Variant report

Variant	rs12899430
Chromosome Location	chr15:75229100-75229101
allele	C/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:24)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

(count:24 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr15:75164573..75166914-chr15:75228746..75230664,2	K562	blood:
2	chr15:75180806..75183670-chr15:75227670..75231591,7	K562	blood:
3	chr15:75072694..75075672-chr15:75228478..75230738,4	K562	blood:
4	chr15:75227655..75229943-chr15:75305697..75307723,2	MCF-7	breast:
5	chr15:74906651..74909310-chr15:75228343..75231322,3	K562	blood:
6	chr15:75180371..75182934-chr15:75228872..75231935,3	MCF-7	breast:
7	chr15:75126487..75129177-chr15:75225564..75229328,3	K562	blood:
8	chr15:75073739..75076026-chr15:75228940..75231737,2	MCF-7	breast:
9	chr15:75226056..75232063-chr15:75248745..75252832,9	MCF-7	breast:
10	chr15:75196219..75200292-chr15:75228985..75231952,6	MCF-7	breast:
11	chr15:75228700..75232954-chr15:75245461..75250546,13	K562	blood:
12	chr15:75196237..75205947-chr15:75227299..75233104,18	K562	blood:
13	chr15:75090885..75095958-chr15:75228068..75231576,5	K562	blood:
14	chr15:75126584..75129177-chr15:75226754..75229328,2	K562	blood:
15	chr15:75133406..75136691-chr15:75228046..75231533,6	MCF-7	breast:
16	chr15:75180021..75183481-chr15:75226759..75230284,3	K562	blood:
17	chr15:75072694..75075868-chr15:75228655..75230932,4	K562	blood:
18	chr15:75226664..75233309-chr15:75245862..75252227,16	K562	blood:
19	chr15:75199684..75201494-chr15:75226994..75229978,2	MCF-7	breast:
20	chr15:75094337..75095958-chr15:75228176..75229862,2	K562	blood:
21	chr15:75188520..75190057-chr15:75227191..75229624,2	K562	blood:
22	chr15:75191256..75201000-chr15:75228549..75233626,13	K562	blood:
23	chr15:75073526..75075460-chr15:75228949..75230471,2	MCF-7	breast:
24	chr15:75131716..75139878-chr15:75227772..75233177,11	MCF-7	breast:

No data

Variant related genes	Relation type
ENSG00000140497	Chromatin interaction
ENSG00000179335	Chromatin interaction
ENSG00000103653	Chromatin interaction
ENSG00000260919	Chromatin interaction
ENSG00000178761	Chromatin interaction
ENSG00000178802	Chromatin interaction
ENSG00000140474	Chromatin interaction
ENSG00000178718	Chromatin interaction
ENSG00000260824	Chromatin interaction
ENSG00000198794	Chromatin interaction

Extended variants
information (count: 38 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:37)

rs_ID	r²[population]
rs11072511	0.83[EUR][1000 genomes]
rs11072512	1.00[AFR][1000 genomes];0.89[AMR][1000 genomes];0.89[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs11072513	0.81[EUR][1000 genomes]
rs11072514	0.81[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs1127796	1.00[AFR][1000 genomes];0.89[AMR][1000 genomes];0.89[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs1130741	0.89[EUR][1000 genomes]
rs1133322	1.00[AFR][1000 genomes];0.89[AMR][1000 genomes];0.90[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs1133323	0.81[EUR][1000 genomes]
rs11854704	0.89[AMR][1000 genomes];0.90[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs11857695	0.85[EUR][1000 genomes]
rs12898539	1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12899787	1.00[AFR][1000 genomes];0.94[AMR][1000 genomes];0.92[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs12900662	0.81[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs12901190	0.83[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs12902515	0.85[EUR][1000 genomes]
rs12903205	0.87[EUR][1000 genomes]
rs12903370	0.81[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs12904326	0.81[EUR][1000 genomes]
rs12904897	0.92[EUR][1000 genomes]
rs12907898	1.00[AFR][1000 genomes];0.89[AMR][1000 genomes];0.90[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs12908365	1.00[AFR][1000 genomes];0.86[AMR][1000 genomes];0.88[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs12909335	0.81[EUR][1000 genomes]
rs12912839	0.82[EUR][1000 genomes]
rs12913293	0.88[EUR][1000 genomes]
rs12914217	0.93[AFR][1000 genomes];0.83[AMR][1000 genomes];0.81[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2044157	0.83[AMR][1000 genomes]
rs4643278	0.83[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs4886608	0.86[EUR][1000 genomes]
rs4886632	0.87[AFR][1000 genomes];0.83[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs4886636	0.89[EUR][1000 genomes]
rs4886639	0.89[AMR][1000 genomes];0.86[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs59945415	1.00[AFR][1000 genomes];0.92[AMR][1000 genomes];0.92[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs62029167	1.00[AFR][1000 genomes];0.94[AMR][1000 genomes];0.93[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs7495664	0.81[EUR][1000 genomes]
rs7495739	0.88[EUR][1000 genomes]
rs7497026	0.86[EUR][1000 genomes]
rs8025447	0.89[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:4)

SNP	Gene	Cis/trans	Tissue	Source
rs12899430	COX5A	Cis_1M	lymphoblastoid	RTeQTL
rs12899430	SCAMP2	Cis_1M	lymphoblastoid	RTeQTL
rs12899430	SCAMP5	cis	Artery Tibial	GTEx
rs12899430	MPI	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:127 , 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	chr15:75204600-75229200	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
3	chr15:75212400-75229600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
4	chr15:75212600-75229200	Weak transcription	Pancreatic Islets	Pancreatic Islet
5	chr15:75217400-75229400	Weak transcription	Placenta Amnion	Placenta Amnion
6	chr15:75221400-75229800	Weak transcription	Spleen	Spleen
7	chr15:75221600-75229200	Weak transcription	Fetal Kidney	kidney
8	chr15:75221600-75229200	Weak transcription	HSMMtube	muscle
9	chr15:75221600-75229400	Weak transcription	Aorta	Aorta
10	chr15:75221600-75229400	Weak transcription	Ovary	ovary
11	chr15:75221600-75229600	Weak transcription	Gastric	stomach
12	chr15:75222000-75229200	Weak transcription	NHDF-Ad	bronchial
13	chr15:75222200-75229200	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
14	chr15:75222200-75229200	Weak transcription	Breast Myoepithelial Primary Cells	Breast
15	chr15:75222200-75229200	Weak transcription	Brain Substantia Nigra	brain
16	chr15:75222200-75229200	Weak transcription	Esophagus	oesophagus
17	chr15:75222200-75229200	Weak transcription	NH-A	brain
18	chr15:75222400-75229200	Weak transcription	HSMM	muscle
19	chr15:75223000-75229200	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
20	chr15:75223000-75229400	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
21	chr15:75223600-75229200	Weak transcription	HMEC	breast
22	chr15:75223800-75229600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
23	chr15:75224200-75229200	Weak transcription	H9 Cell Line	embryonic stem cell
24	chr15:75224200-75229200	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
25	chr15:75224200-75229200	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
26	chr15:75224200-75229200	Weak transcription	NHEK	skin
27	chr15:75224200-75229400	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
28	chr15:75224200-75229600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
29	chr15:75224400-75229200	Weak transcription	H1 Cell Line	embryonic stem cell
30	chr15:75224400-75229200	Weak transcription	HUVEC	blood vessel
31	chr15:75224600-75229200	Weak transcription	iPS-18 Cell Line	embryonic stem cell
32	chr15:75226000-75229200	Enhancers	Primary T helper cells PMA-I stimulated	--
33	chr15:75226000-75229200	Enhancers	Primary T helper cells fromperipheralblood	blood
34	chr15:75226000-75229200	Enhancers	Primary T regulatory cells fromperipheralblood	blood
35	chr15:75226000-75229400	Enhancers	Primary T helper naive cells from peripheral blood	blood
36	chr15:75226400-75229200	Weak transcription	HUES6 Cell Line	embryonic stem cell
37	chr15:75226400-75229200	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
38	chr15:75226600-75231000	Active TSS	GM12878-XiMat	blood
39	chr15:75226800-75229400	Enhancers	Primary T helper naive cells fromperipheralblood	blood
40	chr15:75227000-75229200	Enhancers	Brain Cingulate Gyrus	brain
41	chr15:75227000-75229400	Enhancers	Adipose Nuclei	Adipose
42	chr15:75227400-75229200	Enhancers	Primary T helper 17 cells PMA-I stimulated	--
43	chr15:75227400-75229200	Enhancers	Brain Angular Gyrus	brain
44	chr15:75227400-75229200	Enhancers	Brain Germinal Matrix	brain
45	chr15:75227400-75229400	Enhancers	Primary T cells fromperipheralblood	blood
46	chr15:75227400-75229400	Weak transcription	Stomach Mucosa	stomach
47	chr15:75227600-75229200	Weak transcription	iPS-15b Cell Line	embryonic stem cell
48	chr15:75227600-75229200	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
49	chr15:75227600-75229400	Enhancers	Fetal Muscle Trunk	muscle
50	chr15:75227800-75229200	Weak transcription	ES-I3 Cell Line	embryonic stem cell

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