Variant report

Variant	rs4689665
Chromosome Location	chr4:7243400-7243401
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 20 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:8)

rs_ID	r²[population]
rs11947768	0.97[ASN][1000 genomes]
rs4689100	0.97[ASN][1000 genomes]
rs6414632	0.81[AMR][1000 genomes]
rs6446583	0.93[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs6820163	0.83[CEU][hapmap];0.88[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs6830990	0.95[ASN][1000 genomes]
rs6851490	0.86[AMR][1000 genomes]
rs6852212	1.00[ASW][hapmap]

Variant overlapped rSNPs/rCNVs (count:12 , 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	esv2757919	chr4:6988148-7269901	Genic enhancers Strong transcription Flanking Active TSS Bivalent Enhancer Weak transcription Enhancers Flanking Bivalent TSS/Enh Active TSS ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	38 gene(s)	inside rSNPs	diseases
3	esv2759221	chr4:6988148-7269901	Active TSS Weak transcription Flanking Active TSS Enhancers Bivalent Enhancer Strong transcription Transcr. at gene 5' and 3' Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	38 gene(s)	inside rSNPs	diseases
4	nsv428436	chr4:6988148-7269901	Bivalent Enhancer Weak transcription Bivalent/Poised TSS Active TSS Enhancers Genic enhancers Flanking Active TSS Transcr. at gene 5' and 3' Strong transcription ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	38 gene(s)	inside rSNPs	diseases
5	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
6	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
7	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
8	nsv878542	chr4:7214696-7276541	Enhancers Weak transcription ZNF genes & repeats Bivalent Enhancer Flanking Active TSS Bivalent/Poised TSS Active TSS Strong transcription Flanking Bivalent TSS/Enh Genic enhancers	Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
9	nsv461198	chr4:7219933-7265635	Bivalent Enhancer Weak transcription Enhancers Active TSS Flanking Active TSS ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh Strong transcription Genic enhancers	Chromatin interactive region lncRNA	n/a	inside rSNPs	diseases
10	nsv593565	chr4:7219933-7265635	ZNF genes & repeats Enhancers Bivalent Enhancer Weak transcription Flanking Active TSS Flanking Bivalent TSS/Enh Active TSS Bivalent/Poised TSS Genic enhancers Strong transcription	Chromatin interactive region lncRNA	n/a	inside rSNPs	diseases
11	nsv4218	chr4:7225196-7270057	Flanking Active TSS Enhancers Weak transcription ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Active TSS Flanking Bivalent TSS/Enh Strong transcription Genic enhancers	Chromatin interactive region lncRNA	n/a	inside rSNPs	diseases
12	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

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs4689665	ABLIM2	cis	cerebellum	SCAN
rs4689665	JAKMIP1	cis	cerebellum	SCAN
rs4689665	GPR78	cis	parietal	SCAN

Chromatin state (count:21 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:7238800-7245400	Weak transcription	Fetal Brain Male	brain
2	chr4:7239000-7244600	Weak transcription	Brain Substantia Nigra	brain
3	chr4:7239000-7245400	Weak transcription	Brain Angular Gyrus	brain
4	chr4:7240200-7244800	Weak transcription	Duodenum Smooth Muscle	Duodenum
5	chr4:7240400-7243400	Weak transcription	Brain Cingulate Gyrus	brain
6	chr4:7240600-7244400	Weak transcription	Brain Inferior Temporal Lobe	brain
7	chr4:7240600-7244600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
8	chr4:7240800-7245400	Weak transcription	Right Atrium	heart
9	chr4:7241000-7245400	Weak transcription	Esophagus	oesophagus
10	chr4:7241400-7245800	Weak transcription	Stomach Smooth Muscle	stomach
11	chr4:7241800-7245800	Weak transcription	Fetal Lung	lung
12	chr4:7242000-7245200	Weak transcription	Right Ventricle	heart
13	chr4:7242000-7245400	Weak transcription	Left Ventricle	heart
14	chr4:7242200-7245200	Weak transcription	Fetal Heart	heart
15	chr4:7243000-7243800	Bivalent Enhancer	Fetal Muscle Leg	muscle
16	chr4:7243000-7247600	Bivalent Enhancer	Fetal Muscle Trunk	muscle
17	chr4:7243200-7243800	Enhancers	iPS DF 19.11 Cell Line	embryonic stem cell
18	chr4:7243200-7244800	Weak transcription	Brain Germinal Matrix	brain
19	chr4:7243400-7243600	Enhancers	Fetal Brain Female	brain
20	chr4:7243400-7243600	Bivalent Enhancer	Skeletal Muscle Female	skeletal muscle
21	chr4:7243400-7243800	Enhancers	Brain Cingulate Gyrus	brain

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