU][hapmap];0.89[JPT][hapmap]
rs839149	0.89[JPT][hapmap]
rs839150	0.87[JPT][hapmap]
rs839151	0.89[JPT][hapmap]
rs839152	0.87[JPT][hapmap]
rs839153	0.89[JPT][hapmap]
rs839154	0.83[JPT][hapmap]
rs839156	0.89[JPT][hapmap]
rs839157	0.92[CEU][hapmap];0.81[GIH][hapmap];0.89[JPT][hapmap];0.86[MEX][hapmap];0.85[TSI][hapmap]
rs839158	0.89[JPT][hapmap]
rs839159	0.92[CEU][hapmap];0.89[JPT][hapmap]
rs839163	0.83[EUR][1000 genomes]
rs839164	0.83[EUR][1000 genomes]
rs839165	0.88[CEU][hapmap];0.81[GIH][hapmap];0.89[JPT][hapmap];0.85[TSI][hapmap];0.81[EUR][1000 genomes]
rs839166	0.89[JPT][hapmap]
rs839168	0.92[CEU][hapmap];0.89[JPT][hapmap];0.83[EUR][1000 genomes]
rs839170	0.92[CEU][hapmap];0.89[JPT][hapmap]
rs839171	0.92[CEU][hapmap];0.81[GIH][hapmap];0.89[JPT][hapmap];0.82[MEX][hapmap];0.85[TSI][hapmap]
rs844434	0.89[JPT][hapmap]
rs844435	0.92[CEU][hapmap];0.83[GIH][hapmap];0.89[JPT][hapmap];0.85[TSI][hapmap]
rs863392	0.88[CEU][hapmap];0.89[JPT][hapmap]
rs863394	0.87[CHB][hapmap];0.81[JPT][hapmap]
rs863395	0.92[CEU][hapmap];0.81[GIH][hapmap];0.89[JPT][hapmap];0.82[MEX][hapmap];0.85[TSI][hapmap]
rs865138	0.88[CEU][hapmap];0.89[JPT][hapmap]
rs865721	0.89[JPT][hapmap]
rs9919783	0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs9919793	0.92[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:12 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1049179	chr12:86056376-86799188	Weak transcription Enhancers Active TSS Flanking Active TSS Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Strong transcription Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases
2	esv2761759	chr12:86415936-86747726	Enhancers Active TSS Weak transcription Flanking Active TSS Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
3	nsv518059	chr12:86416212-86747726	Enhancers Weak transcription Active TSS Flanking Bivalent TSS/Enh Flanking Active TSS ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
4	nsv1041397	chr12:86438607-86737558	ZNF genes & repeats Enhancers Weak transcription Flanking Active TSS Active TSS Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
5	nsv1053087	chr12:86569126-86733418	Enhancers Active TSS Weak transcription Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
6	nsv541564	chr12:86569126-86733418	Flanking Active TSS Enhancers Weak transcription Active TSS Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
7	nsv1037003	chr12:86610040-86798121	Enhancers Active TSS Weak transcription Flanking Active TSS Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
8	nsv1045386	chr12:86616015-86733418	Enhancers Weak transcription Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
9	nsv541565	chr12:86616015-86733418	Enhancers Active TSS ZNF genes & repeats Flanking Active TSS Weak transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
10	esv1845250	chr12:86696771-86730126	Active TSS Enhancers Weak transcription Flanking Active TSS	Chromatin interactive region lncRNA	n/a	inside rSNPs	diseases
11	nsv1053234	chr12:86701070-86774957	Flanking Active TSS Enhancers Active TSS Weak transcription ZNF genes & repeats	Chromatin interactive region lncRNA	n/a	inside rSNPs	diseases
12	esv2754127	chr12:86723232-87576932	Enhancers Active TSS Flanking Active TSS Weak transcription ZNF genes & repeats Strong transcription Genic enhancers Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs4628748	SNORA20	trans	cerebellum	SCAN

Chromatin state (count:16 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:86723800-86726000	Enhancers	iPS-20b Cell Line	embryonic stem cell
2	chr12:86724600-86726000	Enhancers	HUES48 Cell Line	embryonic stem cell
3	chr12:86724600-86726400	Enhancers	HUES64 Cell Line	embryonic stem cell
4	chr12:86724800-86725600	Enhancers	H1 Cell Line	embryonic stem cell
5	chr12:86724800-86725600	Enhancers	Fetal Muscle Leg	muscle
6	chr12:86724800-86725800	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
7	chr12:86724800-86725800	Enhancers	HUES6 Cell Line	embryonic stem cell
8	chr12:86724800-86726400	Enhancers	iPS-15b Cell Line	embryonic stem cell
9	chr12:86724800-86727600	Enhancers	Cortex derived primary cultured neurospheres	brain
10	chr12:86725000-86725600	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
11	chr12:86725000-86725600	Enhancers	iPS DF 6.9 Cell Line	embryonic stem cell
12	chr12:86725000-86726000	Enhancers	ES-I3 Cell Line	embryonic stem cell
13	chr12:86725000-86726000	Enhancers	iPS-18 Cell Line	embryonic stem cell
14	chr12:86725200-86726000	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
15	chr12:86725400-86725600	Flanking Active TSS	Brain Germinal Matrix	brain
16	chr12:86725400-86726800	Weak transcription	H9 Cell Line	embryonic stem cell

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