Variant report

Variant	rs1493414
Chromosome Location	chr12:86650395-86650396
allele	A/T
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	chr12:86649901-86650443	H1-neurons	neurons:	n/a	n/a

Variant related genes	Relation type
MGAT4C	TF binding region

Extended variants
information (count: 103 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:94)

rs_ID	r²[population]
rs10745415	0.82[AMR][1000 genomes];0.82[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10776954	0.89[CEU][hapmap];0.86[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs10776958	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs10776960	0.94[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs10776967	0.86[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10776975	0.89[CEU][hapmap]
rs10858409	0.87[EUR][1000 genomes]
rs10858411	1.00[CEU][hapmap];1.00[CHB][hapmap];0.86[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs10858412	0.89[CEU][hapmap]
rs10858417	0.86[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs10858420	0.94[CEU][hapmap];1.00[CHB][hapmap];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10858424	1.00[CHB][hapmap];1.00[YRI][hapmap]
rs1097997	0.84[CEU][hapmap];1.00[CHB][hapmap];1.00[YRI][hapmap]
rs11103946	0.86[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs11117189	1.00[CHB][hapmap]
rs12372566	1.00[CHB][hapmap]
rs1389292	0.94[CEU][hapmap];1.00[CHB][hapmap];0.88[AFR][1000 genomes];0.94[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs1389294	0.88[CEU][hapmap];0.86[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs1389295	0.84[CEU][hapmap];0.90[EUR][1000 genomes]
rs1463750	0.94[CEU][hapmap];1.00[CHB][hapmap];1.00[YRI][hapmap]
rs1493413	0.82[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs1493417	0.89[CEU][hapmap];0.86[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs1493418	0.89[CEU][hapmap];0.86[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs1493419	0.84[CEU][hapmap]
rs1493420	0.81[AMR][1000 genomes]
rs1532263	0.94[CEU][hapmap];1.00[CHB][hapmap];1.00[YRI][hapmap];0.88[AFR][1000 genomes];0.97[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs1628799	0.94[CEU][hapmap]
rs1689364	0.94[CEU][hapmap];1.00[CHB][hapmap]
rs1698757	1.00[CHB][hapmap]
rs1994863	0.88[EUR][1000 genomes]
rs2178748	0.87[CEU][hapmap];1.00[CHB][hapmap];1.00[YRI][hapmap]
rs2250915	0.81[AMR][1000 genomes]
rs2405932	0.83[CEU][hapmap]
rs2405934	0.89[CEU][hapmap]
rs2406120	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2406121	0.93[EUR][1000 genomes]
rs2406128	0.89[CEU][hapmap]
rs2452803	0.89[CEU][hapmap];0.86[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs2452805	0.88[CEU][hapmap];0.86[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs2452808	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[YRI][hapmap];0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2465142	0.90[EUR][1000 genomes]
rs2465145	0.86[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs2465148	0.86[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs2471562	0.80[CEU][hapmap];0.81[AMR][1000 genomes]
rs2471565	0.94[CEU][hapmap];1.00[CHB][hapmap]
rs2471567	0.84[CEU][hapmap];0.90[EUR][1000 genomes]
rs2897269	0.89[CEU][hapmap];1.00[CHB][hapmap]
rs2897273	0.82[CEU][hapmap];1.00[CHB][hapmap];1.00[YRI][hapmap]
rs4329741	0.86[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs4444151	0.89[CEU][hapmap];1.00[CHB][hapmap]
rs6538021	0.84[CEU][hapmap]
rs6538023	0.94[CEU][hapmap];0.83[EUR][1000 genomes]
rs6538027	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[YRI][hapmap]
rs6538040	0.89[CEU][hapmap];1.00[CHB][hapmap]
rs7134045	0.82[CEU][hapmap]
rs7134944	0.94[CEU][hapmap];1.00[CHB][hapmap];1.00[YRI][hapmap]
rs7303642	0.93[EUR][1000 genomes]
rs7309839	0.89[CEU][hapmap];1.00[CHB][hapmap]
rs7312245	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[YRI][hapmap]
rs7953494	0.86[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs7954833	0.94[CEU][hapmap];1.00[CHB][hapmap];1.00[YRI][hapmap];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7963957	0.87[EUR][1000 genomes]
rs7966656	0.80[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7972185	0.94[CEU][hapmap]
rs7975314	0.88[CEU][hapmap];1.00[CHB][hapmap]
rs839099	0.84[CEU][hapmap];1.00[CHB][hapmap];1.00[YRI][hapmap]
rs839100	0.94[CEU][hapmap];1.00[CHB][hapmap]
rs839106	1.00[CHB][hapmap]
rs839107	0.94[CEU][hapmap];1.00[CHB][hapmap];1.00[YRI][hapmap];0.97[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs839109	0.84[CEU][hapmap];1.00[CHB][hapmap];1.00[YRI][hapmap]
rs839112	0.84[CEU][hapmap];1.00[YRI][hapmap]
rs839113	1.00[CHB][hapmap]
rs839114	0.84[CEU][hapmap];1.00[CHB][hapmap];1.00[YRI][hapmap]
rs839115	1.00[CHB][hapmap];1.00[YRI][hapmap]
rs839116	0.84[CEU][hapmap];1.00[CHB][hapmap]
rs839117	0.84[CEU][hapmap]
rs839119	1.00[CHB][hapmap]
rs839120	1.00[CHB][hapmap]
rs839124	1.00[CHB][hapmap]
rs839128	1.00[CHB][hapmap]
rs839134	0.84[CEU][hapmap];1.00[CHB][hapmap]
rs839138	0.84[CEU][hapmap];1.00[CHB][hapmap]
rs839139	0.84[CEU][hapmap];1.00[CHB][hapmap]
rs839147	0.84[CEU][hapmap];1.00[CHB][hapmap]
rs839162	0.89[CEU][hapmap]
rs839166	0.80[CEU][hapmap]
rs839183	0.84[CEU][hapmap];1.00[CHB][hapmap]
rs839189	1.00[CHB][hapmap]
rs839191	1.00[CHB][hapmap]
rs844433	0.94[CEU][hapmap]
rs844434	0.80[CEU][hapmap]
rs844437	0.84[CEU][hapmap];1.00[CHB][hapmap]
rs858213	0.94[CEU][hapmap];1.00[CHB][hapmap];1.00[YRI][hapmap]
rs866893	1.00[CHB][hapmap]

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

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs1493414	MGAT4C	cis	Heart Left Ventricle	GTEx

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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