Variant report

Variant	rs7342591
Chromosome Location	chr15:75306863-75306864
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr15:75304706..75307905-chr15:75494120..75496489,3	MCF-7	breast:
2	chr15:75227655..75229943-chr15:75305697..75307723,2	MCF-7	breast:
3	chr15:75299758..75302262-chr15:75305323..75307805,2	K562	blood:
4	chr15:75306128..75307779-chr15:75522303..75524360,2	MCF-7	breast:
5	chr15:75249504..75251132-chr15:75306617..75309149,2	MCF-7	breast:
6	chr15:75286200..75292858-chr15:75303462..75309796,11	MCF-7	breast:
7	chr15:75304775..75307425-chr15:75315753..75317450,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000198794	Chromatin interaction
ENSG00000167173	Chromatin interaction
ENSG00000138621	Chromatin interaction
ENSG00000178718	Chromatin interaction

Extended variants
information (count: 75 )
Associated
traits (count: 6 )

rSNPs within LD-proxies of this variant (count:72)

rs_ID	r²[population]
rs11072519	0.82[CEU][hapmap];0.82[AMR][1000 genomes]
rs12591175	0.82[CEU][hapmap];0.93[GIH][hapmap];0.90[JPT][hapmap];0.81[LWK][hapmap];0.82[EUR][1000 genomes]
rs12591994	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.92[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs12592477	1.00[CEU][hapmap];0.95[JPT][hapmap];0.89[AMR][1000 genomes];0.94[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12593476	0.82[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs12593542	0.95[CHB][hapmap];1.00[CHD][hapmap];0.89[GIH][hapmap];1.00[JPT][hapmap];0.93[LWK][hapmap];0.85[MKK][hapmap];0.94[TSI][hapmap];0.86[YRI][hapmap];0.82[AFR][1000 genomes];0.98[AMR][1000 genomes];0.82[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs12594117	1.00[CEU][hapmap];0.94[CHB][hapmap];1.00[JPT][hapmap];0.84[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs12917120	0.81[LWK][hapmap];0.80[YRI][hapmap]
rs13056	0.82[ASW][hapmap];0.91[LWK][hapmap];0.82[YRI][hapmap];0.81[AFR][1000 genomes]
rs2120019	0.82[ASW][hapmap];0.86[LWK][hapmap];0.80[YRI][hapmap]
rs2289582	1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[YRI][hapmap];0.94[AFR][1000 genomes];0.99[ASN][1000 genomes]
rs2304903	0.82[ASW][hapmap];0.91[LWK][hapmap]
rs2304904	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.92[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs28394281	0.84[AMR][1000 genomes];0.93[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs34713999	0.81[AFR][1000 genomes]
rs3812943	1.00[CEU][hapmap];0.84[CHB][hapmap];1.00[JPT][hapmap];0.92[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs3812946	0.82[AMR][1000 genomes];0.91[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs3816261	1.00[CEU][hapmap];0.94[JPT][hapmap];0.82[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs3910748	1.00[CEU][hapmap];0.95[CHB][hapmap];0.93[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.87[LWK][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.84[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs55877218	0.95[AMR][1000 genomes];0.89[ASN][1000 genomes]
rs56828495	0.82[AFR][1000 genomes];0.98[AMR][1000 genomes];0.94[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs56970592	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs58068887	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];0.94[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs58294763	0.89[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs58403754	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.94[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs58645417	0.80[AMR][1000 genomes];0.97[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs59094290	0.94[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs59303424	0.80[ASN][1000 genomes]
rs61166993	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6495135	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.98[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6495136	0.89[AMR][1000 genomes];0.95[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6495137	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6495138	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6495140	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6495142	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.84[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6495146	0.80[ASN][1000 genomes]
rs7163390	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[CHD][hapmap];0.93[GIH][hapmap];1.00[JPT][hapmap];0.98[LWK][hapmap];1.00[MEX][hapmap];0.90[MKK][hapmap];1.00[TSI][hapmap];0.86[YRI][hapmap];0.81[AFR][1000 genomes];0.93[AMR][1000 genomes];0.81[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7166105	1.00[CEU][hapmap];0.93[GIH][hapmap];0.90[JPT][hapmap];0.83[LWK][hapmap];0.86[MEX][hapmap];0.83[TSI][hapmap];0.84[AMR][1000 genomes];0.88[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs7167415	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7168638	0.84[AMR][1000 genomes];0.82[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7172065	1.00[CEU][hapmap];0.92[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs7172715	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.82[AMR][1000 genomes];0.91[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7172989	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7173218	1.00[CEU][hapmap];0.95[CHB][hapmap];0.91[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.87[LWK][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.84[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7174129	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.96[MKK][hapmap];1.00[TSI][hapmap];0.96[YRI][hapmap];0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7177109	0.84[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs7179097	0.95[AMR][1000 genomes];0.82[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7181942	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7182286	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72475969	0.80[ASN][1000 genomes]
rs7342601	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.98[LWK][hapmap];1.00[MEX][hapmap];0.98[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73436579	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73436586	0.92[AFR][1000 genomes];0.91[AMR][1000 genomes];0.93[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs73438537	0.94[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs73438554	0.84[AMR][1000 genomes];0.88[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs73438569	0.82[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs74023908	0.89[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs74023935	0.82[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs74025863	0.86[AFR][1000 genomes];1.00[AMR][1000 genomes];0.94[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs8028632	0.82[ASW][hapmap];0.91[LWK][hapmap];0.80[YRI][hapmap]
rs8030089	0.82[YRI][hapmap]
rs8031545	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.94[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs8033925	0.81[AFR][1000 genomes]
rs8034149	0.83[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs8036573	0.94[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs8039433	0.80[ASN][1000 genomes]
rs8040961	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.94[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs9672926	0.98[AFR][1000 genomes];0.93[AMR][1000 genomes];0.92[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs9672995	0.87[AFR][1000 genomes];0.99[ASN][1000 genomes]
rs9672996	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9673012	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9788648	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[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
rs7342591	SCAMP5	cis	lymphoblastoid	seeQTL
rs7342591	SCAMP5	cis	Thyroid	GTEx
rs7342591	SCAMP5	cis	multi-tissue	Pritchard
rs7342591	SCAMP5	cis	Artery Tibial	GTEx
rs7342591	SCAMP5	cis	Esophagus Mucosa	GTEx
rs7342591	PPCDC	cis	Adipose Subcutaneous	GTEx

Chromatin state (count:52 , 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	chr15:75290000-75309400	Weak transcription	Gastric	stomach
4	chr15:75290000-75316000	Weak transcription	Small Intestine	intestine
5	chr15:75293200-75315800	Weak transcription	Duodenum Mucosa	Duodenum
6	chr15:75294600-75312200	Weak transcription	Adipose Nuclei	Adipose
7	chr15:75294600-75315600	Weak transcription	ES-I3 Cell Line	embryonic stem cell
8	chr15:75300400-75312200	Weak transcription	Spleen	Spleen
9	chr15:75301000-75315400	Weak transcription	Thymus	Thymus
10	chr15:75302000-75314000	Strong transcription	Fetal Intestine Small	intestine
11	chr15:75302200-75313200	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
12	chr15:75302200-75313400	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
13	chr15:75303600-75309800	Strong transcription	Brain Germinal Matrix	brain
14	chr15:75303600-75313800	Strong transcription	Cortex derived primary cultured neurospheres	brain
15	chr15:75303800-75309400	Strong transcription	Brain Cingulate Gyrus	brain
16	chr15:75303800-75313800	Strong transcription	Ganglion Eminence derived primary cultured neurospheres	brain
17	chr15:75303800-75314000	Strong transcription	Fetal Brain Female	brain
18	chr15:75304000-75307600	Strong transcription	Brain Dorsolateral Prefrontal Cortex	brain
19	chr15:75304000-75308800	Strong transcription	iPS-15b Cell Line	embryonic stem cell
20	chr15:75304000-75309400	Strong transcription	Brain Hippocampus Middle	brain
21	chr15:75304000-75309400	Strong transcription	Brain Inferior Temporal Lobe	brain
22	chr15:75304000-75315800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
23	chr15:75304000-75316000	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
24	chr15:75304200-75307400	Strong transcription	H9 Cell Line	embryonic stem cell
25	chr15:75304200-75310000	Weak transcription	Fetal Muscle Trunk	muscle
26	chr15:75304400-75307000	Strong transcription	HepG2	liver
27	chr15:75304400-75307400	Strong transcription	iPS-18 Cell Line	embryonic stem cell
28	chr15:75304400-75313600	Strong transcription	Fetal Stomach	stomach
29	chr15:75304600-75313200	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
30	chr15:75304800-75310200	Strong transcription	Brain Angular Gyrus	brain
31	chr15:75304800-75312600	Strong transcription	Brain Anterior Caudate	brain
32	chr15:75304800-75314000	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
33	chr15:75305000-75307600	Strong transcription	HUES48 Cell Line	embryonic stem cell
34	chr15:75305000-75315800	Weak transcription	Right Ventricle	heart
35	chr15:75305400-75307200	Strong transcription	HUES64 Cell Line	embryonic stem cell
36	chr15:75305400-75307400	Weak transcription	HUES6 Cell Line	embryonic stem cell
37	chr15:75305400-75309200	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
38	chr15:75305600-75310800	Strong transcription	Primary hematopoietic stem cells short term culture	blood
39	chr15:75305600-75311400	Strong transcription	Breast Myoepithelial Primary Cells	Breast
40	chr15:75305800-75308200	Weak transcription	Pancreatic Islets	Pancreatic Islet
41	chr15:75306000-75307400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
42	chr15:75306000-75309200	Weak transcription	Brain Substantia Nigra	brain
43	chr15:75306000-75309600	Weak transcription	iPS-20b Cell Line	embryonic stem cell
44	chr15:75306000-75312400	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
45	chr15:75306200-75316000	Weak transcription	Fetal Brain Male	brain
46	chr15:75306600-75309000	Enhancers	Placenta	Placenta
47	chr15:75306600-75309400	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
48	chr15:75306800-75308600	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
49	chr15:75306800-75308800	Weak transcription	H1 Cell Line	embryonic stem cell
50	chr15:75306800-75308800	Weak transcription	Pancreas	Pancrea

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