Variant report

Variant	rs3816261
Chromosome Location	chr15:75336173-75336174
allele	A/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:0)
CpG islands
(count:0)
Chromatin interactive
region (count:10)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

(count:10 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr15:75333855..75341122-chr15:75492635..75495814,9	MCF-7	breast:
2	chr15:75318584..75321988-chr15:75334747..75339188,4	K562	blood:
3	chr15:75321657..75322201-chr15:75335761..75336283,2	K562	blood:
4	chr15:75335261..75336225-chr15:75493661..75494947,6	MCF-7	breast:
5	chr15:75314438..75320960-chr15:75334023..75339188,6	K562	blood:
6	chr15:75335868..75337626-chr15:75660366..75661953,2	MCF-7	breast:
7	chr15:75331603..75340227-chr15:75492938..75499942,15	K562	blood:
8	chr15:75334055..75342899-chr15:75492444..75498798,20	K562	blood:
9	chr15:75332512..75342228-chr15:75491817..75496419,22	MCF-7	breast:
10	chr15:75335299..75336533-chr15:75494000..75494818,4	K562	blood:

No data

Variant related genes	Relation type
ENSG00000260483	Chromatin interaction
ENSG00000167173	Chromatin interaction
ENSG00000138621	Chromatin interaction
ENSG00000260274	Chromatin interaction
ENSG00000140400	Chromatin interaction

Extended variants
information (count: 69 )
Associated
traits (count: 4 )

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

rs_ID	r²[population]
rs11072519	0.82[CEU][hapmap]
rs12148355	0.80[ASN][1000 genomes]
rs12591175	0.95[CHB][hapmap];1.00[JPT][hapmap];0.87[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12591994	1.00[CEU][hapmap];0.95[JPT][hapmap];0.97[AMR][1000 genomes];0.89[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs12592477	1.00[CEU][hapmap];0.90[JPT][hapmap];0.81[AMR][1000 genomes];0.82[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs12593476	0.85[AMR][1000 genomes]
rs12593542	0.95[JPT][hapmap]
rs12594117	1.00[CEU][hapmap];0.94[JPT][hapmap];0.85[AMR][1000 genomes];0.83[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs2289582	0.94[JPT][hapmap];0.82[ASN][1000 genomes]
rs2304904	1.00[CEU][hapmap];0.94[JPT][hapmap];0.97[AMR][1000 genomes];0.89[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs28394281	0.85[AMR][1000 genomes];0.86[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs3743212	0.88[JPT][hapmap]
rs3812943	1.00[CEU][hapmap];0.94[JPT][hapmap];0.97[AMR][1000 genomes];0.89[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs3812946	0.87[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs3910748	1.00[CEU][hapmap];0.81[CHB][hapmap];0.94[JPT][hapmap];0.85[AMR][1000 genomes];0.83[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs56828495	0.82[EUR][1000 genomes]
rs56970592	0.83[EUR][1000 genomes]
rs58068887	0.82[EUR][1000 genomes]
rs58294763	0.81[AMR][1000 genomes];0.83[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs58403754	0.82[EUR][1000 genomes]
rs58645417	0.81[AMR][1000 genomes];0.85[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs59094290	0.81[ASN][1000 genomes]
rs59303424	0.98[ASN][1000 genomes]
rs61166993	0.83[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs6495135	1.00[CEU][hapmap];0.94[JPT][hapmap];0.83[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs6495136	0.81[AMR][1000 genomes];0.83[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs6495137	0.83[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs6495138	1.00[CEU][hapmap];0.94[JPT][hapmap];0.83[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs6495140	0.83[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs6495142	1.00[CEU][hapmap];0.94[JPT][hapmap];0.85[AMR][1000 genomes];0.83[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs6495146	0.98[ASN][1000 genomes]
rs6495148	0.95[ASN][1000 genomes]
rs7163390	1.00[CEU][hapmap];0.94[JPT][hapmap]
rs7166105	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.94[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7167415	1.00[CEU][hapmap];0.94[JPT][hapmap];0.83[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs7168638	0.81[AMR][1000 genomes]
rs7172065	1.00[CEU][hapmap];0.97[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs7172715	1.00[CEU][hapmap];0.94[JPT][hapmap];0.87[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs7172989	0.83[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs7173218	1.00[CEU][hapmap];0.81[CHB][hapmap];0.94[JPT][hapmap];0.85[AMR][1000 genomes];0.83[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs7174129	1.00[CEU][hapmap];0.94[JPT][hapmap];0.83[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs7177109	0.89[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7181942	1.00[CEU][hapmap];0.95[JPT][hapmap];0.83[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs7182286	0.82[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs72475969	0.98[ASN][1000 genomes]
rs7342591	1.00[CEU][hapmap];0.94[JPT][hapmap];0.82[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs7342601	1.00[CEU][hapmap];0.94[JPT][hapmap];0.83[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs73432941	0.97[ASN][1000 genomes]
rs73436579	0.83[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs73438537	0.92[AMR][1000 genomes];0.88[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs73438554	0.94[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs73438569	0.87[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs74023908	0.81[AMR][1000 genomes];0.83[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs74023935	0.87[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs74023936	0.90[ASN][1000 genomes]
rs74025863	0.82[EUR][1000 genomes]
rs8024931	0.92[ASN][1000 genomes]
rs8031545	1.00[CEU][hapmap];0.94[JPT][hapmap];0.82[EUR][1000 genomes]
rs8033125	0.96[ASN][1000 genomes]
rs8034149	0.83[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs8036573	0.81[ASN][1000 genomes]
rs8038365	0.96[ASN][1000 genomes]
rs8039433	0.98[ASN][1000 genomes]
rs8040961	0.82[EUR][1000 genomes]
rs9672926	0.80[EUR][1000 genomes]
rs9672996	0.83[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs9673012	1.00[CEU][hapmap];0.94[JPT][hapmap];0.83[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs9788648	0.83[EUR][1000 genomes];0.81[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:1 , 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

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs3816261	SCAMP5	cis	Esophagus Mucosa	GTEx
rs3816261	PPCDC	cis	Adipose Subcutaneous	GTEx
rs3816261	PPCDC	cis	Thyroid	GTEx
rs3816261	SCAMP5	cis	Artery Tibial	GTEx

Chromatin state (count:123 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:75316600-75336800	Weak transcription	Fetal Brain Female	brain
2	chr15:75316800-75338800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
3	chr15:75318000-75341400	Weak transcription	Brain Germinal Matrix	brain
4	chr15:75322200-75339000	Weak transcription	Primary T helper naive cells from peripheral blood	blood
5	chr15:75322400-75336800	Weak transcription	Primary T cells from cord blood	blood
6	chr15:75322400-75339200	Weak transcription	Primary T helper cells PMA-I stimulated	--
7	chr15:75322600-75338600	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
8	chr15:75323000-75336600	Weak transcription	Dnd41	blood
9	chr15:75324600-75339200	Weak transcription	iPS-18 Cell Line	embryonic stem cell
10	chr15:75328600-75338800	Weak transcription	ES-I3 Cell Line	embryonic stem cell
11	chr15:75328800-75350400	Weak transcription	HUES64 Cell Line	embryonic stem cell
12	chr15:75329200-75338800	Weak transcription	iPS-20b Cell Line	embryonic stem cell
13	chr15:75329200-75350400	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
14	chr15:75329400-75346800	Weak transcription	HUES48 Cell Line	embryonic stem cell
15	chr15:75329600-75336400	Enhancers	Primary monocytes fromperipheralblood	blood
16	chr15:75330600-75340000	Weak transcription	NHEK	skin
17	chr15:75332000-75337000	Weak transcription	Psoas Muscle	Psoas
18	chr15:75333600-75338400	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
19	chr15:75333600-75341000	Enhancers	Fetal Adrenal Gland	Adrenal Gland
20	chr15:75333800-75337200	Enhancers	Breast Myoepithelial Primary Cells	Breast
21	chr15:75333800-75337400	Enhancers	Stomach Mucosa	stomach
22	chr15:75334000-75344600	Enhancers	Placenta	Placenta
23	chr15:75334200-75336600	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
24	chr15:75334200-75336800	Enhancers	Pancreas	Pancrea
25	chr15:75334200-75337000	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
26	chr15:75334200-75337000	Enhancers	Fetal Muscle Trunk	muscle
27	chr15:75334200-75340400	Genic enhancers	Fetal Intestine Small	intestine
28	chr15:75334200-75340600	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
29	chr15:75334200-75344600	Enhancers	Right Ventricle	heart
30	chr15:75334400-75336800	Enhancers	Fetal Intestine Large	intestine
31	chr15:75334400-75337000	Enhancers	NHDF-Ad	bronchial
32	chr15:75334400-75343200	Enhancers	Fetal Heart	heart
33	chr15:75334600-75336800	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
34	chr15:75334600-75337000	Enhancers	Primary B cells from peripheral blood	blood
35	chr15:75334600-75340400	Enhancers	Liver	Liver
36	chr15:75334600-75340800	Enhancers	Fetal Muscle Leg	muscle
37	chr15:75334600-75341000	Enhancers	Lung	lung
38	chr15:75334600-75343200	Enhancers	Right Atrium	heart
39	chr15:75334800-75344600	Enhancers	Left Ventricle	heart
40	chr15:75335000-75336200	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
41	chr15:75335000-75336200	Genic enhancers	A549	lung
42	chr15:75335000-75336400	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
43	chr15:75335000-75336400	Flanking Active TSS	HepG2	liver
44	chr15:75335000-75336400	Enhancers	HSMM	muscle
45	chr15:75335000-75336600	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
46	chr15:75335000-75336600	Enhancers	Skeletal Muscle Female	skeletal muscle
47	chr15:75335000-75336800	Enhancers	NHLF	lung
48	chr15:75335000-75337200	Enhancers	Placenta Amnion	Placenta Amnion
49	chr15:75335000-75337200	Enhancers	HUVEC	blood vessel
50	chr15:75335000-75337600	Enhancers	Sigmoid Colon	Sigmoid Colon

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