Variant report

Variant	rs6495138
Chromosome Location	chr15:75304692-75304693
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr15:75300826..75305111-chr15:75313603..75318752,6	MCF-7	breast:
2	chr15:75287065..75288881-chr15:75303278..75305678,2	MCF-7	breast:
3	chr15:75286200..75292858-chr15:75303462..75309796,11	MCF-7	breast:

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-RPP25-2	chr15:75303307-75304737	ucscGeneNc_uc002bcp_2

Variant related genes	Relation type
ENSG00000138621	Chromatin interaction
ENSG00000260483	Chromatin interaction
ENSG00000198794	Chromatin interaction

Extended variants
information (count: 73 )
Associated
traits (count: 5 )

rSNPs within LD-proxies of this variant (count:71)

rs_ID	r²[population]
rs11072519	0.87[CEU][hapmap];0.82[AMR][1000 genomes]
rs12591175	0.82[CEU][hapmap];0.90[JPT][hapmap];0.84[EUR][1000 genomes]
rs12591994	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.94[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs12592477	1.00[CEU][hapmap];0.95[JPT][hapmap];0.89[AMR][1000 genomes];0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12593476	0.84[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs12593542	0.95[CHB][hapmap];1.00[JPT][hapmap];0.87[YRI][hapmap];0.82[AFR][1000 genomes];0.98[AMR][1000 genomes];0.84[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];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs12917120	0.80[YRI][hapmap]
rs13056	0.82[YRI][hapmap];0.81[AFR][1000 genomes]
rs2120019	0.80[YRI][hapmap]
rs2289582	1.00[CHB][hapmap];1.00[JPT][hapmap];0.97[YRI][hapmap];0.94[AFR][1000 genomes];0.99[ASN][1000 genomes]
rs2304904	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.94[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs28394281	0.84[AMR][1000 genomes];0.94[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs34713999	0.81[AFR][1000 genomes]
rs3812943	1.00[CEU][hapmap];0.83[CHB][hapmap];1.00[JPT][hapmap];0.94[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs3812946	0.82[AMR][1000 genomes];0.92[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs3816261	1.00[CEU][hapmap];0.94[JPT][hapmap];0.83[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs3910748	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.84[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs55877218	0.95[AMR][1000 genomes];0.81[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs56828495	0.82[AFR][1000 genomes];0.98[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs56970592	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs58068887	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs58294763	0.89[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs58403754	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs58645417	0.80[AMR][1000 genomes];0.98[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];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6495135	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6495136	0.89[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6495137	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6495140	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[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];1.00[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[JPT][hapmap];0.86[YRI][hapmap];0.81[AFR][1000 genomes];0.93[AMR][1000 genomes];0.82[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7166105	1.00[CEU][hapmap];0.90[JPT][hapmap];0.84[AMR][1000 genomes];0.89[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];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7168638	0.84[AMR][1000 genomes];0.84[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7172065	1.00[CEU][hapmap];0.94[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];0.92[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7172989	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7173218	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.84[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7174129	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[YRI][hapmap];0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7177109	0.85[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs7179097	0.95[AMR][1000 genomes];0.84[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];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7182286	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72475969	0.80[ASN][1000 genomes]
rs7342591	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]
rs7342601	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];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73436579	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73436586	0.92[AFR][1000 genomes];0.91[AMR][1000 genomes];0.94[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs73438537	0.95[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs73438554	0.84[AMR][1000 genomes];0.89[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs73438569	0.84[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs74023908	0.89[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs74023935	0.84[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs74025863	0.86[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs8028632	0.80[YRI][hapmap]
rs8030089	0.84[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];0.95[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs8033925	0.81[AFR][1000 genomes]
rs8034149	0.83[AMR][1000 genomes];1.00[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];0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs9672926	0.98[AFR][1000 genomes];0.93[AMR][1000 genomes];0.94[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];1.00[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];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9788648	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:2 , 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

mRNA abundance (count:5)

SNP	Gene	Cis/trans	Tissue	Source
rs6495138	SCAMP5	cis	Esophagus Mucosa	GTEx
rs6495138	SCAMP5	cis	Artery Tibial	GTEx
rs6495138	SCAMP5	cis	Thyroid	GTEx
rs6495138	PPCDC	cis	Adipose Subcutaneous	GTEx
rs6495138	SCAMP5	cis	multi-tissue	Pritchard

Chromatin state (count:48 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:75289000-75315800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
2	chr15:75289400-75305000	Weak transcription	HUES48 Cell Line	embryonic stem cell
3	chr15:75289400-75305000	Weak transcription	Brain Substantia Nigra	brain
4	chr15:75289400-75305600	Weak transcription	Breast Myoepithelial Primary Cells	Breast
5	chr15:75289400-75315400	Weak transcription	Fetal Kidney	kidney
6	chr15:75289600-75305400	Weak transcription	HUES64 Cell Line	embryonic stem cell
7	chr15:75290000-75309400	Weak transcription	Gastric	stomach
8	chr15:75290000-75316000	Weak transcription	Small Intestine	intestine
9	chr15:75290400-75304800	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
10	chr15:75290400-75304800	Weak transcription	Brain Anterior Caudate	brain
11	chr15:75291400-75305400	Weak transcription	Fetal Brain Male	brain
12	chr15:75292000-75305000	Weak transcription	HUES6 Cell Line	embryonic stem cell
13	chr15:75292600-75305400	Weak transcription	Pancreatic Islets	Pancreatic Islet
14	chr15:75293200-75315800	Weak transcription	Duodenum Mucosa	Duodenum
15	chr15:75294600-75312200	Weak transcription	Adipose Nuclei	Adipose
16	chr15:75294600-75315600	Weak transcription	ES-I3 Cell Line	embryonic stem cell
17	chr15:75297400-75305000	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
18	chr15:75298200-75305600	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
19	chr15:75300400-75312200	Weak transcription	Spleen	Spleen
20	chr15:75301000-75315400	Weak transcription	Thymus	Thymus
21	chr15:75301800-75304800	Weak transcription	H1 Cell Line	embryonic stem cell
22	chr15:75301800-75306600	Weak transcription	Placenta	Placenta
23	chr15:75302000-75314000	Strong transcription	Fetal Intestine Small	intestine
24	chr15:75302200-75313200	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
25	chr15:75302200-75313400	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
26	chr15:75303400-75305200	Weak transcription	Primary hematopoietic stem cells short term culture	blood
27	chr15:75303600-75309800	Strong transcription	Brain Germinal Matrix	brain
28	chr15:75303600-75313800	Strong transcription	Cortex derived primary cultured neurospheres	brain
29	chr15:75303800-75309400	Strong transcription	Brain Cingulate Gyrus	brain
30	chr15:75303800-75313800	Strong transcription	Ganglion Eminence derived primary cultured neurospheres	brain
31	chr15:75303800-75314000	Strong transcription	Fetal Brain Female	brain
32	chr15:75304000-75306800	Strong transcription	Fetal Intestine Large	intestine
33	chr15:75304000-75306800	Strong transcription	Pancreas	Pancrea
34	chr15:75304000-75307600	Strong transcription	Brain Dorsolateral Prefrontal Cortex	brain
35	chr15:75304000-75308800	Strong transcription	iPS-15b Cell Line	embryonic stem cell
36	chr15:75304000-75309400	Strong transcription	Brain Hippocampus Middle	brain
37	chr15:75304000-75309400	Strong transcription	Brain Inferior Temporal Lobe	brain
38	chr15:75304000-75315800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
39	chr15:75304000-75316000	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
40	chr15:75304200-75304800	Weak transcription	Brain Angular Gyrus	brain
41	chr15:75304200-75307400	Strong transcription	H9 Cell Line	embryonic stem cell
42	chr15:75304200-75310000	Weak transcription	Fetal Muscle Trunk	muscle
43	chr15:75304400-75306000	Strong transcription	iPS DF 19.11 Cell Line	embryonic stem cell
44	chr15:75304400-75307000	Strong transcription	HepG2	liver
45	chr15:75304400-75307400	Strong transcription	iPS-18 Cell Line	embryonic stem cell
46	chr15:75304400-75313600	Strong transcription	Fetal Stomach	stomach
47	chr15:75304600-75306000	Strong transcription	iPS-20b Cell Line	embryonic stem cell
48	chr15:75304600-75313200	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived

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