Variant report

Variant	rs3812943
Chromosome Location	chr15:75312715-75312716
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr15:75289096..75291038-chr15:75311135..75313518,2	K562	blood:
2	chr15:75197976..75200333-chr15:75311534..75313971,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000178761	Chromatin interaction

Extended variants
information (count: 71 )
Associated
traits (count: 6 )

rSNPs within LD-proxies of this variant (count:68)

rs_ID	r²[population]
rs11072519	0.87[CEU][hapmap]
rs12591175	0.82[CEU][hapmap];0.94[JPT][hapmap];0.81[ASN][1000 genomes]
rs12591994	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12592477	1.00[CEU][hapmap];1.00[JPT][hapmap];0.83[AMR][1000 genomes];0.92[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12593476	0.82[AMR][1000 genomes];0.81[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs12593542	0.83[CHB][hapmap];1.00[JPT][hapmap];0.81[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs12594117	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[AMR][1000 genomes];0.94[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2289582	0.84[CHB][hapmap];1.00[JPT][hapmap];0.99[ASN][1000 genomes]
rs2304904	1.00[CEU][hapmap];0.89[CHB][hapmap];1.00[JPT][hapmap];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs28394281	0.88[AMR][1000 genomes];0.88[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs3743212	0.89[JPT][hapmap]
rs3812946	0.90[AMR][1000 genomes];0.98[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs3816261	1.00[CEU][hapmap];0.94[JPT][hapmap];0.97[AMR][1000 genomes];0.89[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs3910748	1.00[CEU][hapmap];0.89[CHB][hapmap];1.00[JPT][hapmap];0.88[AMR][1000 genomes];0.94[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs55877218	0.89[ASN][1000 genomes]
rs56828495	0.92[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs56970592	0.94[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs58068887	0.92[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs58294763	0.83[AMR][1000 genomes];0.94[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs58403754	0.92[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs58645417	0.84[AMR][1000 genomes];0.92[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs59094290	0.98[ASN][1000 genomes]
rs59303424	0.82[ASN][1000 genomes]
rs61166993	0.94[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6495135	1.00[CEU][hapmap];0.84[CHB][hapmap];1.00[JPT][hapmap];0.94[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6495136	0.83[AMR][1000 genomes];0.94[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6495137	0.94[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6495138	1.00[CEU][hapmap];0.83[CHB][hapmap];1.00[JPT][hapmap];0.94[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6495140	0.94[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6495142	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[AMR][1000 genomes];0.94[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6495146	0.82[ASN][1000 genomes]
rs7163390	1.00[CEU][hapmap];0.84[CHB][hapmap];1.00[JPT][hapmap];0.93[ASN][1000 genomes]
rs7166105	1.00[CEU][hapmap];0.94[JPT][hapmap];0.83[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs7167415	1.00[CEU][hapmap];0.84[CHB][hapmap];1.00[JPT][hapmap];0.94[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7168638	0.81[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7172065	1.00[CEU][hapmap];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs7172715	1.00[CEU][hapmap];0.89[CHB][hapmap];1.00[JPT][hapmap];0.90[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7172989	0.94[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7173218	1.00[CEU][hapmap];0.89[CHB][hapmap];1.00[JPT][hapmap];0.88[AMR][1000 genomes];0.94[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7174129	1.00[CEU][hapmap];0.84[CHB][hapmap];1.00[JPT][hapmap];0.94[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7177109	0.83[ASN][1000 genomes]
rs7179097	0.81[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7181942	1.00[CEU][hapmap];0.84[CHB][hapmap];1.00[JPT][hapmap];0.94[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7182286	0.92[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs72475969	0.82[ASN][1000 genomes]
rs7342591	1.00[CEU][hapmap];0.84[CHB][hapmap];1.00[JPT][hapmap];0.92[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7342601	1.00[CEU][hapmap];0.84[CHB][hapmap];1.00[JPT][hapmap];0.94[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs73432941	0.81[ASN][1000 genomes]
rs73436579	0.94[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs73436586	0.88[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs73438537	0.90[AMR][1000 genomes];0.89[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs73438554	0.83[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs73438569	0.83[ASN][1000 genomes]
rs74023908	0.83[AMR][1000 genomes];0.94[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs74023935	0.83[ASN][1000 genomes]
rs74025863	0.92[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs8031545	1.00[CEU][hapmap];0.84[CHB][hapmap];1.00[JPT][hapmap];0.92[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs8033125	0.80[ASN][1000 genomes]
rs8034149	0.94[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs8036573	0.98[ASN][1000 genomes]
rs8038365	0.81[ASN][1000 genomes]
rs8039433	0.82[ASN][1000 genomes]
rs8040961	0.92[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs9672926	0.91[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs9672995	0.96[ASN][1000 genomes]
rs9672996	0.94[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs9673012	1.00[CEU][hapmap];0.82[CHB][hapmap];1.00[JPT][hapmap];0.94[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs9788648	0.94[EUR][1000 genomes];0.98[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv569993	chr15:75242155-75483752	Enhancers Weak transcription Flanking Active TSS Active TSS Strong transcription Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	72 gene(s)	inside rSNPs	diseases
2	nsv542435	chr15:75271788-75321117	Enhancers Weak transcription Flanking Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Genic enhancers Strong transcription ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	27 gene(s)	inside rSNPs	diseases
3	nsv527237	chr15:75305040-75321262	Flanking Active TSS Strong transcription Weak transcription Active TSS Enhancers Bivalent/Poised TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	23 gene(s)	inside rSNPs	diseases

mRNA abundance (count:6)

SNP	Gene	Cis/trans	Tissue	Source
rs3812943	SCAMP5	cis	multi-tissue	Pritchard
rs3812943	PPCDC	cis	Adipose Subcutaneous	GTEx
rs3812943	PPCDC	cis	Thyroid	GTEx
rs3812943	PPCDC	cis	multi-tissue	Pritchard
rs3812943	SCAMP5	cis	Artery Tibial	GTEx
rs3812943	SCAMP5	cis	Esophagus Mucosa	GTEx

Chromatin state (count:58 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:75289000-75315800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
2	chr15:75289400-75315400	Weak transcription	Fetal Kidney	kidney
3	chr15:75290000-75316000	Weak transcription	Small Intestine	intestine
4	chr15:75293200-75315800	Weak transcription	Duodenum Mucosa	Duodenum
5	chr15:75294600-75315600	Weak transcription	ES-I3 Cell Line	embryonic stem cell
6	chr15:75301000-75315400	Weak transcription	Thymus	Thymus
7	chr15:75302000-75314000	Strong transcription	Fetal Intestine Small	intestine
8	chr15:75302200-75313200	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
9	chr15:75302200-75313400	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
10	chr15:75303600-75313800	Strong transcription	Cortex derived primary cultured neurospheres	brain
11	chr15:75303800-75313800	Strong transcription	Ganglion Eminence derived primary cultured neurospheres	brain
12	chr15:75303800-75314000	Strong transcription	Fetal Brain Female	brain
13	chr15:75304000-75315800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
14	chr15:75304000-75316000	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
15	chr15:75304400-75313600	Strong transcription	Fetal Stomach	stomach
16	chr15:75304600-75313200	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
17	chr15:75304800-75314000	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
18	chr15:75305000-75315800	Weak transcription	Right Ventricle	heart
19	chr15:75306200-75316000	Weak transcription	Fetal Brain Male	brain
20	chr15:75307800-75315800	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
21	chr15:75308200-75315800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
22	chr15:75308600-75313800	Strong transcription	Brain Dorsolateral Prefrontal Cortex	brain
23	chr15:75308800-75312800	Strong transcription	H1 Cell Line	embryonic stem cell
24	chr15:75309000-75315800	Weak transcription	Placenta	Placenta
25	chr15:75309400-75315600	Weak transcription	Stomach Smooth Muscle	stomach
26	chr15:75309800-75313600	Strong transcription	Brain Hippocampus Middle	brain
27	chr15:75310000-75313600	Strong transcription	Brain Cingulate Gyrus	brain
28	chr15:75310000-75313600	Strong transcription	Brain Inferior Temporal Lobe	brain
29	chr15:75310000-75315200	Weak transcription	Brain Substantia Nigra	brain
30	chr15:75310200-75315200	Weak transcription	HepG2	liver
31	chr15:75310400-75315800	Weak transcription	Pancreatic Islets	Pancreatic Islet
32	chr15:75310800-75312800	Genic enhancers	Primary hematopoietic stem cells short term culture	blood
33	chr15:75310800-75313600	Strong transcription	iPS-15b Cell Line	embryonic stem cell
34	chr15:75310800-75314000	Strong transcription	Brain Germinal Matrix	brain
35	chr15:75311000-75315600	Weak transcription	Liver	Liver
36	chr15:75311000-75315600	Weak transcription	Fetal Muscle Trunk	muscle
37	chr15:75311200-75315800	Weak transcription	H9 Cell Line	embryonic stem cell
38	chr15:75311200-75315800	Weak transcription	iPS-20b Cell Line	embryonic stem cell
39	chr15:75311400-75312800	Strong transcription	Foreskin Fibroblast Primary Cells skin02	Skin
40	chr15:75311400-75313200	Weak transcription	Primary hematopoietic stem cells	blood
41	chr15:75311400-75315400	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
42	chr15:75311400-75315800	Weak transcription	HUES64 Cell Line	embryonic stem cell
43	chr15:75311400-75315800	Weak transcription	Breast Myoepithelial Primary Cells	Breast
44	chr15:75311400-75315800	Weak transcription	Fetal Intestine Large	intestine
45	chr15:75311600-75314400	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
46	chr15:75311600-75315400	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
47	chr15:75311800-75313200	Strong transcription	Brain Angular Gyrus	brain
48	chr15:75312000-75312800	Strong transcription	iPS-18 Cell Line	embryonic stem cell
49	chr15:75312200-75312800	Enhancers	Adipose Nuclei	Adipose
50	chr15:75312200-75312800	ZNF genes & repeats	Spleen	Spleen

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