Variant report

Variant	rs12912839
Chromosome Location	chr15:75221245-75221246
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr15:75219083..75221777-chr15:75225866..75227747,2	K562	blood:
2	chr15:75210612..75213940-chr15:75219994..75223601,6	K562	blood:
3	chr15:75219020..75222087-chr15:75227777..75231704,4	K562	blood:
4	chr15:75197679..75199782-chr15:75220402..75222080,2	MCF-7	breast:
5	chr15:75219020..75221811-chr15:75227777..75230276,3	K562	blood:
6	chr15:75220124..75223006-chr15:75247944..75250326,2	MCF-7	breast:
7	chr15:75219486..75222765-chr15:75228648..75231849,3	MCF-7	breast:

Variant related genes	Relation type
ENSG00000178718	Chromatin interaction
ENSG00000178761	Chromatin interaction
ENSG00000178741	Chromatin interaction
ENSG00000198794	Chromatin interaction

Extended variants
information (count: 58 )
Associated
traits (count: 5 )

rSNPs within LD-proxies of this variant (count:57)

rs_ID	r²[population]
rs11072511	0.82[EUR][1000 genomes]
rs11072512	0.85[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs11072513	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11072514	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1127796	0.85[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs1130741	0.87[EUR][1000 genomes]
rs1133322	0.85[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs1133323	0.85[AFR][1000 genomes];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11630087	0.80[AMR][1000 genomes]
rs11630592	0.87[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs11630918	0.88[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs11633472	0.84[AFR][1000 genomes];0.93[AMR][1000 genomes];0.95[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs11636892	0.80[AMR][1000 genomes]
rs11638130	0.84[AFR][1000 genomes];0.93[AMR][1000 genomes];0.93[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs11639413	0.86[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs11854704	0.85[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs11856413	1.00[AFR][1000 genomes];0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs11857695	0.84[EUR][1000 genomes]
rs12148513	0.83[AFR][1000 genomes]
rs12898539	0.82[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs12899430	0.82[EUR][1000 genomes]
rs12899787	0.85[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs12900662	0.82[EUR][1000 genomes]
rs12901190	1.00[AFR][1000 genomes];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12902515	0.84[EUR][1000 genomes]
rs12903205	0.85[EUR][1000 genomes]
rs12903370	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12904326	1.00[AFR][1000 genomes];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12904897	0.90[EUR][1000 genomes]
rs12907898	0.85[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs12908365	0.86[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs12909335	1.00[AFR][1000 genomes];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12911254	0.84[AFR][1000 genomes];0.89[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs12912343	0.81[AMR][1000 genomes]
rs12913293	0.86[EUR][1000 genomes]
rs12914217	0.85[AFR][1000 genomes];0.85[AMR][1000 genomes]
rs2044157	0.91[AFR][1000 genomes];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2415251	0.86[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs34063670	0.81[AMR][1000 genomes]
rs34799293	0.80[AMR][1000 genomes]
rs35556055	0.80[AMR][1000 genomes]
rs35882241	0.81[AMR][1000 genomes]
rs4643278	0.84[EUR][1000 genomes]
rs4886413	0.80[AMR][1000 genomes]
rs4886608	0.83[EUR][1000 genomes]
rs4886632	0.85[EUR][1000 genomes]
rs4886636	0.87[EUR][1000 genomes]
rs4886639	0.85[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs4886640	0.93[EUR][1000 genomes]
rs59945415	0.84[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs62029167	0.85[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs62029217	0.80[AMR][1000 genomes]
rs7495664	1.00[AFR][1000 genomes];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7495739	0.86[EUR][1000 genomes]
rs7497026	0.85[EUR][1000 genomes]
rs7497393	0.84[AFR][1000 genomes];0.89[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs8025447	0.87[EUR][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	nsv904381	chr15:75108636-75242155	Weak transcription Genic enhancers Enhancers Flanking Active TSS Active TSS Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	55 gene(s)	inside rSNPs	diseases

mRNA abundance (count:5)

SNP	Gene	Cis/trans	Tissue	Source
rs12912839	SCAMP2	Cis_1M	lymphoblastoid	RTeQTL
rs12912839	COX5A	Cis_1M	lymphoblastoid	RTeQTL
rs12912839	SCAMP2	cis	Whole Blood	GTEx
rs12912839	SCAMP5	cis	Artery Tibial	GTEx
rs12912839	MPI	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:126 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:75199600-75229400	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
2	chr15:75200000-75224000	Weak transcription	Stomach Mucosa	stomach
3	chr15:75201000-75224600	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
4	chr15:75202000-75224400	Strong transcription	Fetal Muscle Trunk	muscle
5	chr15:75202200-75224400	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
6	chr15:75202600-75224800	Strong transcription	Primary hematopoietic stem cells short term culture	blood
7	chr15:75202600-75225000	Strong transcription	Monocytes-CD14+_RO01746	blood
8	chr15:75203000-75224400	Strong transcription	Fetal Muscle Leg	muscle
9	chr15:75203000-75224600	Strong transcription	iPS-18 Cell Line	embryonic stem cell
10	chr15:75203200-75222200	Strong transcription	Left Ventricle	heart
11	chr15:75203800-75223000	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
12	chr15:75203800-75224200	Strong transcription	Duodenum Mucosa	Duodenum
13	chr15:75203800-75224400	Strong transcription	Fetal Intestine Large	intestine
14	chr15:75203800-75224600	Strong transcription	HUES64 Cell Line	embryonic stem cell
15	chr15:75204000-75221800	Strong transcription	Skeletal Muscle Female	skeletal muscle
16	chr15:75204000-75222200	Strong transcription	Breast Myoepithelial Primary Cells	Breast
17	chr15:75204000-75222400	Strong transcription	HUES6 Cell Line	embryonic stem cell
18	chr15:75204000-75224200	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
19	chr15:75204000-75224200	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
20	chr15:75204000-75224400	Strong transcription	Placenta	Placenta
21	chr15:75204000-75224600	Strong transcription	Liver	Liver
22	chr15:75204000-75224600	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
23	chr15:75204000-75224800	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
24	chr15:75204000-75224800	Strong transcription	Fetal Thymus	thymus
25	chr15:75204000-75228400	Strong transcription	HUES48 Cell Line	embryonic stem cell
26	chr15:75204200-75224200	Strong transcription	Sigmoid Colon	Sigmoid Colon
27	chr15:75204400-75224600	Strong transcription	Primary T cells fromperipheralblood	blood
28	chr15:75204600-75229200	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
29	chr15:75205600-75222000	Strong transcription	Primary neutrophils fromperipheralblood	blood
30	chr15:75205600-75223200	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
31	chr15:75206200-75222200	Strong transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
32	chr15:75206200-75224400	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
33	chr15:75206400-75224200	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
34	chr15:75206600-75221800	Strong transcription	Cortex derived primary cultured neurospheres	brain
35	chr15:75206800-75224600	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
36	chr15:75207000-75225800	Strong transcription	Hela-S3	cervix
37	chr15:75207200-75224200	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
38	chr15:75207200-75224400	Strong transcription	Primary T helper cells fromperipheralblood	blood
39	chr15:75207800-75227400	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
40	chr15:75209200-75224600	Strong transcription	Adipose Nuclei	Adipose
41	chr15:75209400-75221600	Strong transcription	Primary T helper naive cells fromperipheralblood	blood
42	chr15:75209400-75224600	Strong transcription	iPS-20b Cell Line	embryonic stem cell
43	chr15:75209600-75222400	Strong transcription	Dnd41	blood
44	chr15:75209800-75222000	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
45	chr15:75212400-75229600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
46	chr15:75212600-75229200	Weak transcription	Pancreatic Islets	Pancreatic Islet
47	chr15:75212800-75224200	Strong transcription	Fetal Intestine Small	intestine
48	chr15:75212800-75224200	Strong transcription	Fetal Stomach	stomach
49	chr15:75212800-75226000	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
50	chr15:75213200-75222400	Strong transcription	HUVEC	blood vessel

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