Variant report

Variant	rs3892041
Chromosome Location	chr4:7314962-7314963
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 55 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:39)

rs_ID	r²[population]
rs10006875	0.88[EUR][1000 genomes]
rs10009323	0.82[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs10026693	0.89[CEU][hapmap];0.91[TSI][hapmap];0.91[EUR][1000 genomes]
rs11722747	0.81[ASN][1000 genomes]
rs11942816	0.81[CEU][hapmap];0.81[TSI][hapmap];0.82[EUR][1000 genomes]
rs12648239	0.84[CEU][hapmap];0.83[EUR][1000 genomes]
rs12650279	0.83[AMR][1000 genomes];0.92[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs1875342	0.83[AFR][1000 genomes];0.85[AMR][1000 genomes];1.00[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2336114	0.92[CEU][hapmap];0.94[EUR][1000 genomes]
rs2336115	0.91[CEU][hapmap];0.94[EUR][1000 genomes]
rs2336116	0.94[EUR][1000 genomes]
rs2878617	0.88[CEU][hapmap];0.94[EUR][1000 genomes]
rs2878618	0.81[CEU][hapmap];0.94[EUR][1000 genomes]
rs2878619	0.94[EUR][1000 genomes]
rs2878620	0.89[CEU][hapmap];0.97[TSI][hapmap];0.94[EUR][1000 genomes]
rs3846428	0.82[EUR][1000 genomes]
rs3857194	0.89[CEU][hapmap];0.95[TSI][hapmap];0.93[EUR][1000 genomes]
rs3894740	0.94[EUR][1000 genomes]
rs3913442	0.89[EUR][1000 genomes]
rs3916117	0.88[CEU][hapmap];0.94[EUR][1000 genomes]
rs3916118	0.89[CEU][hapmap];0.97[TSI][hapmap];0.94[EUR][1000 genomes]
rs4689699	0.83[AFR][1000 genomes];0.84[AMR][1000 genomes];1.00[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs6814710	0.88[CEU][hapmap];0.94[EUR][1000 genomes]
rs6816762	0.94[EUR][1000 genomes]
rs6822054	0.86[CEU][hapmap];0.94[EUR][1000 genomes]
rs6822695	0.92[CEU][hapmap];0.94[EUR][1000 genomes]
rs6827884	0.92[CEU][hapmap];0.81[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs6832272	0.82[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs6832897	0.96[CEU][hapmap];1.00[TSI][hapmap];0.81[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs6833329	0.96[CEU][hapmap];0.97[TSI][hapmap];0.98[EUR][1000 genomes]
rs6841639	0.94[EUR][1000 genomes]
rs6842090	0.96[CEU][hapmap];0.82[JPT][hapmap];0.83[AMR][1000 genomes];0.98[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs6846306	0.88[CEU][hapmap];0.94[EUR][1000 genomes]
rs6846329	0.91[CEU][hapmap];0.81[JPT][hapmap];0.94[EUR][1000 genomes]
rs6847128	0.88[CEU][hapmap];0.94[EUR][1000 genomes]
rs6850248	0.81[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs9784559	0.94[EUR][1000 genomes]
rs9884489	0.89[CEU][hapmap];0.97[TSI][hapmap];0.95[EUR][1000 genomes]
rs9995241	0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.87[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:16 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv34033	chr4:6973270-7390621	Weak transcription Enhancers Strong transcription Flanking Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh Genic enhancers ZNF genes & repeats Active TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	40 gene(s)	inside rSNPs	diseases
2	nsv432556	chr4:7174993-7391948	Weak transcription Flanking Active TSS Bivalent/Poised TSS Enhancers ZNF genes & repeats Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh Genic enhancers Strong transcription Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	2 gene(s)	inside rSNPs	diseases
3	nsv878541	chr4:7211197-7341243	ZNF genes & repeats Flanking Active TSS Enhancers Weak transcription Bivalent Enhancer Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Genic enhancers Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA miRNA	2 gene(s)	inside rSNPs	diseases
4	nsv916610	chr4:7238883-7731946	Bivalent Enhancer Enhancers Active TSS Weak transcription Flanking Active TSS ZNF genes & repeats Genic enhancers Flanking Bivalent TSS/Enh Strong transcription Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA	7 gene(s)	inside rSNPs	diseases
5	nsv878543	chr4:7282506-7353052	Weak transcription Enhancers Flanking Active TSS Bivalent Enhancer Genic enhancers Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Strong transcription	TF binding region CpG island Chromatin interactive region miRNA	2 gene(s)	inside rSNPs	diseases
6	nsv878544	chr4:7285356-7359966	Enhancers Weak transcription Bivalent Enhancer ZNF genes & repeats Flanking Active TSS Active TSS Strong transcription Flanking Bivalent TSS/Enh Genic enhancers	TF binding region CpG island Chromatin interactive region miRNA	2 gene(s)	inside rSNPs	diseases
7	nsv878545	chr4:7285356-7363007	Enhancers Weak transcription Bivalent Enhancer Flanking Active TSS ZNF genes & repeats Active TSS Flanking Bivalent TSS/Enh Genic enhancers Strong transcription	TF binding region CpG island Chromatin interactive region miRNA	2 gene(s)	inside rSNPs	diseases
8	nsv878546	chr4:7285356-7376694	Enhancers Weak transcription ZNF genes & repeats Flanking Active TSS Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh Strong transcription Genic enhancers Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region miRNA	2 gene(s)	inside rSNPs	diseases
9	nsv878547	chr4:7289113-7376694	Enhancers ZNF genes & repeats Weak transcription Bivalent Enhancer Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh Strong transcription Genic enhancers Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region miRNA	2 gene(s)	inside rSNPs	diseases
10	nsv593569	chr4:7291363-7626136	Flanking Active TSS Weak transcription Bivalent Enhancer Enhancers Flanking Bivalent TSS/Enh Genic enhancers Active TSS ZNF genes & repeats Bivalent/Poised TSS Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA miRNA	7 gene(s)	inside rSNPs	diseases
11	nsv878548	chr4:7295154-7333152	Enhancers Weak transcription Bivalent Enhancer Active TSS Flanking Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Genic enhancers	TF binding region CpG island Chromatin interactive region miRNA	2 gene(s)	inside rSNPs	diseases
12	nsv878549	chr4:7295154-7376694	Enhancers Weak transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Strong transcription ZNF genes & repeats Flanking Active TSS Active TSS Bivalent/Poised TSS Genic enhancers	TF binding region CpG island Chromatin interactive region miRNA	2 gene(s)	inside rSNPs	diseases
13	nsv878550	chr4:7297506-7363952	Enhancers Weak transcription Bivalent Enhancer Flanking Active TSS ZNF genes & repeats Active TSS Strong transcription Flanking Bivalent TSS/Enh Genic enhancers	TF binding region CpG island Chromatin interactive region miRNA	2 gene(s)	inside rSNPs	diseases
14	nsv878551	chr4:7297506-7376694	Bivalent Enhancer Enhancers Weak transcription ZNF genes & repeats Genic enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Active TSS Strong transcription Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region miRNA	2 gene(s)	inside rSNPs	diseases
15	nsv461202	chr4:7311399-7333152	Weak transcription Enhancers Bivalent Enhancer ZNF genes & repeats Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh Genic enhancers	TF binding region CpG island Chromatin interactive region miRNA	1 gene(s)	inside rSNPs	diseases
16	nsv593570	chr4:7311399-7333152	Weak transcription Bivalent Enhancer Enhancers ZNF genes & repeats Active TSS Flanking Active TSS Genic enhancers Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region miRNA	1 gene(s)	inside rSNPs	diseases

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs3892041	SORCS2	cis	Brain Pons	GTEx
rs3892041	MAN2B2	cis	cerebellum	SCAN
rs3892041	LYAR	cis	parietal	SCAN
rs3892041	SORCS2	cis	parietal	SCAN

Chromatin state (count:28 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:7307200-7316200	Enhancers	Brain Inferior Temporal Lobe	brain
2	chr4:7311400-7315000	Weak transcription	ES-I3 Cell Line	embryonic stem cell
3	chr4:7311400-7315000	Weak transcription	Right Ventricle	heart
4	chr4:7311800-7315000	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
5	chr4:7311800-7326400	Weak transcription	Fetal Brain Male	brain
6	chr4:7312400-7315400	Weak transcription	Ovary	ovary
7	chr4:7313800-7316000	Enhancers	Brain Cingulate Gyrus	brain
8	chr4:7313800-7316000	Enhancers	Brain Substantia Nigra	brain
9	chr4:7313800-7316400	Enhancers	Brain Angular Gyrus	brain
10	chr4:7314000-7315200	Enhancers	H9 Cell Line	embryonic stem cell
11	chr4:7314000-7316000	Enhancers	Breast Myoepithelial Primary Cells	Breast
12	chr4:7314000-7316000	Enhancers	Brain Anterior Caudate	brain
13	chr4:7314000-7316000	Enhancers	Brain Hippocampus Middle	brain
14	chr4:7314200-7315800	Enhancers	iPS DF 19.11 Cell Line	embryonic stem cell
15	chr4:7314200-7316000	Bivalent Enhancer	Fetal Muscle Trunk	muscle
16	chr4:7314400-7315200	Bivalent Enhancer	H1 Derived Mesenchymal Stem Cells	ES cell derived
17	chr4:7314400-7315200	Enhancers	iPS DF 6.9 Cell Line	embryonic stem cell
18	chr4:7314400-7315800	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
19	chr4:7314400-7316000	Enhancers	Brain Dorsolateral Prefrontal Cortex	brain
20	chr4:7314400-7316000	Bivalent Enhancer	Fetal Stomach	stomach
21	chr4:7314400-7316000	Enhancers	Fetal Thymus	thymus
22	chr4:7314400-7316000	Enhancers	Stomach Smooth Muscle	stomach
23	chr4:7314600-7315200	Enhancers	Fetal Muscle Leg	muscle
24	chr4:7314600-7315800	Enhancers	Fetal Lung	lung
25	chr4:7314800-7315000	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
26	chr4:7314800-7315000	Enhancers	Fetal Kidney	kidney
27	chr4:7314800-7315600	Enhancers	HUES6 Cell Line	embryonic stem cell
28	chr4:7314800-7315800	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived

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