Variant report

Variant	rs62013227
Chromosome Location	chr15:79231046-79231047
allele	G/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	POLR2A	chr15:79230701-79233525	GM12891	blood:	n/a	n/a
2	NFATC1	chr15:79230870-79232005	GM12878	blood:	n/a	n/a
3	STAT5A	chr15:79230798-79232053	GM12878	blood:	n/a	chr15:79231305-79231313
4	EP300	chr15:79230886-79231959	GM12878	blood:	n/a	chr15:79231518-79231532
5	IRF4	chr15:79230842-79231984	GM12878	blood:	n/a	n/a
6	POLR2A	chr15:79230656-79233528	GM12878	blood:	n/a	n/a
7	MXI1	chr15:79231044-79231909	GM12878	blood:	n/a	n/a
8	IKZF1	chr15:79230970-79231944	GM12878	blood:	n/a	n/a
9	ZNF384	chr15:79231018-79231899	GM12878	blood:	n/a	n/a
10	SPI1	chr15:79230949-79232020	GM12878	blood:	n/a	chr15:79231458-79231471
11	RELA	chr15:79230876-79232017	GM18951	blood:	n/a	chr15:79231380-79231389 chr15:79231380-79231389
12	RELA	chr15:79230974-79232372	GM12891	blood:	n/a	chr15:79231380-79231389 chr15:79231380-79231389
13	FOXM1	chr15:79231039-79231995	GM12878	blood:	n/a	n/a
14	NFIC	chr15:79230826-79232074	GM12878	blood:	n/a	chr15:79231263-79231280
15	RELA	chr15:79230981-79232021	GM12892	blood:	n/a	chr15:79231380-79231389 chr15:79231380-79231389
16	RUNX3	chr15:79230912-79231999	GM12878	blood:	n/a	n/a
17	ATF2	chr15:79230969-79231985	GM12878	blood:	n/a	n/a
18	NFIC	chr15:79230850-79232052	GM12878	blood:	n/a	chr15:79231263-79231280
19	BATF	chr15:79230916-79231919	GM12878	blood:	n/a	n/a
20	CHD1	chr15:79230955-79232605	GM12878	blood:	n/a	n/a
21	MTA3	chr15:79230609-79232903	GM12878	blood:	n/a	n/a
22	CEBPB	chr15:79230851-79231801	GM12878	blood:	n/a	n/a
23	RELA	chr15:79230940-79231983	GM18505	blood:	n/a	chr15:79231380-79231389 chr15:79231380-79231389
24	RELA	chr15:79230864-79232002	GM19099	blood:	n/a	chr15:79231380-79231389 chr15:79231380-79231389
25	BCLAF1	chr15:79230776-79232047	GM12878	blood:	n/a	n/a
26	POLR2A	chr15:79230799-79232596	GM12878	blood:	n/a	n/a
27	MTA3	chr15:79230651-79231991	GM12878	blood:	n/a	n/a
28	RELA	chr15:79230835-79232024	GM12878	blood:	n/a	chr15:79231380-79231389 chr15:79231380-79231389
29	RUNX3	chr15:79230924-79232016	GM12878	blood:	n/a	n/a
30	BHLHE40	chr15:79231043-79231873	GM12878	blood:	n/a	n/a
31	EBF1	chr15:79230926-79231944	GM12878	blood:	n/a	n/a
32	FOXM1	chr15:79231019-79232411	GM12878	blood:	n/a	n/a
33	BATF	chr15:79230974-79231641	GM12878	blood:	n/a	n/a
34	POLR2A	chr15:79230702-79232674	GM12878	blood:	n/a	n/a
35	RELA	chr15:79230861-79232405	GM15510	blood:	n/a	chr15:79231380-79231389 chr15:79231380-79231389
36	PML	chr15:79230773-79232418	GM12878	blood:	n/a	n/a
37	ATF2	chr15:79230807-79232004	GM12878	blood:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr15:79229734..79233307-chr15:79235000..79238757,6	MCF-7	breast:
2	chr15:79228950..79233188-chr15:79235013..79237607,6	K562	blood:
3	chr15:79228914..79232769-chr15:79235901..79239047,4	MCF-7	breast:

Variant related genes	Relation type
CTSH	TF binding region
ENSG00000103811	Chromatin interaction

Extended variants
information (count: 6 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:5)

rs_ID	r²[population]
rs2289696	0.96[ASN][1000 genomes]
rs62013198	0.84[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs62013199	0.83[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62013200	0.85[AFR][1000 genomes];0.87[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs62013235	0.89[ASN][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	esv33573	chr15:79053484-79293881	Weak transcription Strong transcription Enhancers Flanking Active TSS Active TSS ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	20 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs62013227	CTSH	cis	Adipose Subcutaneous	GTEx
rs62013227	CTSH	cis	Nerve Tibial	GTEx

Chromatin state (count:80 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:79215400-79233200	Weak transcription	H1 Cell Line	embryonic stem cell
2	chr15:79215400-79236600	Weak transcription	Small Intestine	intestine
3	chr15:79215600-79232800	Weak transcription	HUES48 Cell Line	embryonic stem cell
4	chr15:79219600-79236200	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
5	chr15:79220200-79231800	Weak transcription	Rectal Mucosa Donor 31	rectum
6	chr15:79220200-79235200	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
7	chr15:79220600-79236200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
8	chr15:79220600-79236400	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
9	chr15:79222000-79232000	Strong transcription	HepG2	liver
10	chr15:79222200-79233400	Weak transcription	Thymus	Thymus
11	chr15:79222400-79236400	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
12	chr15:79223800-79236000	Weak transcription	HSMMtube	muscle
13	chr15:79223800-79236200	Weak transcription	Brain Angular Gyrus	brain
14	chr15:79224200-79236400	Weak transcription	Colonic Mucosa	Colon
15	chr15:79224400-79236600	Weak transcription	HMEC	breast
16	chr15:79224600-79236200	Weak transcription	Psoas Muscle	Psoas
17	chr15:79225600-79236400	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
18	chr15:79226400-79236000	Weak transcription	Fetal Kidney	kidney
19	chr15:79226600-79236200	Weak transcription	Rectal Smooth Muscle	rectum
20	chr15:79227000-79236000	Weak transcription	Colon Smooth Muscle	Colon
21	chr15:79227200-79231800	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
22	chr15:79227200-79236000	Weak transcription	Duodenum Smooth Muscle	Duodenum
23	chr15:79227200-79236200	Weak transcription	Placenta	Placenta
24	chr15:79227400-79234800	Weak transcription	Rectal Mucosa Donor 29	rectum
25	chr15:79227400-79236400	Weak transcription	Aorta	Aorta
26	chr15:79227400-79236600	Weak transcription	Sigmoid Colon	Sigmoid Colon
27	chr15:79227600-79236200	Weak transcription	Right Ventricle	heart
28	chr15:79228000-79231800	Weak transcription	Left Ventricle	heart
29	chr15:79228000-79236000	Weak transcription	Stomach Smooth Muscle	stomach
30	chr15:79228200-79235400	Weak transcription	Brain Anterior Caudate	brain
31	chr15:79229000-79233200	Flanking Active TSS	Monocytes-CD14+_RO01746	blood
32	chr15:79229200-79232800	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
33	chr15:79229400-79231200	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
34	chr15:79229400-79232200	Enhancers	Primary T helper cells fromperipheralblood	blood
35	chr15:79229400-79232400	Enhancers	Primary T helper cells PMA-I stimulated	--
36	chr15:79229800-79236200	Weak transcription	Esophagus	oesophagus
37	chr15:79230000-79231200	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
38	chr15:79230000-79231200	Strong transcription	Liver	Liver
39	chr15:79230000-79231600	Enhancers	Primary B cells from peripheral blood	blood
40	chr15:79230000-79231800	Enhancers	Primary T helper 17 cells PMA-I stimulated	--
41	chr15:79230000-79231800	Weak transcription	Lung	lung
42	chr15:79230000-79232000	Enhancers	Primary monocytes fromperipheralblood	blood
43	chr15:79230000-79232000	Enhancers	Primary T cells from cord blood	blood
44	chr15:79230000-79235000	Weak transcription	Brain Hippocampus Middle	brain
45	chr15:79230000-79235600	Weak transcription	Fetal Stomach	stomach
46	chr15:79230000-79235600	Weak transcription	Skeletal Muscle Female	skeletal muscle
47	chr15:79230000-79235600	Weak transcription	Stomach Mucosa	stomach
48	chr15:79230000-79236200	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
49	chr15:79230200-79231200	Enhancers	Primary B cells from cord blood	blood
50	chr15:79230200-79231200	Weak transcription	Brain Inferior Temporal Lobe	brain

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