Variant report

Variant	rs3816452
Chromosome Location	chr15:99653511-99653512
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr15:99653397..99656049-chr15:99657808..99660823,3	MCF-7	breast:
2	chr15:99652267..99657709-chr15:99661798..99664247,5	MCF-7	breast:

Extended variants
information (count: 36 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:17)

rs_ID	r²[population]
rs12148328	0.86[ASN][1000 genomes]
rs12441651	0.83[ASN][1000 genomes]
rs1670232	0.82[ASN][1000 genomes]
rs1670233	0.83[ASN][1000 genomes]
rs1670234	0.83[ASN][1000 genomes]
rs1670244	0.85[ASN][1000 genomes]
rs1670248	0.90[AMR][1000 genomes];1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs1670251	0.87[ASN][1000 genomes]
rs1670253	0.85[ASN][1000 genomes]
rs1670254	0.87[ASN][1000 genomes]
rs1703761	0.83[GIH][hapmap]
rs2292288	0.81[CHD][hapmap];0.91[MEX][hapmap]
rs2305445	0.96[CEU][hapmap];0.86[CHB][hapmap];0.97[CHD][hapmap];1.00[GIH][hapmap];0.95[JPT][hapmap];0.94[LWK][hapmap];1.00[MEX][hapmap];0.94[MKK][hapmap];1.00[TSI][hapmap];0.84[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2654967	0.87[ASN][1000 genomes]
rs55803543	0.80[ASN][1000 genomes]
rs7178187	0.87[MEX][hapmap]
rs921578	0.83[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:19 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv531079	chr15:98907913-99878547	Strong transcription Weak transcription Genic enhancers Active TSS Enhancers ZNF genes & repeats Flanking Active TSS Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	97 gene(s)	inside rSNPs	diseases
2	nsv1039575	chr15:98982045-99924685	Weak transcription Bivalent Enhancer Enhancers Genic enhancers Flanking Active TSS Active TSS Strong transcription ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	96 gene(s)	inside rSNPs	diseases
3	nsv869529	chr15:99416774-99903351	Genic enhancers Weak transcription Enhancers Flanking Active TSS Strong transcription Bivalent Enhancer Active TSS ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	60 gene(s)	inside rSNPs	diseases
4	nsv533375	chr15:99443534-99696221	Enhancers Genic enhancers Bivalent/Poised TSS Weak transcription Active TSS Flanking Active TSS Strong transcription ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	29 gene(s)	inside rSNPs	diseases
5	nsv1050982	chr15:99450004-99725825	Enhancers Strong transcription Genic enhancers Bivalent Enhancer Weak transcription Flanking Bivalent TSS/Enh Flanking Active TSS 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	26 gene(s)	inside rSNPs	diseases
6	nsv530685	chr15:99452377-99713365	Bivalent/Poised TSS Strong transcription Genic enhancers Weak transcription ZNF genes & repeats Flanking Active TSS Enhancers Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	26 gene(s)	inside rSNPs	diseases
7	nsv1055008	chr15:99477144-100019861	Enhancers Weak transcription Strong transcription Flanking Active TSS Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh Active TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	46 gene(s)	inside rSNPs	diseases
8	nsv1045124	chr15:99504843-99847210	Strong transcription Active TSS Weak transcription Enhancers Genic enhancers Flanking Active TSS Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	39 gene(s)	inside rSNPs	diseases
9	nsv1038870	chr15:99510479-99768374	Enhancers Bivalent Enhancer Weak transcription Active TSS Bivalent/Poised TSS Strong transcription Flanking Active TSS ZNF genes & repeats Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	23 gene(s)	inside rSNPs	diseases
10	nsv904543	chr15:99513231-99991506	Weak transcription Flanking Active TSS Enhancers Strong transcription Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	45 gene(s)	inside rSNPs	diseases
11	nsv533926	chr15:99519820-99997114	Enhancers Active TSS Weak transcription Bivalent Enhancer Flanking Active TSS Strong transcription Bivalent/Poised TSS Flanking Bivalent TSS/Enh Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	45 gene(s)	inside rSNPs	diseases
12	nsv915926	chr15:99519820-100138705	Active TSS Enhancers Weak transcription Flanking Bivalent TSS/Enh Strong transcription Flanking Active TSS Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	55 gene(s)	inside rSNPs	diseases
13	nsv904544	chr15:99524865-99655744	Flanking Active TSS Enhancers Active TSS Genic enhancers Bivalent Enhancer Weak transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS Strong transcription Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	20 gene(s)	inside rSNPs	diseases
14	nsv1051782	chr15:99621061-99792967	Enhancers Active TSS Weak transcription Strong transcription Flanking Active TSS Bivalent Enhancer Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	26 gene(s)	inside rSNPs	diseases
15	nsv916822	chr15:99621061-99878564	Enhancers Flanking Active TSS Weak transcription Strong transcription Genic enhancers Bivalent Enhancer ZNF genes & repeats 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	30 gene(s)	inside rSNPs	diseases
16	nsv949203	chr15:99621061-99932797	Strong transcription Weak transcription Enhancers Bivalent Enhancer Active TSS Genic enhancers ZNF genes & repeats Flanking 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	31 gene(s)	inside rSNPs	diseases
17	nsv817289	chr15:99621061-100138705	Weak transcription Flanking Active TSS Enhancers ZNF genes & repeats Strong transcription Bivalent/Poised TSS Active TSS Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	44 gene(s)	inside rSNPs	diseases
18	nsv431411	chr15:99621061-100143999	Enhancers Flanking Active TSS Weak transcription Active TSS Bivalent/Poised TSS Strong transcription Genic enhancers ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	44 gene(s)	inside rSNPs	diseases
19	nsv570716	chr15:99629901-99916332	Weak transcription Active TSS Transcr. at gene 5' and 3' Strong transcription Enhancers Flanking Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS Genic enhancers Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	30 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs3816452	SYNM	cis	parietal	SCAN
rs3816452	SYNM	cis	cerebellum	SCAN

Chromatin state (count:66 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:99646400-99663200	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
2	chr15:99646600-99653800	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
3	chr15:99646600-99662200	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
4	chr15:99646800-99663600	Weak transcription	Ovary	ovary
5	chr15:99646800-99663600	Weak transcription	Spleen	Spleen
6	chr15:99647000-99662000	Weak transcription	HUVEC	blood vessel
7	chr15:99647000-99663200	Weak transcription	HSMM	muscle
8	chr15:99647200-99654000	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
9	chr15:99647600-99654600	Weak transcription	Stomach Mucosa	stomach
10	chr15:99647600-99672400	Weak transcription	Esophagus	oesophagus
11	chr15:99647800-99653800	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
12	chr15:99647800-99654800	Weak transcription	Placenta	Placenta
13	chr15:99648000-99653800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
14	chr15:99648000-99653800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
15	chr15:99648000-99653800	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
16	chr15:99648000-99653800	Weak transcription	Pancreas	Pancrea
17	chr15:99648000-99658000	Weak transcription	Fetal Brain Female	brain
18	chr15:99648000-99663200	Weak transcription	Rectal Mucosa Donor 29	rectum
19	chr15:99648200-99654000	Weak transcription	Fetal Intestine Small	intestine
20	chr15:99648200-99654000	Weak transcription	NHLF	lung
21	chr15:99648200-99656200	Weak transcription	Hela-S3	cervix
22	chr15:99648200-99663000	Weak transcription	NHDF-Ad	bronchial
23	chr15:99648200-99663200	Weak transcription	Duodenum Mucosa	Duodenum
24	chr15:99648600-99653600	Weak transcription	Brain Hippocampus Middle	brain
25	chr15:99648600-99655400	Transcr. at gene 5' and 3'	Stomach Smooth Muscle	stomach
26	chr15:99649000-99663800	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
27	chr15:99649200-99658400	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
28	chr15:99649800-99653800	Weak transcription	Brain Inferior Temporal Lobe	brain
29	chr15:99650200-99653800	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
30	chr15:99650200-99653800	Weak transcription	Fetal Stomach	stomach
31	chr15:99650200-99654200	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
32	chr15:99650400-99653800	Weak transcription	Fetal Muscle Trunk	muscle
33	chr15:99650400-99653800	Weak transcription	Right Atrium	heart
34	chr15:99650400-99653800	Weak transcription	Right Ventricle	heart
35	chr15:99650400-99663400	Weak transcription	HSMMtube	muscle
36	chr15:99650600-99653800	Weak transcription	Lung	lung
37	chr15:99650600-99663400	Weak transcription	Colonic Mucosa	Colon
38	chr15:99650800-99662000	Strong transcription	A549	lung
39	chr15:99651200-99653800	Weak transcription	Adipose Nuclei	Adipose
40	chr15:99651200-99653800	Weak transcription	Fetal Muscle Leg	muscle
41	chr15:99651200-99653800	Weak transcription	Psoas Muscle	Psoas
42	chr15:99651200-99659600	Weak transcription	Liver	Liver
43	chr15:99651200-99663200	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
44	chr15:99651200-99663800	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
45	chr15:99651400-99654000	Weak transcription	Brain Angular Gyrus	brain
46	chr15:99651400-99663200	Weak transcription	NH-A	brain
47	chr15:99651800-99653600	Weak transcription	Brain Cingulate Gyrus	brain
48	chr15:99651800-99654200	Transcr. at gene 5' and 3'	Breast Myoepithelial Primary Cells	Breast
49	chr15:99651800-99654600	Weak transcription	Brain Anterior Caudate	brain
50	chr15:99651800-99655000	Weak transcription	Aorta	Aorta

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