Variant report

Variant	rs3812946
Chromosome Location	chr15:75288610-75288611
allele	C/G
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:8)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

(count:8 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr15:75287065..75288881-chr15:75303278..75305678,2	MCF-7	breast:
2	chr15:75249528..75251223-chr15:75287946..75289828,2	K562	blood:
3	chr15:75287417..75289225-chr15:75314885..75317439,2	MCF-7	breast:
4	chr15:75286200..75292858-chr15:75303462..75309796,11	MCF-7	breast:
5	chr15:75286466..75289268-chr15:75313854..75316191,2	MCF-7	breast:
6	chr15:75274950..75276613-chr15:75287594..75290045,3	K562	blood:
7	chr15:75287456..75290010-chr15:75314463..75316098,2	K562	blood:
8	chr15:75275080..75277543-chr15:75287594..75290421,2	K562	blood:

No data

Variant related genes	Relation type
ENSG00000178718	Chromatin interaction
ENSG00000198794	Chromatin interaction
ENSG00000138621	Chromatin interaction
ENSG00000260483	Chromatin interaction
ENSG00000199580	Chromatin interaction

Extended variants
information (count: 58 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:56)

rs_ID	r²[population]
rs11072519	0.81[AMR][1000 genomes]
rs12591994	0.90[AMR][1000 genomes];0.98[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs12592477	0.93[AMR][1000 genomes];0.94[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs12593476	0.83[AMR][1000 genomes];0.82[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs12593542	0.82[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs12594117	0.88[AMR][1000 genomes];0.92[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2289582	0.91[ASN][1000 genomes]
rs2304904	0.90[AMR][1000 genomes];0.98[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs28394281	0.88[AMR][1000 genomes];0.86[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs3812943	0.90[AMR][1000 genomes];0.98[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs3816261	0.87[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs3910748	0.88[AMR][1000 genomes];0.92[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs55877218	0.86[ASN][1000 genomes]
rs56828495	0.84[AMR][1000 genomes];0.94[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs56970592	0.82[AMR][1000 genomes];0.92[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs58068887	0.82[AMR][1000 genomes];0.94[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs58294763	0.93[AMR][1000 genomes];0.92[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs58403754	0.82[AMR][1000 genomes];0.94[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs58645417	0.84[AMR][1000 genomes];0.91[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs59094290	0.92[ASN][1000 genomes]
rs61166993	0.82[AMR][1000 genomes];0.92[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs6495135	0.82[AMR][1000 genomes];0.92[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs6495136	0.93[AMR][1000 genomes];0.92[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs6495137	0.82[AMR][1000 genomes];0.92[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs6495138	0.82[AMR][1000 genomes];0.92[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs6495140	0.82[AMR][1000 genomes];0.92[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs6495142	0.88[AMR][1000 genomes];0.92[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs7163390	0.81[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs7166105	0.82[EUR][1000 genomes]
rs7167415	0.82[AMR][1000 genomes];0.92[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs7168638	0.88[AMR][1000 genomes];0.82[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs7172065	0.90[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs7172715	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7172989	0.82[AMR][1000 genomes];0.92[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs7173218	0.88[AMR][1000 genomes];0.92[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs7174129	0.82[AMR][1000 genomes];0.92[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs7179097	0.82[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs7181942	0.82[AMR][1000 genomes];0.92[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs7182286	0.82[AMR][1000 genomes];0.91[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs7342591	0.82[AMR][1000 genomes];0.91[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs7342601	0.82[AMR][1000 genomes];0.92[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs73436579	0.82[AMR][1000 genomes];0.92[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs73436586	0.87[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs73438537	0.80[AMR][1000 genomes];0.88[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs73438554	0.82[EUR][1000 genomes]
rs74023908	0.93[AMR][1000 genomes];0.92[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs74025863	0.82[AMR][1000 genomes];0.94[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs8031545	0.82[AMR][1000 genomes];0.94[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs8034149	0.92[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs8036573	0.92[ASN][1000 genomes]
rs8040961	0.82[AMR][1000 genomes];0.94[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs9672926	0.89[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs9672995	0.91[ASN][1000 genomes]
rs9672996	0.82[AMR][1000 genomes];0.92[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs9673012	0.82[AMR][1000 genomes];0.92[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs9788648	0.82[AMR][1000 genomes];0.92[EUR][1000 genomes];0.92[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:3)

SNP	Gene	Cis/trans	Tissue	Source
rs3812946	SCAMP5	cis	Esophagus Mucosa	GTEx
rs3812946	SCAMP5	cis	Artery Tibial	GTEx
rs3812946	PPCDC	cis	Thyroid	GTEx

Chromatin state (count:111 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:75286600-75289000	Active TSS	Brain Substantia Nigra	brain
2	chr15:75286600-75289600	Active TSS	Pancreatic Islets	Pancreatic Islet
3	chr15:75286800-75288800	Active TSS	Brain Angular Gyrus	brain
4	chr15:75287200-75289800	Active TSS	H9 Cell Line	embryonic stem cell
5	chr15:75287400-75288800	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Female	--
6	chr15:75287400-75288800	Bivalent/Poised TSS	Muscle Satellite Cultured Cells	--
7	chr15:75287400-75288800	Flanking Active TSS	Adipose Nuclei	Adipose
8	chr15:75287400-75288800	Enhancers	Fetal Lung	lung
9	chr15:75287400-75288800	Flanking Active TSS	Dnd41	blood
10	chr15:75287400-75290000	Bivalent Enhancer	Stomach Mucosa	stomach
11	chr15:75287600-75288800	Active TSS	H1 Cell Line	embryonic stem cell
12	chr15:75287600-75288800	Active TSS	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
13	chr15:75287600-75288800	Active TSS	iPS-15b Cell Line	embryonic stem cell
14	chr15:75287600-75288800	Active TSS	Fetal Brain Male	brain
15	chr15:75287600-75288800	Active TSS	Fetal Brain Female	brain
16	chr15:75287600-75288800	Active TSS	Fetal Intestine Small	intestine
17	chr15:75287600-75288800	Active TSS	Hela-S3	cervix
18	chr15:75287600-75289000	Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
19	chr15:75287600-75289000	Active TSS	Fetal Kidney	kidney
20	chr15:75287800-75288800	Bivalent/Poised TSS	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
21	chr15:75287800-75288800	Active TSS	iPS DF 6.9 Cell Line	embryonic stem cell
22	chr15:75287800-75288800	Flanking Active TSS	Liver	Liver
23	chr15:75287800-75289000	Active TSS	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
24	chr15:75287800-75289400	Bivalent/Poised TSS	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
25	chr15:75288000-75288800	Active TSS	ES-WA7 Cell Line	embryonic stem cell
26	chr15:75288000-75288800	Flanking Active TSS	Primary T helper naive cells from peripheral blood	blood
27	chr15:75288000-75288800	Flanking Active TSS	Primary T helper naive cells fromperipheralblood	blood
28	chr15:75288000-75288800	Flanking Bivalent TSS/Enh	Fetal Muscle Leg	muscle
29	chr15:75288000-75288800	Flanking Active TSS	Gastric	stomach
30	chr15:75288000-75288800	Flanking Bivalent TSS/Enh	Skeletal Muscle Male	skeletal muscle
31	chr15:75288000-75289000	Bivalent/Poised TSS	HUES6 Cell Line	embryonic stem cell
32	chr15:75288000-75289000	Transcr. at gene 5' and 3'	iPS DF 19.11 Cell Line	embryonic stem cell
33	chr15:75288000-75289000	Flanking Bivalent TSS/Enh	Foreskin Fibroblast Primary Cells skin02	Skin
34	chr15:75288000-75289000	Flanking Bivalent TSS/Enh	Fetal Adrenal Gland	Adrenal Gland
35	chr15:75288000-75289200	Flanking Active TSS	Primary hematopoietic stem cells short term culture	blood
36	chr15:75288000-75289200	Flanking Active TSS	Cortex derived primary cultured neurospheres	brain
37	chr15:75288200-75288800	Flanking Bivalent TSS/Enh	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
38	chr15:75288200-75288800	Flanking Bivalent TSS/Enh	Foreskin Fibroblast Primary Cells skin01	Skin
39	chr15:75288200-75288800	Flanking Bivalent TSS/Enh	Foreskin Melanocyte Primary Cells skin03	Skin
40	chr15:75288200-75288800	Flanking Bivalent TSS/Enh	Fetal Muscle Trunk	muscle
41	chr15:75288200-75288800	Flanking Bivalent TSS/Enh	Fetal Stomach	stomach
42	chr15:75288200-75289000	Bivalent/Poised TSS	ES-I3 Cell Line	embryonic stem cell
43	chr15:75288200-75289000	Enhancers	Primary T killer memory cells from peripheral blood	blood
44	chr15:75288200-75289000	Bivalent/Poised TSS	Fetal Intestine Large	intestine
45	chr15:75288200-75290000	Enhancers	Lung	lung
46	chr15:75288200-75290200	Enhancers	Spleen	Spleen
47	chr15:75288400-75288800	Bivalent/Poised TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
48	chr15:75288400-75288800	Bivalent Enhancer	Primary monocytes fromperipheralblood	blood
49	chr15:75288400-75288800	Enhancers	Primary T killer naive cells fromperipheralblood	blood
50	chr15:75288400-75288800	Flanking Active TSS	Brain Dorsolateral Prefrontal Cortex	brain

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