Variant report

Variant	rs4689705
Chromosome Location	chr4:7325002-7325003
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 37 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:12)

rs_ID	r²[population]
rs10937805	0.87[ASN][1000 genomes]
rs1104939	0.94[CEU][hapmap];1.00[YRI][hapmap];0.93[EUR][1000 genomes]
rs16840033	0.94[CEU][hapmap];0.93[EUR][1000 genomes]
rs3913444	0.94[CEU][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap]
rs3913445	0.89[CEU][hapmap];0.80[CHB][hapmap];1.00[JPT][hapmap];0.84[AMR][1000 genomes];0.90[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs4689702	1.00[CEU][hapmap];0.89[CHB][hapmap];1.00[JPT][hapmap];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4689703	1.00[CEU][hapmap];0.89[CHB][hapmap];1.00[JPT][hapmap];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4689704	1.00[CEU][hapmap];1.00[JPT][hapmap];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4689706	0.87[ASN][1000 genomes]
rs4689708	0.95[CEU][hapmap];0.90[CHB][hapmap];1.00[JPT][hapmap];0.83[AMR][1000 genomes];0.90[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6819749	1.00[YRI][hapmap]
rs6843614	0.84[ASW][hapmap];0.80[GIH][hapmap];0.88[MEX][hapmap];0.88[TSI][hapmap];0.80[AMR][1000 genomes];0.81[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:25 , 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
17	nsv1011547	chr4:7318232-7637410	Active TSS ZNF genes & repeats Weak transcription Enhancers Bivalent Enhancer Flanking Active TSS Genic enhancers Strong transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA	6 gene(s)	inside rSNPs	diseases
18	nsv537017	chr4:7318232-7637410	Weak transcription Flanking Active TSS Bivalent Enhancer Enhancers ZNF genes & repeats Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Genic enhancers Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA miRNA	6 gene(s)	inside rSNPs	diseases
19	nsv1003679	chr4:7319111-7449262	Bivalent Enhancer Weak transcription Flanking Active TSS Enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS Active TSS Genic enhancers Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
20	nsv878552	chr4:7321511-7341243	Weak transcription Enhancers Bivalent Enhancer Flanking Active TSS Genic enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh	Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
21	nsv878553	chr4:7321511-7376694	Weak transcription Bivalent Enhancer Enhancers ZNF genes & repeats Strong transcription Flanking Active TSS Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Active TSS	Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
22	nsv878554	chr4:7323450-7338852	Flanking Active TSS Enhancers Weak transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Genic enhancers	Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
23	nsv878555	chr4:7325002-7338619	Enhancers Weak transcription Bivalent Enhancer Flanking Active TSS Flanking Bivalent TSS/Enh Genic enhancers	Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
24	nsv878556	chr4:7325002-7339378	Enhancers Weak transcription Flanking Active TSS Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats	Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
25	nsv878557	chr4:7325002-7348593	Enhancers Weak transcription ZNF genes & repeats Bivalent Enhancer Genic enhancers Flanking Active TSS Strong transcription Flanking Bivalent TSS/Enh	Chromatin interactive region	1 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs4689705	SORCS2	cis	parietal	SCAN
rs4689705	HTRA3	cis	parietal	SCAN

Chromatin state (count:25 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:7311800-7326400	Weak transcription	Fetal Brain Male	brain
2	chr4:7322400-7328400	Weak transcription	HSMMtube	muscle
3	chr4:7322600-7325800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
4	chr4:7323000-7330800	Weak transcription	Right Atrium	heart
5	chr4:7323600-7325400	Enhancers	Fetal Lung	lung
6	chr4:7323600-7325400	Enhancers	Fetal Stomach	stomach
7	chr4:7323600-7325600	Enhancers	Brain Inferior Temporal Lobe	brain
8	chr4:7323600-7327200	Enhancers	Brain Anterior Caudate	brain
9	chr4:7323600-7331600	Enhancers	Brain Cingulate Gyrus	brain
10	chr4:7323800-7326400	Enhancers	Brain Hippocampus Middle	brain
11	chr4:7323800-7326800	Enhancers	Cortex derived primary cultured neurospheres	brain
12	chr4:7323800-7327000	Enhancers	Brain Angular Gyrus	brain
13	chr4:7324200-7325200	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
14	chr4:7324200-7325200	Enhancers	Fetal Kidney	kidney
15	chr4:7324400-7327000	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
16	chr4:7324400-7327200	Enhancers	Brain Substantia Nigra	brain
17	chr4:7324400-7328400	Weak transcription	NH-A	brain
18	chr4:7324400-7328600	Weak transcription	Brain Germinal Matrix	brain
19	chr4:7324400-7335600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
20	chr4:7324600-7325200	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
21	chr4:7324600-7325800	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
22	chr4:7324600-7326200	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
23	chr4:7324800-7328600	Weak transcription	Ovary	ovary
24	chr4:7325000-7325200	Bivalent Enhancer	Placenta	Placenta
25	chr4:7325000-7328000	Enhancers	Primary Natural Killer cells fromperipheralblood	blood

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