Variant report

Variant	rs12442901
Chromosome Location	chr15:75083912-75083913
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:1)
CpG islands
(count:0)
Chromatin interactive
region (count:5)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

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

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	POLR2A	chr15:75078633-75084441	GM12878	blood:	n/a	n/a

No data

(count:5 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr15:75080218..75087203-chr15:75106250..75113071,13	MCF-7	breast:
2	chr15:75081397..75085815-chr15:75182279..75185381,4	MCF-7	breast:
3	chr15:75079215..75085047-chr15:75133215..75137478,7	MCF-7	breast:
4	chr15:75081235..75085402-chr15:75108223..75111318,4	MCF-7	breast:
5	chr15:75082759..75085102-chr15:75229620..75232231,2	K562	blood:

No data

Variant related genes	Relation type
CSK	TF binding region
MIR4513	TF binding region
ENSG00000178802	Chromatin interaction
ENSG00000140506	Chromatin interaction
ENSG00000140474	Chromatin interaction
ENSG00000178741	Chromatin interaction
ENSG00000261606	Chromatin interaction

Extended variants
information (count: 36 )
Associated
traits (count: 6 )

rSNPs within LD-proxies of this variant (count:34)

rs_ID	r²[population]
rs11072509	0.86[AMR][1000 genomes];0.85[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs11634474	0.90[CEU][hapmap];0.95[CHB][hapmap];0.90[JPT][hapmap];0.85[AMR][1000 genomes];0.83[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs12441505	0.86[AMR][1000 genomes];0.86[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs12591078	0.80[EUR][1000 genomes]
rs1350193	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1378938	0.95[CEU][hapmap];0.95[CHB][hapmap];0.95[CHD][hapmap];0.97[GIH][hapmap];0.90[JPT][hapmap];0.82[MEX][hapmap];0.88[TSI][hapmap];0.91[AMR][1000 genomes];0.87[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs1543927	0.90[CEU][hapmap];0.81[CHB][hapmap];0.84[EUR][1000 genomes]
rs2071501	0.85[JPT][hapmap];0.81[ASN][1000 genomes]
rs2168519	0.95[CEU][hapmap];1.00[CHB][hapmap];0.98[CHD][hapmap];1.00[GIH][hapmap];0.95[JPT][hapmap];0.91[MEX][hapmap];0.83[MKK][hapmap];0.97[TSI][hapmap];0.99[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2301249	0.95[CEU][hapmap];0.95[CHB][hapmap];0.93[CHD][hapmap];1.00[GIH][hapmap];0.95[JPT][hapmap];0.82[MEX][hapmap];0.88[MKK][hapmap];0.88[TSI][hapmap];0.82[YRI][hapmap];0.91[AMR][1000 genomes];0.90[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2472299	0.81[CHD][hapmap];0.83[TSI][hapmap]
rs3784790	0.91[AFR][1000 genomes];0.99[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs3935077	0.84[AMR][1000 genomes];0.83[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs4886406	0.90[CEU][hapmap];0.86[CHB][hapmap];0.83[CHD][hapmap];0.86[TSI][hapmap];0.82[EUR][1000 genomes]
rs4886615	0.92[GIH][hapmap];0.85[MKK][hapmap]
rs4886619	0.90[CEU][hapmap];0.95[CHB][hapmap];0.95[CHD][hapmap];0.97[GIH][hapmap];0.90[JPT][hapmap];0.82[MEX][hapmap];0.86[TSI][hapmap];0.88[AMR][1000 genomes];0.86[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs4886629	0.95[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs6495126	0.88[GIH][hapmap]
rs6495127	0.88[GIH][hapmap]
rs7085	0.95[CEU][hapmap];0.95[CHB][hapmap];0.95[CHD][hapmap];0.97[GIH][hapmap];0.95[JPT][hapmap];0.82[MKK][hapmap];0.88[TSI][hapmap];0.91[AMR][1000 genomes];0.89[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7162232	0.90[CEU][hapmap];0.95[CHB][hapmap];0.88[CHD][hapmap];0.95[GIH][hapmap];0.90[JPT][hapmap];0.86[TSI][hapmap];0.85[AMR][1000 genomes];0.85[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs7176022	0.90[CEU][hapmap];0.95[CHB][hapmap];0.95[CHD][hapmap];0.92[GIH][hapmap];0.95[JPT][hapmap];0.82[MEX][hapmap];0.81[MKK][hapmap];0.86[TSI][hapmap];0.82[YRI][hapmap];0.86[AMR][1000 genomes];0.83[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7180484	0.90[CEU][hapmap];0.90[CHB][hapmap];0.88[CHD][hapmap];0.97[GIH][hapmap];0.90[JPT][hapmap];0.82[MEX][hapmap];0.82[MKK][hapmap];0.86[TSI][hapmap];0.86[AMR][1000 genomes];0.85[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs72730503	0.99[AMR][1000 genomes];0.95[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7497201	0.88[GIH][hapmap]
rs762551	0.81[CHD][hapmap];0.83[TSI][hapmap]
rs8031937	0.88[GIH][hapmap]
rs8033381	0.93[ASW][hapmap];0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.95[JPT][hapmap];0.89[LWK][hapmap];0.91[MEX][hapmap];0.96[MKK][hapmap];0.97[TSI][hapmap];0.89[AFR][1000 genomes];0.99[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs8042694	0.88[GIH][hapmap]
rs9210	0.81[CEU][hapmap];0.95[GIH][hapmap];0.84[MKK][hapmap]
rs936226	0.95[CEU][hapmap];0.90[CHB][hapmap];0.82[YRI][hapmap];0.82[AFR][1000 genomes];0.96[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs936228	0.92[GIH][hapmap];0.82[MKK][hapmap]
rs936229	0.92[GIH][hapmap];0.82[MKK][hapmap]
rs936230	0.87[GIH][hapmap]

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	nsv904380	chr15:74869438-75142761	Flanking Active TSS Weak transcription Active TSS Enhancers Strong transcription Genic enhancers Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	69 gene(s)	inside rSNPs	diseases
2	nsv833055	chr15:74988344-75166288	Weak transcription Active TSS Genic enhancers Flanking Active TSS Strong transcription Enhancers Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	46 gene(s)	inside rSNPs	diseases

mRNA abundance (count:6)

SNP	Gene	Cis/trans	Tissue	Source
rs12442901	ULK3	cis	Whole Blood	GTEx
rs12442901	TMEM202	cis	parietal	SCAN
rs12442901	COX5A	Cis_1M	lymphoblastoid	RTeQTL
rs12442901	SCAMP5	cis	cerebellum	SCAN
rs12442901	NEO1	cis	parietal	SCAN
rs12442901	SCAMP2	cis	parietal	SCAN

Chromatin state (count:121 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:75076400-75084200	Enhancers	Spleen	Spleen
2	chr15:75076400-75085800	Enhancers	Left Ventricle	heart
3	chr15:75076600-75084800	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
4	chr15:75077800-75084400	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
5	chr15:75077800-75092000	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
6	chr15:75078000-75084200	Flanking Active TSS	Monocytes-CD14+_RO01746	blood
7	chr15:75078000-75085600	Enhancers	NHDF-Ad	bronchial
8	chr15:75078200-75084400	Flanking Active TSS	Primary B cells from cord blood	blood
9	chr15:75078600-75085000	Enhancers	NHLF	lung
10	chr15:75078800-75084600	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
11	chr15:75079400-75093800	Weak transcription	Aorta	Aorta
12	chr15:75080000-75084000	Flanking Active TSS	Primary hematopoietic stem cells	blood
13	chr15:75080200-75084600	Weak transcription	Psoas Muscle	Psoas
14	chr15:75080800-75086000	Enhancers	Adipose Nuclei	Adipose
15	chr15:75080800-75088600	Enhancers	Stomach Mucosa	stomach
16	chr15:75081200-75085000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
17	chr15:75081200-75091400	Weak transcription	H9 Cell Line	embryonic stem cell
18	chr15:75081800-75087600	Enhancers	Brain Substantia Nigra	brain
19	chr15:75081800-75092000	Weak transcription	iPS-18 Cell Line	embryonic stem cell
20	chr15:75081800-75092000	Weak transcription	iPS-20b Cell Line	embryonic stem cell
21	chr15:75082000-75085600	Weak transcription	Placenta Amnion	Placenta Amnion
22	chr15:75082200-75084000	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
23	chr15:75082200-75085800	Weak transcription	HUES48 Cell Line	embryonic stem cell
24	chr15:75082200-75092200	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
25	chr15:75082400-75084200	Enhancers	Fetal Intestine Large	intestine
26	chr15:75082400-75085800	Enhancers	Liver	Liver
27	chr15:75082400-75088000	Genic enhancers	Fetal Intestine Small	intestine
28	chr15:75082400-75098400	Weak transcription	Fetal Kidney	kidney
29	chr15:75082600-75084000	Enhancers	Muscle Satellite Cultured Cells	--
30	chr15:75082600-75085600	Enhancers	Fetal Heart	heart
31	chr15:75082600-75086000	Enhancers	Skeletal Muscle Male	skeletal muscle
32	chr15:75082600-75088400	Genic enhancers	Fetal Thymus	thymus
33	chr15:75082600-75090400	Weak transcription	HepG2	liver
34	chr15:75082600-75093200	Weak transcription	HUES64 Cell Line	embryonic stem cell
35	chr15:75082800-75084000	Enhancers	Primary T killer naive cells fromperipheralblood	blood
36	chr15:75082800-75084200	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
37	chr15:75082800-75084600	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
38	chr15:75082800-75084600	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
39	chr15:75082800-75084800	Weak transcription	Fetal Brain Male	brain
40	chr15:75082800-75085000	Weak transcription	Ovary	ovary
41	chr15:75082800-75086000	Enhancers	Rectal Mucosa Donor 31	rectum
42	chr15:75082800-75086000	Enhancers	Skeletal Muscle Female	skeletal muscle
43	chr15:75082800-75086800	Weak transcription	Brain Germinal Matrix	brain
44	chr15:75083000-75084200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
45	chr15:75083000-75084200	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
46	chr15:75083000-75084200	Enhancers	Primary T helper 17 cells PMA-I stimulated	--
47	chr15:75083000-75084400	Weak transcription	Pancreas	Pancrea
48	chr15:75083000-75084400	Weak transcription	NHEK	skin
49	chr15:75083000-75085000	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
50	chr15:75083000-75085600	Weak transcription	Rectal Smooth Muscle	rectum

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