Variant report

Variant	rs13115302
Chromosome Location	chr4:7746083-7746084
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 18 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:10)

rs_ID	r²[population]
rs10049998	0.92[LWK][hapmap];0.91[MKK][hapmap]
rs13151500	0.84[ASN][1000 genomes]
rs17466783	0.82[AFR][1000 genomes];0.82[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs34769859	0.84[ASN][1000 genomes]
rs4361385	0.92[LWK][hapmap];0.91[MKK][hapmap]
rs4696772	0.92[LWK][hapmap];0.91[MKK][hapmap]
rs6446627	0.82[MKK][hapmap]
rs6446629	0.92[LWK][hapmap];0.91[MKK][hapmap]
rs6832352	0.92[LWK][hapmap];0.91[MKK][hapmap]
rs7697255	0.92[LWK][hapmap];0.91[MKK][hapmap]

Variant overlapped rSNPs/rCNVs (count:8 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv34156	chr4:7526515-7750588	Active TSS Flanking Active TSS Strong transcription Enhancers Bivalent Enhancer Weak transcription ZNF genes & repeats Bivalent/Poised TSS Genic enhancers Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region	5 gene(s)	inside rSNPs	diseases
2	nsv878570	chr4:7534603-7836835	Bivalent Enhancer Flanking Active TSS Enhancers Weak transcription Strong transcription ZNF genes & repeats Genic enhancers Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	12 gene(s)	inside rSNPs	diseases
3	nsv491712	chr4:7582506-8155069	Enhancers Bivalent Enhancer Genic enhancers Weak transcription Flanking Active TSS Flanking Bivalent TSS/Enh Active TSS ZNF genes & repeats Strong transcription Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	16 gene(s)	inside rSNPs	diseases
4	nsv1007319	chr4:7705550-7832097	Strong transcription Flanking Active TSS Weak transcription Enhancers Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	8 gene(s)	inside rSNPs	diseases
5	nsv537018	chr4:7705550-7832097	Genic enhancers Strong transcription Weak transcription Enhancers Flanking Active TSS Bivalent Enhancer Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	8 gene(s)	inside rSNPs	diseases
6	nsv878574	chr4:7715181-7751894	Weak transcription Enhancers Active TSS ZNF genes & repeats Bivalent Enhancer Genic enhancers Strong transcription Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region	2 gene(s)	inside rSNPs	diseases
7	nsv878575	chr4:7715181-7767755	Weak transcription Bivalent Enhancer Enhancers Strong transcription Active TSS Genic enhancers Flanking Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region miRNA target site	2 gene(s)	inside rSNPs	diseases
8	nsv878576	chr4:7720919-7746820	Weak transcription Bivalent Enhancer Flanking Active TSS Flanking Bivalent TSS/Enh Genic enhancers Strong transcription Enhancers ZNF genes & repeats Active TSS Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region	2 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs13115302	AFAP1	cis	parietal	SCAN
rs13115302	CLNK	cis	cerebellum	SCAN

Chromatin state (count:35 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:7726600-7757200	Weak transcription	Fetal Brain Female	brain
2	chr4:7740200-7765000	Weak transcription	Aorta	Aorta
3	chr4:7740400-7746400	Weak transcription	Colonic Mucosa	Colon
4	chr4:7740600-7762400	Weak transcription	Pancreas	Pancrea
5	chr4:7741000-7757800	Weak transcription	Lung	lung
6	chr4:7741400-7755000	Weak transcription	Fetal Intestine Small	intestine
7	chr4:7741400-7755200	Weak transcription	Brain Germinal Matrix	brain
8	chr4:7742000-7746400	Weak transcription	Ovary	ovary
9	chr4:7742000-7749400	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
10	chr4:7744000-7752800	Enhancers	Primary monocytes fromperipheralblood	blood
11	chr4:7744200-7746400	Enhancers	Breast Myoepithelial Primary Cells	Breast
12	chr4:7744800-7746200	Enhancers	Brain Cingulate Gyrus	brain
13	chr4:7744800-7746200	Enhancers	Colon Smooth Muscle	Colon
14	chr4:7744800-7746400	Enhancers	Rectal Smooth Muscle	rectum
15	chr4:7745000-7746200	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
16	chr4:7745000-7746200	Enhancers	Brain Anterior Caudate	brain
17	chr4:7745000-7746600	Enhancers	Brain Hippocampus Middle	brain
18	chr4:7745000-7747400	Bivalent Enhancer	Placenta	Placenta
19	chr4:7745200-7746400	Enhancers	Brain Inferior Temporal Lobe	brain
20	chr4:7745200-7746400	Flanking Active TSS	Monocytes-CD14+_RO01746	blood
21	chr4:7745200-7746600	Enhancers	GM12878-XiMat	blood
22	chr4:7745200-7749400	Enhancers	Fetal Brain Male	brain
23	chr4:7745400-7746600	Enhancers	Spleen	Spleen
24	chr4:7745400-7746600	Enhancers	HepG2	liver
25	chr4:7745800-7746200	Active TSS	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
26	chr4:7745800-7746200	Enhancers	Fetal Muscle Leg	muscle
27	chr4:7745800-7746400	Enhancers	Right Atrium	heart
28	chr4:7745800-7746600	Strong transcription	Fetal Stomach	stomach
29	chr4:7745800-7748400	Weak transcription	Brain Angular Gyrus	brain
30	chr4:7746000-7747800	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
31	chr4:7746000-7748400	Weak transcription	Brain Substantia Nigra	brain
32	chr4:7746000-7751400	Weak transcription	HMEC	breast
33	chr4:7746000-7752200	Weak transcription	Esophagus	oesophagus
34	chr4:7746000-7753200	Weak transcription	Stomach Smooth Muscle	stomach
35	chr4:7746000-7758800	Weak transcription	Cortex derived primary cultured neurospheres	brain

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