Variant report

Variant	rs4689694
Chromosome Location	chr4:7309659-7309660
allele	A/G
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	BCL3	chr4:7309436-7309751	GM12878	blood:	n/a	n/a
2	BCL3	chr4:7309477-7309799	GM12878	blood:	n/a	n/a
3	PBX3	chr4:7309438-7309667	GM12878	blood:	n/a	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr4:7308048..7310472-chr4:7320955..7323841,2	MCF-7	breast:

Variant related genes	Relation type
MIR4798	TF binding region

Extended variants
information (count: 40 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:23)

rs_ID	r²[population]
rs10937803	0.81[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs10937804	0.81[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs11722747	0.84[CEU][hapmap]
rs11942816	0.90[CHB][hapmap];0.86[CHD][hapmap];0.90[JPT][hapmap];0.91[ASN][1000 genomes]
rs12504886	0.82[AMR][1000 genomes];0.86[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs34168071	0.89[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs3843439	0.89[AFR][1000 genomes];0.97[ASN][1000 genomes]
rs3846426	0.83[ASW][hapmap];0.91[CEU][hapmap];1.00[CHB][hapmap];0.98[CHD][hapmap];1.00[JPT][hapmap];0.91[MEX][hapmap];0.99[ASN][1000 genomes]
rs3846427	0.91[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.83[YRI][hapmap];0.92[AFR][1000 genomes];0.80[AMR][1000 genomes];0.85[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs3846428	0.90[ASN][1000 genomes]
rs3846429	0.81[AMR][1000 genomes];0.95[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs4689103	0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs4689692	0.91[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4689693	0.81[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs4689695	0.95[JPT][hapmap]
rs4689696	0.98[ASN][1000 genomes]
rs4689697	0.89[AFR][1000 genomes];0.97[ASN][1000 genomes]
rs4689698	0.95[JPT][hapmap]
rs6845859	0.84[TSI][hapmap]
rs881240	0.91[CEU][hapmap];0.86[CHB][hapmap];0.90[JPT][hapmap];0.80[ASN][1000 genomes]
rs885310	0.81[CEU][hapmap]
rs952587	0.89[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs952588	0.88[ASW][hapmap];0.95[CHB][hapmap];0.98[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.91[MEX][hapmap];0.84[MKK][hapmap];0.86[YRI][hapmap];0.81[EUR][1000 genomes];0.97[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:17 , 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	nsv829850	chr4:7112509-7314016	Bivalent Enhancer Enhancers Active TSS Weak transcription Bivalent/Poised TSS Flanking Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Genic enhancers Strong transcription Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	8 gene(s)	inside rSNPs	diseases
3	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
4	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
5	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
6	nsv461201	chr4:7256620-7311399	Enhancers Flanking Active TSS Weak transcription Bivalent Enhancer ZNF genes & repeats Active TSS Flanking Bivalent TSS/Enh Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
7	nsv593568	chr4:7256620-7311399	Weak transcription Enhancers Flanking Active TSS Bivalent Enhancer Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
8	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
9	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
10	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
11	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
12	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
13	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
14	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
15	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
16	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
17	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

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs4689694	SORCS2	cis	parietal	SCAN
rs4689694	MRFAP1	cis	cerebellum	SCAN

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:7307200-7316200	Enhancers	Brain Inferior Temporal Lobe	brain
2	chr4:7307400-7310000	Enhancers	Brain Cingulate Gyrus	brain
3	chr4:7307600-7309800	Enhancers	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
4	chr4:7307600-7309800	Enhancers	Brain Anterior Caudate	brain
5	chr4:7307600-7309800	Enhancers	Brain Hippocampus Middle	brain
6	chr4:7307600-7310200	Enhancers	Brain Angular Gyrus	brain
7	chr4:7307600-7311800	Enhancers	Brain Substantia Nigra	brain
8	chr4:7307600-7312000	Bivalent Enhancer	Fetal Muscle Leg	muscle
9	chr4:7307600-7312400	Bivalent Enhancer	Fetal Muscle Trunk	muscle
10	chr4:7307800-7310000	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
11	chr4:7308200-7309800	Enhancers	HSMMtube	muscle
12	chr4:7308400-7311400	Enhancers	Right Ventricle	heart
13	chr4:7308400-7313000	Enhancers	Breast Myoepithelial Primary Cells	Breast
14	chr4:7308600-7311600	Enhancers	Fetal Heart	heart
15	chr4:7308600-7313000	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
16	chr4:7308600-7313200	Enhancers	Brain Dorsolateral Prefrontal Cortex	brain
17	chr4:7308800-7309800	Enhancers	Right Atrium	heart
18	chr4:7309000-7309800	Enhancers	Fetal Brain Male	brain
19	chr4:7309400-7309800	Enhancers	Brain Germinal Matrix	brain
20	chr4:7309400-7309800	Bivalent Enhancer	Skeletal Muscle Female	skeletal muscle
21	chr4:7309600-7309800	Flanking Bivalent TSS/Enh	H1 Derived Mesenchymal Stem Cells	ES cell derived
22	chr4:7309600-7309800	Enhancers	Fetal Lung	lung
23	chr4:7309600-7310600	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
24	chr4:7309600-7310600	Weak transcription	Left Ventricle	heart
25	chr4:7309600-7311800	Weak transcription	Fetal Brain Female	brain

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