Variant report

Variant	rs62013200
Chromosome Location	chr15:79230737-79230738
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	POLR2A	chr15:79230656-79233528	GM12878	blood:	n/a	n/a
3	MTA3	chr15:79230609-79232903	GM12878	blood:	n/a	n/a
4	MTA3	chr15:79230651-79231991	GM12878	blood:	n/a	n/a
5	POLR2A	chr15:79230702-79232674	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: 3 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:2)

rs_ID	r²[population]
rs62013199	0.93[AFR][1000 genomes];0.87[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs62013227	0.85[AFR][1000 genomes];0.87[AMR][1000 genomes];0.91[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	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
rs62013200	CTSH	cis	Nerve Tibial	GTEx
rs62013200	CTSH	cis	Adipose Subcutaneous	GTEx

Chromatin state (count:81 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:79203600-79231000	Weak transcription	Primary T killer memory cells from peripheral blood	blood
2	chr15:79215400-79233200	Weak transcription	H1 Cell Line	embryonic stem cell
3	chr15:79215400-79236600	Weak transcription	Small Intestine	intestine
4	chr15:79215600-79232800	Weak transcription	HUES48 Cell Line	embryonic stem cell
5	chr15:79219600-79236200	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
6	chr15:79220200-79231800	Weak transcription	Rectal Mucosa Donor 31	rectum
7	chr15:79220200-79235200	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
8	chr15:79220600-79236200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
9	chr15:79220600-79236400	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
10	chr15:79222000-79232000	Strong transcription	HepG2	liver
11	chr15:79222200-79233400	Weak transcription	Thymus	Thymus
12	chr15:79222400-79236400	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
13	chr15:79223800-79236000	Weak transcription	HSMMtube	muscle
14	chr15:79223800-79236200	Weak transcription	Brain Angular Gyrus	brain
15	chr15:79224200-79236400	Weak transcription	Colonic Mucosa	Colon
16	chr15:79224400-79231000	Weak transcription	Brain Cingulate Gyrus	brain
17	chr15:79224400-79236600	Weak transcription	HMEC	breast
18	chr15:79224600-79236200	Weak transcription	Psoas Muscle	Psoas
19	chr15:79225600-79236400	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
20	chr15:79226400-79236000	Weak transcription	Fetal Kidney	kidney
21	chr15:79226600-79236200	Weak transcription	Rectal Smooth Muscle	rectum
22	chr15:79227000-79236000	Weak transcription	Colon Smooth Muscle	Colon
23	chr15:79227200-79231800	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
24	chr15:79227200-79236000	Weak transcription	Duodenum Smooth Muscle	Duodenum
25	chr15:79227200-79236200	Weak transcription	Placenta	Placenta
26	chr15:79227400-79231000	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
27	chr15:79227400-79234800	Weak transcription	Rectal Mucosa Donor 29	rectum
28	chr15:79227400-79236400	Weak transcription	Aorta	Aorta
29	chr15:79227400-79236600	Weak transcription	Sigmoid Colon	Sigmoid Colon
30	chr15:79227600-79236200	Weak transcription	Right Ventricle	heart
31	chr15:79228000-79231800	Weak transcription	Left Ventricle	heart
32	chr15:79228000-79236000	Weak transcription	Stomach Smooth Muscle	stomach
33	chr15:79228200-79235400	Weak transcription	Brain Anterior Caudate	brain
34	chr15:79229000-79233200	Flanking Active TSS	Monocytes-CD14+_RO01746	blood
35	chr15:79229200-79230800	Enhancers	Dnd41	blood
36	chr15:79229200-79232800	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
37	chr15:79229400-79231200	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
38	chr15:79229400-79232200	Enhancers	Primary T helper cells fromperipheralblood	blood
39	chr15:79229400-79232400	Enhancers	Primary T helper cells PMA-I stimulated	--
40	chr15:79229600-79231000	Enhancers	Brain Substantia Nigra	brain
41	chr15:79229800-79236200	Weak transcription	Esophagus	oesophagus
42	chr15:79230000-79231000	Weak transcription	Primary T helper naive cells from peripheral blood	blood
43	chr15:79230000-79231200	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
44	chr15:79230000-79231200	Strong transcription	Liver	Liver
45	chr15:79230000-79231600	Enhancers	Primary B cells from peripheral blood	blood
46	chr15:79230000-79231800	Enhancers	Primary T helper 17 cells PMA-I stimulated	--
47	chr15:79230000-79231800	Weak transcription	Lung	lung
48	chr15:79230000-79232000	Enhancers	Primary monocytes fromperipheralblood	blood
49	chr15:79230000-79232000	Enhancers	Primary T cells from cord blood	blood
50	chr15:79230000-79235000	Weak transcription	Brain Hippocampus Middle	brain

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