Variant report

Variant	rs4775053
Chromosome Location	chr15:58769583-58769584
allele	C/T
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	MAX	chr15:58769306-58769878	NB4	blood:	n/a	n/a
2	SPI1	chr15:58769398-58769790	HL-60	blood:	n/a	chr15:58769519-58769528 chr15:58769520-58769527 chr15:58769639-58769652
3	SPI1	chr15:58769519-58769695	K562	blood:	n/a	chr15:58769519-58769528 chr15:58769520-58769527 chr15:58769639-58769652
4	SPI1	chr15:58769429-58769708	GM12891	blood:	n/a	chr15:58769519-58769528 chr15:58769520-58769527 chr15:58769639-58769652
5	SPI1	chr15:58769297-58769788	HL-60	blood:	n/a	chr15:58769519-58769528 chr15:58769520-58769527 chr15:58769639-58769652
6	MYC	chr15:58769066-58770120	NB4	blood:	n/a	chr15:58769885-58769894
7	SPI1	chr15:58769401-58769764	GM12878	blood:	n/a	chr15:58769519-58769528 chr15:58769520-58769527 chr15:58769639-58769652
8	POLR2A	chr15:58767587-58769732	HepG2	liver:	n/a	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr15:58767133..58770014-chr15:58770584..58772843,2	MCF-7	breast:
2	chr15:58767751..58769658-chr15:58771265..58773299,2	MCF-7	breast:

Variant related genes	Relation type
ALDH1A2	TF binding region

Extended variants
information (count: 59 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:48)

rs_ID	r²[population]
rs10518978	0.90[CHB][hapmap];0.81[CHD][hapmap];1.00[JPT][hapmap];0.87[ASN][1000 genomes]
rs11634902	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12591216	0.90[CHB][hapmap];1.00[CHD][hapmap];0.85[ASN][1000 genomes]
rs12591624	0.90[CHB][hapmap];0.81[CHD][hapmap];0.82[JPT][hapmap];0.85[ASN][1000 genomes]
rs12592407	1.00[CHB][hapmap];1.00[CHD][hapmap];0.85[JPT][hapmap];0.98[ASN][1000 genomes]
rs12593736	0.90[CHB][hapmap];1.00[JPT][hapmap];0.87[ASN][1000 genomes]
rs12593880	0.90[CHB][hapmap];1.00[CHD][hapmap];0.85[JPT][hapmap];0.96[ASN][1000 genomes]
rs12594222	0.90[CHB][hapmap];1.00[JPT][hapmap];0.94[ASN][1000 genomes]
rs12595191	0.90[CHB][hapmap];1.00[JPT][hapmap];0.87[ASN][1000 genomes]
rs12900891	0.90[CHB][hapmap];0.81[CHD][hapmap];1.00[JPT][hapmap];0.87[ASN][1000 genomes]
rs12902119	0.90[CHB][hapmap];0.81[CHD][hapmap];1.00[JPT][hapmap];0.87[ASN][1000 genomes]
rs12903955	0.93[ASN][1000 genomes]
rs12906459	0.82[CHB][hapmap];1.00[JPT][hapmap];0.87[ASN][1000 genomes]
rs12908427	0.93[ASN][1000 genomes]
rs12910028	0.89[ASN][1000 genomes]
rs12910602	0.93[ASN][1000 genomes]
rs12913605	0.90[CHB][hapmap];1.00[JPT][hapmap];0.87[ASN][1000 genomes]
rs16940338	0.90[CHB][hapmap];1.00[JPT][hapmap];0.87[ASN][1000 genomes]
rs17190580	1.00[CHB][hapmap];0.81[CHD][hapmap];1.00[JPT][hapmap];0.93[ASN][1000 genomes]
rs17190587	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs2414581	0.98[ASN][1000 genomes]
rs28478642	0.89[ASN][1000 genomes]
rs28713618	0.83[ASN][1000 genomes]
rs2899630	0.98[ASN][1000 genomes]
rs34053638	0.87[ASN][1000 genomes]
rs34297592	0.87[ASN][1000 genomes]
rs34570549	0.87[ASN][1000 genomes]
rs34577128	0.85[ASN][1000 genomes]
rs34744603	0.87[ASN][1000 genomes]
rs35633916	0.87[ASN][1000 genomes]
rs35732576	0.87[ASN][1000 genomes]
rs35771822	0.98[ASN][1000 genomes]
rs35795657	0.98[ASN][1000 genomes]
rs6494009	0.90[CHB][hapmap];0.81[CHD][hapmap];1.00[JPT][hapmap];0.87[ASN][1000 genomes]
rs6494010	1.00[JPT][hapmap];0.87[ASN][1000 genomes]
rs6494011	0.90[CHB][hapmap];1.00[JPT][hapmap];0.87[ASN][1000 genomes]
rs71478668	0.94[ASN][1000 genomes]
rs71478670	0.82[AMR][1000 genomes];0.93[ASN][1000 genomes]
rs71478671	0.96[ASN][1000 genomes]
rs71478672	0.93[ASN][1000 genomes]
rs7162384	0.93[ASN][1000 genomes]
rs7162603	1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[ASN][1000 genomes]
rs7169744	0.80[CHB][hapmap];0.85[JPT][hapmap];0.85[ASN][1000 genomes]
rs7172556	0.90[CHB][hapmap];1.00[JPT][hapmap];0.87[ASN][1000 genomes]
rs7174539	0.87[ASN][1000 genomes]
rs8029592	0.98[ASN][1000 genomes]
rs8029837	0.98[ASN][1000 genomes]
rs8041525	1.00[CHB][hapmap];1.00[CHD][hapmap];0.85[JPT][hapmap];0.98[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:11 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1051058	chr15:58519922-59092530	Strong transcription Weak transcription Enhancers Flanking Active TSS ZNF genes & repeats Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	50 gene(s)	inside rSNPs	diseases
2	nsv542401	chr15:58519922-59092530	Strong transcription Weak transcription Active TSS Flanking Active TSS Enhancers Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	50 gene(s)	inside rSNPs	diseases
3	nsv1042201	chr15:58520746-58780710	Enhancers Weak transcription Flanking Active TSS Bivalent Enhancer ZNF genes & repeats Active TSS Bivalent/Poised TSS Strong transcription Genic enhancers Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases
4	nsv569598	chr15:58552606-58852463	Enhancers Weak transcription Flanking Active TSS ZNF genes & repeats Active TSS Bivalent Enhancer Genic enhancers Strong transcription Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	12 gene(s)	inside rSNPs	diseases
5	nsv904267	chr15:58699010-58769583	Enhancers Weak transcription Flanking Active TSS Active TSS Bivalent Enhancer Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
6	nsv1047048	chr15:58701400-58784800	Weak transcription Active TSS Enhancers ZNF genes & repeats Flanking Active TSS Bivalent Enhancer Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
7	esv3362898	chr15:58705732-58850860	ZNF genes & repeats Flanking Active TSS Enhancers Weak transcription Genic enhancers Bivalent Enhancer Active TSS Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
8	nsv457173	chr15:58731567-58779039	Enhancers Weak transcription Flanking Active TSS Active TSS Bivalent Enhancer ZNF genes & repeats Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
9	nsv569600	chr15:58731567-58779039	Enhancers Weak transcription Flanking Active TSS Active TSS Bivalent Enhancer Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
10	nsv1043041	chr15:58744505-58876327	Weak transcription Enhancers Flanking Active TSS Bivalent Enhancer Strong transcription ZNF genes & repeats Active TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
11	nsv904268	chr15:58763678-58803225	Weak transcription Enhancers Flanking Active TSS ZNF genes & repeats Bivalent Enhancer Active TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs4775053	KIAA1370	cis	cerebellum	SCAN
rs4775053	FAM63B	cis	parietal	SCAN

Chromatin state (count:71 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:58743800-58770400	Enhancers	Fetal Thymus	thymus
2	chr15:58759400-58770400	Enhancers	Placenta	Placenta
3	chr15:58760400-58770200	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
4	chr15:58764000-58770200	Enhancers	Fetal Muscle Leg	muscle
5	chr15:58764000-58770200	Enhancers	Thymus	Thymus
6	chr15:58764600-58769600	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
7	chr15:58764600-58769600	Enhancers	Cortex derived primary cultured neurospheres	brain
8	chr15:58764600-58770200	Enhancers	Spleen	Spleen
9	chr15:58764800-58769600	Enhancers	HSMMtube	muscle
10	chr15:58765000-58769600	Enhancers	Duodenum Mucosa	Duodenum
11	chr15:58765000-58769600	Enhancers	Right Atrium	heart
12	chr15:58765000-58769800	Enhancers	Adipose Nuclei	Adipose
13	chr15:58765000-58769800	Enhancers	Pancreas	Pancrea
14	chr15:58765000-58770000	Enhancers	Primary neutrophils fromperipheralblood	blood
15	chr15:58765000-58770400	Enhancers	Primary hematopoietic stem cells	blood
16	chr15:58765000-58770600	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
17	chr15:58765000-58770600	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
18	chr15:58765600-58770400	Enhancers	Primary T helper 17 cells PMA-I stimulated	--
19	chr15:58765800-58769600	Enhancers	HUVEC	blood vessel
20	chr15:58765800-58770000	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
21	chr15:58765800-58770200	Enhancers	Primary T cells fromperipheralblood	blood
22	chr15:58765800-58770200	Enhancers	Primary T helper naive cells fromperipheralblood	blood
23	chr15:58765800-58770200	Enhancers	Primary T helper cells PMA-I stimulated	--
24	chr15:58765800-58770400	Enhancers	Primary T killer naive cells fromperipheralblood	blood
25	chr15:58766000-58769800	Enhancers	Primary T regulatory cells fromperipheralblood	blood
26	chr15:58766000-58770000	Enhancers	Primary T cells from cord blood	blood
27	chr15:58766000-58770400	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
28	chr15:58766200-58769600	Enhancers	Primary T helper cells fromperipheralblood	blood
29	chr15:58766200-58769800	Enhancers	Primary T helper naive cells from peripheral blood	blood
30	chr15:58766200-58769800	Enhancers	A549	lung
31	chr15:58766200-58770000	Enhancers	Primary T killer memory cells from peripheral blood	blood
32	chr15:58766600-58769800	Enhancers	Primary monocytes fromperipheralblood	blood
33	chr15:58766600-58769800	Enhancers	Primary B cells from cord blood	blood
34	chr15:58766800-58769600	Enhancers	Fetal Muscle Trunk	muscle
35	chr15:58767000-58769600	Enhancers	Brain Cingulate Gyrus	brain
36	chr15:58767000-58769600	Enhancers	Fetal Intestine Large	intestine
37	chr15:58767000-58769600	Enhancers	HSMM	muscle
38	chr15:58767000-58770000	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
39	chr15:58767000-58770200	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
40	chr15:58767000-58770400	Enhancers	Left Ventricle	heart
41	chr15:58767200-58769600	Enhancers	Brain Hippocampus Middle	brain
42	chr15:58767200-58769600	Enhancers	Skeletal Muscle Male	skeletal muscle
43	chr15:58767200-58769600	Enhancers	Small Intestine	intestine
44	chr15:58767400-58769600	Enhancers	NHDF-Ad	bronchial
45	chr15:58767400-58769800	Enhancers	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
46	chr15:58767400-58769800	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
47	chr15:58767400-58769800	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
48	chr15:58767400-58770000	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
49	chr15:58767600-58769800	Flanking Active TSS	HepG2	liver
50	chr15:58767600-58770000	Enhancers	GM12878-XiMat	blood

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