Variant report

Variant	rs12441505
Chromosome Location	chr15:75107311-75107312
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	EP300	chr15:75107255-75108063	SK-N-SH	brain:	n/a	chr15:75107620-75107630 chr15:75107742-75107758

No.	Distal block	Cell Line	Cell type
1	chr15:75090919..75095080-chr15:75105772..75108722,6	MCF-7	breast:
2	chr15:75106165..75113668-chr15:75132311..75136608,10	MCF-7	breast:
3	chr15:75080218..75087203-chr15:75106250..75113071,13	MCF-7	breast:
4	chr15:75105168..75109047-chr15:75134120..75137766,4	K562	blood:

Variant related genes	Relation type
LMAN1L	TF binding region
ENSG00000261606	TF binding region
ENSG00000264386	Chromatin interaction
ENSG00000140474	Chromatin interaction
ENSG00000103653	Chromatin interaction

Extended variants
information (count: 24 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:22)

rs_ID	r²[population]
rs11072509	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs11634474	0.90[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12442901	0.86[AMR][1000 genomes];0.86[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs1350193	0.86[AMR][1000 genomes];0.87[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs1378938	0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2071501	0.86[ASN][1000 genomes]
rs2168519	0.87[AMR][1000 genomes];0.89[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2301249	0.97[AFR][1000 genomes];0.94[AMR][1000 genomes];0.93[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs3784790	0.82[AFR][1000 genomes];0.87[AMR][1000 genomes];0.89[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs3935077	0.87[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4886615	0.81[EUR][1000 genomes]
rs4886619	0.90[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4886629	0.85[AMR][1000 genomes];0.87[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs7085	0.95[AFR][1000 genomes];0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7162232	0.86[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7176022	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7180484	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs72625792	0.83[ASN][1000 genomes]
rs72730503	0.87[AMR][1000 genomes];0.90[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs8033381	0.80[AFR][1000 genomes];0.87[AMR][1000 genomes];0.89[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs936226	0.86[EUR][1000 genomes]
rs936228	0.80[EUR][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	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:3)

SNP	Gene	Cis/trans	Tissue	Source
rs12441505	COX5A	Cis_1M	lymphoblastoid	RTeQTL
rs12441505	ULK3	cis	Whole Blood	GTEx
rs12441505	MPI	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:58 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:75086000-75107400	Weak transcription	Fetal Brain Male	brain
2	chr15:75096000-75109000	Weak transcription	H1 Cell Line	embryonic stem cell
3	chr15:75096200-75109600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
4	chr15:75096600-75107400	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
5	chr15:75096800-75107400	Weak transcription	Cortex derived primary cultured neurospheres	brain
6	chr15:75096800-75107400	Weak transcription	HSMMtube	muscle
7	chr15:75096800-75109000	Weak transcription	Fetal Intestine Large	intestine
8	chr15:75096800-75109200	Weak transcription	HUES64 Cell Line	embryonic stem cell
9	chr15:75096800-75109400	Weak transcription	HUVEC	blood vessel
10	chr15:75096800-75109800	Weak transcription	NH-A	brain
11	chr15:75097000-75107600	Weak transcription	Brain Cingulate Gyrus	brain
12	chr15:75097000-75109200	Weak transcription	iPS-20b Cell Line	embryonic stem cell
13	chr15:75097000-75109400	Weak transcription	Brain Anterior Caudate	brain
14	chr15:75097200-75108000	Weak transcription	Monocytes-CD14+_RO01746	blood
15	chr15:75097200-75109400	Weak transcription	Lung	lung
16	chr15:75097600-75108600	Weak transcription	HUES6 Cell Line	embryonic stem cell
17	chr15:75097600-75111000	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
18	chr15:75097800-75107800	Weak transcription	Primary hematopoietic stem cells short term culture	blood
19	chr15:75097800-75109200	Weak transcription	Brain Germinal Matrix	brain
20	chr15:75100800-75107800	Weak transcription	GM12878-XiMat	blood
21	chr15:75101200-75109000	Weak transcription	HMEC	breast
22	chr15:75101800-75109200	Weak transcription	H9 Cell Line	embryonic stem cell
23	chr15:75101800-75113200	Weak transcription	iPS-18 Cell Line	embryonic stem cell
24	chr15:75102000-75107400	Weak transcription	Placenta	Placenta
25	chr15:75102000-75108800	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
26	chr15:75102400-75107600	Weak transcription	Primary B cells from peripheral blood	blood
27	chr15:75102600-75109600	Weak transcription	NHLF	lung
28	chr15:75105400-75107400	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
29	chr15:75105400-75108600	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
30	chr15:75105600-75107400	Weak transcription	Fetal Stomach	stomach
31	chr15:75105800-75107400	Weak transcription	Brain Inferior Temporal Lobe	brain
32	chr15:75107000-75107600	Weak transcription	Breast Myoepithelial Primary Cells	Breast
33	chr15:75107000-75108600	Enhancers	Hela-S3	cervix
34	chr15:75107000-75112200	Enhancers	Fetal Adrenal Gland	Adrenal Gland
35	chr15:75107200-75107800	Enhancers	Fetal Lung	lung
36	chr15:75107200-75107800	Enhancers	Left Ventricle	heart
37	chr15:75107200-75107800	Enhancers	A549	lung
38	chr15:75107200-75108000	Enhancers	Liver	Liver
39	chr15:75107200-75108000	Enhancers	Duodenum Mucosa	Duodenum
40	chr15:75107200-75108000	Enhancers	Pancreas	Pancrea
41	chr15:75107200-75108000	Enhancers	Right Atrium	heart
42	chr15:75107200-75108000	Enhancers	Stomach Smooth Muscle	stomach
43	chr15:75107200-75108200	Enhancers	Fetal Heart	heart
44	chr15:75107200-75108200	Enhancers	Skeletal Muscle Female	skeletal muscle
45	chr15:75107200-75108200	Enhancers	Stomach Mucosa	stomach
46	chr15:75107200-75108400	Enhancers	Gastric	stomach
47	chr15:75107200-75108400	Enhancers	Rectal Smooth Muscle	rectum
48	chr15:75107200-75108400	Enhancers	Right Ventricle	heart
49	chr15:75107200-75108600	Enhancers	Spleen	Spleen
50	chr15:75107200-75108800	Enhancers	Sigmoid Colon	Sigmoid Colon

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