Variant report

Variant	rs1493415
Chromosome Location	chr12:86650365-86650366
allele	A/C
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	POLR2A	chr12:86649868-86650387	H1-neurons	neurons:	n/a	n/a
2	KAP1	chr12:86649928-86650379	U2OS	brain:	n/a	n/a
3	POLR2A	chr12:86649901-86650443	H1-neurons	neurons:	n/a	n/a

Variant related genes	Relation type
MGAT4C	TF binding region

Extended variants
information (count: 157 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:148)

rs_ID	r²[population]
rs10431399	0.81[CEU][hapmap];0.82[JPT][hapmap]
rs10745407	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs10745408	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[YRI][hapmap];0.91[AFR][1000 genomes];0.87[AMR][1000 genomes];0.96[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs10776955	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.85[AMR][1000 genomes];0.97[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs10776957	0.82[AMR][1000 genomes];0.97[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs10776959	0.83[AFR][1000 genomes];0.82[AMR][1000 genomes];0.95[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs10776961	0.90[CEU][hapmap];0.94[CHB][hapmap];0.87[JPT][hapmap];0.94[EUR][1000 genomes]
rs10776966	0.90[CEU][hapmap];0.92[EUR][1000 genomes]
rs10776968	0.89[EUR][1000 genomes]
rs10776969	0.90[CEU][hapmap];0.82[JPT][hapmap]
rs10776971	0.81[CEU][hapmap]
rs10858408	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs10858409	0.87[ASN][1000 genomes]
rs10858412	0.94[CHB][hapmap];0.87[JPT][hapmap]
rs10858419	0.93[EUR][1000 genomes]
rs10858425	0.82[JPT][hapmap]
rs10858427	0.81[CEU][hapmap];0.82[JPT][hapmap]
rs10858428	0.81[CEU][hapmap]
rs11103912	0.80[EUR][1000 genomes]
rs11830448	0.80[JPT][hapmap]
rs12317113	0.82[JPT][hapmap]
rs12319410	0.80[JPT][hapmap]
rs12578669	0.81[CEU][hapmap];0.82[JPT][hapmap]
rs12581639	0.80[JPT][hapmap]
rs12582690	0.84[CHB][hapmap];0.88[JPT][hapmap]
rs12582767	0.81[JPT][hapmap]
rs1463749	1.00[CEU][hapmap];0.99[EUR][1000 genomes]
rs1493416	0.99[EUR][1000 genomes]
rs1532262	0.95[CEU][hapmap];0.92[EUR][1000 genomes]
rs1552839	0.95[CEU][hapmap];0.92[EUR][1000 genomes]
rs1602848	0.80[AFR][1000 genomes];0.96[AMR][1000 genomes];0.92[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs1602850	0.99[EUR][1000 genomes]
rs1628799	0.80[JPT][hapmap]
rs1689340	0.84[CEU][hapmap]
rs1689357	0.86[AMR][1000 genomes];0.88[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs1698787	0.90[CEU][hapmap];1.00[JPT][hapmap];0.90[AMR][1000 genomes];0.88[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs17013858	0.81[JPT][hapmap]
rs17013981	0.81[JPT][hapmap]
rs17014005	0.81[JPT][hapmap]
rs17014008	0.81[JPT][hapmap]
rs17014009	0.81[JPT][hapmap]
rs1922749	0.81[CEU][hapmap];0.82[JPT][hapmap]
rs1948448	0.81[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1986602	0.81[JPT][hapmap]
rs1986603	0.84[CHB][hapmap];0.81[JPT][hapmap]
rs2091818	0.81[JPT][hapmap]
rs2131565	1.00[CEU][hapmap];0.81[YRI][hapmap];0.84[AFR][1000 genomes];0.92[EUR][1000 genomes]
rs2220782	0.89[CHB][hapmap];1.00[JPT][hapmap]
rs2405923	0.85[CEU][hapmap]
rs2405925	0.90[CEU][hapmap];0.81[CHB][hapmap];0.88[JPT][hapmap]
rs2405928	0.90[CEU][hapmap];0.90[CHB][hapmap];0.88[JPT][hapmap]
rs2405929	0.80[JPT][hapmap]
rs2405930	0.90[CHB][hapmap];0.87[JPT][hapmap];0.93[EUR][1000 genomes]
rs2405931	0.80[JPT][hapmap]
rs2405933	0.90[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2406115	0.95[CEU][hapmap];0.94[CHB][hapmap];0.87[JPT][hapmap];0.82[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs2406116	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.83[AMR][1000 genomes];0.97[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2406117	0.80[AFR][1000 genomes];0.87[AMR][1000 genomes];0.97[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2406118	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[YRI][hapmap];0.87[AFR][1000 genomes];0.88[AMR][1000 genomes];0.97[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2406119	0.85[AMR][1000 genomes];0.97[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2406121	0.92[ASN][1000 genomes]
rs2406122	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.85[AMR][1000 genomes];0.97[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2406123	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[AMR][1000 genomes];0.97[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2406127	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs2406128	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs2452806	1.00[CEU][hapmap];0.99[EUR][1000 genomes]
rs2452807	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[YRI][hapmap];0.87[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2452811	0.95[CEU][hapmap];0.92[EUR][1000 genomes]
rs2452815	0.95[CEU][hapmap];0.93[EUR][1000 genomes]
rs2465143	1.00[CEU][hapmap];1.00[CHB][hapmap];0.93[JPT][hapmap];0.81[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2465144	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2465146	0.98[EUR][1000 genomes]
rs2465147	0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2465149	0.95[CEU][hapmap];0.81[YRI][hapmap]
rs2471560	0.95[CEU][hapmap];0.83[CHB][hapmap];1.00[JPT][hapmap];0.96[AMR][1000 genomes];0.91[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2471564	0.95[CEU][hapmap];0.81[YRI][hapmap]
rs2471568	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[YRI][hapmap];0.89[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2471569	1.00[CEU][hapmap];0.94[CHB][hapmap];1.00[JPT][hapmap];0.81[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2471570	0.91[AFR][1000 genomes];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2897240	0.81[JPT][hapmap]
rs2897274	0.80[JPT][hapmap]
rs2897278	0.85[CEU][hapmap];0.92[EUR][1000 genomes]
rs2897280	0.95[CEU][hapmap];0.90[CHB][hapmap];0.88[JPT][hapmap]
rs4265650	0.94[CEU][hapmap];1.00[CHB][hapmap];0.93[JPT][hapmap];0.81[AMR][1000 genomes];0.95[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs4334094	0.82[AMR][1000 genomes];0.97[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs4503614	0.85[AMR][1000 genomes];0.97[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs4526834	0.80[JPT][hapmap]
rs4628748	0.90[CEU][hapmap];0.94[CHB][hapmap];0.87[JPT][hapmap];0.94[EUR][1000 genomes]
rs4636736	0.80[JPT][hapmap]
rs4842483	0.84[CEU][hapmap];0.92[EUR][1000 genomes]
rs6538024	0.84[JPT][hapmap]
rs6538025	0.95[CEU][hapmap];0.83[CHB][hapmap];1.00[JPT][hapmap]
rs6538028	1.00[CEU][hapmap]
rs6538029	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs6538031	0.83[AFR][1000 genomes];0.83[AMR][1000 genomes];0.95[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs6538032	0.82[AMR][1000 genomes];0.95[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs6538033	0.95[CEU][hapmap];1.00[CHB][hapmap];0.88[JPT][hapmap]
rs7134946	0.86[AFR][1000 genomes];0.82[AMR][1000 genomes];0.90[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs7135177	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[YRI][hapmap];0.90[AFR][1000 genomes];0.88[AMR][1000 genomes];0.97[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs7135733	0.90[AFR][1000 genomes];0.88[AMR][1000 genomes];0.97[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs7135741	0.84[AFR][1000 genomes];0.87[AMR][1000 genomes];0.97[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs7137308	1.00[CEU][hapmap];0.99[EUR][1000 genomes]
rs7299319	0.90[CEU][hapmap];0.87[JPT][hapmap]
rs7301129	0.81[JPT][hapmap]
rs7303642	0.92[ASN][1000 genomes]
rs7310186	0.81[AMR][1000 genomes];0.95[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs7953196	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.87[YRI][hapmap]
rs7957560	0.95[CEU][hapmap];1.00[CHB][hapmap];0.94[JPT][hapmap]
rs7963957	0.88[ASN][1000 genomes]
rs7964553	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs7972484	0.95[CEU][hapmap];1.00[CHB][hapmap];0.94[JPT][hapmap];0.81[AMR][1000 genomes];0.94[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs7973773	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs839101	0.86[AMR][1000 genomes];0.85[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs839104	0.89[CEU][hapmap];0.83[CHB][hapmap];1.00[JPT][hapmap]
rs839105	0.89[CEU][hapmap];0.83[CHB][hapmap];0.94[JPT][hapmap]
rs839113	0.81[CEU][hapmap]
rs839118	0.80[CEU][hapmap]
rs839119	0.81[CEU][hapmap]
rs839123	0.81[CEU][hapmap]
rs839124	0.81[CEU][hapmap]
rs839148	0.89[CEU][hapmap];0.83[CHB][hapmap];1.00[JPT][hapmap]
rs839149	0.83[CHB][hapmap];1.00[JPT][hapmap]
rs839150	1.00[JPT][hapmap]
rs839151	0.84[CHB][hapmap];1.00[JPT][hapmap]
rs839152	0.86[CHB][hapmap];1.00[JPT][hapmap]
rs839153	0.84[CHB][hapmap];1.00[JPT][hapmap]
rs839154	0.83[CHB][hapmap];0.94[JPT][hapmap]
rs839156	0.84[CHB][hapmap];1.00[JPT][hapmap]
rs839157	0.89[CEU][hapmap];0.83[CHB][hapmap];1.00[JPT][hapmap]
rs839158	0.84[CHB][hapmap];1.00[JPT][hapmap]
rs839159	0.90[CEU][hapmap];0.84[CHB][hapmap];1.00[JPT][hapmap]
rs839162	0.80[JPT][hapmap]
rs839163	0.88[AMR][1000 genomes];0.83[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs839164	0.88[AMR][1000 genomes];0.83[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs839165	0.95[CEU][hapmap];0.83[CHB][hapmap];1.00[JPT][hapmap];0.91[AMR][1000 genomes];0.87[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs839166	0.84[CHB][hapmap];1.00[JPT][hapmap]
rs839168	0.90[CEU][hapmap];0.84[CHB][hapmap];1.00[JPT][hapmap];0.93[AMR][1000 genomes];0.83[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs839170	0.90[CEU][hapmap];0.83[CHB][hapmap];1.00[JPT][hapmap]
rs839171	0.89[CEU][hapmap];0.83[CHB][hapmap];1.00[JPT][hapmap]
rs844434	0.83[CHB][hapmap];1.00[JPT][hapmap]
rs844435	0.89[CEU][hapmap];0.83[CHB][hapmap];1.00[JPT][hapmap]
rs863392	0.95[CEU][hapmap];0.84[CHB][hapmap];1.00[JPT][hapmap]
rs863394	0.87[CHB][hapmap];0.92[JPT][hapmap];0.87[ASN][1000 genomes]
rs863395	0.89[CEU][hapmap];0.83[CHB][hapmap];1.00[JPT][hapmap]
rs865138	0.95[CEU][hapmap];0.84[CHB][hapmap];1.00[JPT][hapmap]
rs865721	0.84[CHB][hapmap];1.00[JPT][hapmap]
rs9919783	0.82[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs9919793	0.81[AMR][1000 genomes];0.96[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:9 , 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

No data

Chromatin state (count:24 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:86644200-86655400	Weak transcription	HUES6 Cell Line	embryonic stem cell
2	chr12:86648200-86650600	Active TSS	Pancreatic Islets	Pancreatic Islet
3	chr12:86648400-86650400	Active TSS	Brain Anterior Caudate	brain
4	chr12:86648600-86650400	Active TSS	Right Atrium	heart
5	chr12:86649000-86651000	Weak transcription	ES-I3 Cell Line	embryonic stem cell
6	chr12:86649600-86650400	Active TSS	Brain Cingulate Gyrus	brain
7	chr12:86649600-86650400	Active TSS	Right Ventricle	heart
8	chr12:86649800-86650400	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
9	chr12:86649800-86651000	Enhancers	iPS-20b Cell Line	embryonic stem cell
10	chr12:86649800-86651400	Enhancers	HUES48 Cell Line	embryonic stem cell
11	chr12:86650000-86650400	Active TSS	Brain Angular Gyrus	brain
12	chr12:86650000-86650400	Active TSS	Brain Hippocampus Middle	brain
13	chr12:86650000-86650400	Enhancers	Brain Substantia Nigra	brain
14	chr12:86650000-86650400	Enhancers	Fetal Lung	lung
15	chr12:86650000-86651200	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
16	chr12:86650200-86650400	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
17	chr12:86650200-86650400	Active TSS	Brain Germinal Matrix	brain
18	chr12:86650200-86650600	Weak transcription	Cortex derived primary cultured neurospheres	brain
19	chr12:86650200-86650600	Flanking Active TSS	Fetal Heart	heart
20	chr12:86650200-86651000	Weak transcription	HUES64 Cell Line	embryonic stem cell
21	chr12:86650200-86653600	Weak transcription	iPS-15b Cell Line	embryonic stem cell
22	chr12:86650200-86655400	Weak transcription	iPS-18 Cell Line	embryonic stem cell
23	chr12:86650200-86658200	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
24	chr12:86650200-86658400	Weak transcription	Left Ventricle	heart

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