Variant report

Variant	rs3803472
Chromosome Location	chr15:99701857-99701858
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	chr15:99694775..99697545-chr15:99701020..99702847,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000103852	Chromatin interaction

Extended variants
information (count: 42 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:24)

rs_ID	r²[population]
rs12324187	0.81[CEU][hapmap];0.83[CHB][hapmap]
rs12324825	0.92[CEU][hapmap];0.85[AMR][1000 genomes]
rs12591477	0.92[CEU][hapmap];0.84[AMR][1000 genomes]
rs12594336	0.88[CEU][hapmap];0.82[CHB][hapmap];0.90[JPT][hapmap];0.91[AMR][1000 genomes];0.86[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs12594960	0.82[YRI][hapmap];0.81[AFR][1000 genomes]
rs12595385	0.96[CEU][hapmap];0.80[JPT][hapmap];0.91[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs1377267	0.92[CEU][hapmap];0.97[GIH][hapmap];0.82[TSI][hapmap];0.81[EUR][1000 genomes]
rs1530920	0.92[CEU][hapmap];0.95[GIH][hapmap];0.87[MEX][hapmap];0.82[TSI][hapmap];0.85[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs2602029	0.81[CHD][hapmap]
rs2602034	0.81[JPT][hapmap]
rs28517698	0.86[AMR][1000 genomes];0.85[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs28612155	0.81[AFR][1000 genomes];0.99[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs28819101	0.84[AMR][1000 genomes]
rs4500700	0.81[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs7170336	0.83[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs7174431	0.81[CEU][hapmap]
rs8023421	0.81[CEU][hapmap];0.87[CHB][hapmap]
rs8023490	0.96[CEU][hapmap];0.84[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs8026991	0.96[CEU][hapmap];1.00[GIH][hapmap];0.80[JPT][hapmap];0.95[MEX][hapmap];0.85[TSI][hapmap];0.88[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs8032154	1.00[ASW][hapmap];0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.89[LWK][hapmap];1.00[MEX][hapmap];0.86[MKK][hapmap];1.00[TSI][hapmap];0.93[YRI][hapmap];0.89[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs8038002	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs8038392	0.83[CEU][hapmap]
rs8038732	0.85[ASN][1000 genomes]
rs9672800	0.92[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.89[YRI][hapmap];0.84[AFR][1000 genomes];0.88[AMR][1000 genomes];0.93[EUR][1000 genomes];0.87[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:18 , 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	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
5	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
6	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
7	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
8	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
9	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
10	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
11	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
12	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
13	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
14	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
15	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
16	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
17	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
18	nsv904546	chr15:99696046-100166300	Flanking Active TSS Weak transcription Enhancers Bivalent Enhancer Strong transcription Active TSS ZNF genes & repeats Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	41 gene(s)	inside rSNPs	diseases

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs3803472	TTC23	cis	cerebellum	SCAN
rs3803472	TTC23	cis	parietal	SCAN
rs3803472	SYNM	cis	cerebellum	SCAN
rs3803472	SYNM	cis	parietal	SCAN

Chromatin state (count:91 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:99665000-99714200	Weak transcription	NHEK	skin
2	chr15:99673200-99789400	Weak transcription	Small Intestine	intestine
3	chr15:99674400-99704200	Weak transcription	Fetal Kidney	kidney
4	chr15:99676200-99703400	Weak transcription	GM12878-XiMat	blood
5	chr15:99678200-99708800	Weak transcription	Primary hematopoietic stem cells short term culture	blood
6	chr15:99684600-99706600	Weak transcription	Right Atrium	heart
7	chr15:99684800-99709200	Weak transcription	Colonic Mucosa	Colon
8	chr15:99684800-99721600	Weak transcription	iPS-15b Cell Line	embryonic stem cell
9	chr15:99685000-99720200	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
10	chr15:99689600-99707600	Weak transcription	Brain Hippocampus Middle	brain
11	chr15:99689600-99709600	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
12	chr15:99689800-99703400	Weak transcription	Brain Cingulate Gyrus	brain
13	chr15:99689800-99709400	Weak transcription	Brain Angular Gyrus	brain
14	chr15:99690000-99708200	Weak transcription	Right Ventricle	heart
15	chr15:99690000-99709400	Weak transcription	Brain Inferior Temporal Lobe	brain
16	chr15:99690200-99704800	Weak transcription	Rectal Smooth Muscle	rectum
17	chr15:99690400-99705400	Weak transcription	Skeletal Muscle Female	skeletal muscle
18	chr15:99690400-99706600	Weak transcription	Spleen	Spleen
19	chr15:99690400-99707400	Weak transcription	Gastric	stomach
20	chr15:99690400-99709800	Weak transcription	Placenta Amnion	Placenta Amnion
21	chr15:99690600-99709000	Weak transcription	Fetal Heart	heart
22	chr15:99692000-99707200	Weak transcription	HSMMtube	muscle
23	chr15:99692000-99717000	Weak transcription	HSMM	muscle
24	chr15:99694800-99702800	Weak transcription	HUVEC	blood vessel
25	chr15:99694800-99711000	Weak transcription	HUES6 Cell Line	embryonic stem cell
26	chr15:99694800-99721200	Weak transcription	H1 Cell Line	embryonic stem cell
27	chr15:99694800-99732600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
28	chr15:99694800-99732600	Weak transcription	H9 Cell Line	embryonic stem cell
29	chr15:99695200-99721600	Weak transcription	HUES64 Cell Line	embryonic stem cell
30	chr15:99695200-99721800	Weak transcription	HUES48 Cell Line	embryonic stem cell
31	chr15:99695200-99732400	Weak transcription	iPS-20b Cell Line	embryonic stem cell
32	chr15:99696200-99705600	Strong transcription	Fetal Muscle Trunk	muscle
33	chr15:99696600-99706800	Weak transcription	Osteobl	bone
34	chr15:99696600-99707400	Weak transcription	HepG2	liver
35	chr15:99696600-99709200	Weak transcription	NH-A	brain
36	chr15:99696600-99710800	Weak transcription	HMEC	breast
37	chr15:99697000-99707200	Weak transcription	Muscle Satellite Cultured Cells	--
38	chr15:99697000-99716800	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
39	chr15:99697000-99756400	Weak transcription	Stomach Mucosa	stomach
40	chr15:99697200-99712400	Weak transcription	Hela-S3	cervix
41	chr15:99698000-99706400	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
42	chr15:99698200-99702600	Weak transcription	Duodenum Smooth Muscle	Duodenum
43	chr15:99698400-99704800	Weak transcription	Colon Smooth Muscle	Colon
44	chr15:99698400-99705200	Strong transcription	Fetal Muscle Leg	muscle
45	chr15:99698600-99702600	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
46	chr15:99698600-99704000	Strong transcription	Fetal Stomach	stomach
47	chr15:99698600-99709200	Weak transcription	NHLF	lung
48	chr15:99698800-99704800	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
49	chr15:99699000-99702000	Strong transcription	Adipose Nuclei	Adipose
50	chr15:99699000-99708800	Strong transcription	Liver	Liver

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