Variant report

Variant	rs55658494
Chromosome Location	chr15:79238879-79238880
allele	A/C/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	RCOR1	chr15:79238859-79239181	K562	blood:	n/a	n/a

No data

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

No.	Distal block	Cell Line	Cell type
1	chr15:79238657..79240315-chr15:79242629..79245251,2	K562	blood:
2	chr15:79238426..79240913-chr15:79263614..79265466,3	MCF-7	breast:
3	chr15:79228914..79232769-chr15:79235901..79239047,4	MCF-7	breast:
4	chr15:79219205..79223895-chr15:79234790..79239038,6	MCF-7	breast:
5	chr15:79236829..79239228-chr15:79240562..79242151,2	K562	blood:

No data

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

Extended variants
information (count: 13 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:11)

rs_ID	r²[population]
rs16970344	0.96[AFR][1000 genomes];0.89[EUR][1000 genomes]
rs56148823	0.89[AFR][1000 genomes];0.95[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs56248637	0.86[EUR][1000 genomes]
rs56289610	0.86[EUR][1000 genomes]
rs62013229	0.92[AFR][1000 genomes];0.86[EUR][1000 genomes]
rs62013230	0.96[AFR][1000 genomes];0.89[EUR][1000 genomes]
rs62013231	0.89[EUR][1000 genomes]
rs62013236	0.82[EUR][1000 genomes]
rs62013237	0.82[EUR][1000 genomes]
rs62013238	0.82[EUR][1000 genomes]
rs8035576	0.89[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	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
2	esv3428448	chr15:79236847-79239745	Active TSS Bivalent/Poised TSS Flanking Active TSS Weak transcription Enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region	3 gene(s)	inside rSNPs	n/a

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs55658494	CTSH	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:28 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:79237800-79239000	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
2	chr15:79237800-79241000	Weak transcription	Liver	Liver
3	chr15:79237800-79241800	Weak transcription	Fetal Intestine Large	intestine
4	chr15:79237800-79242200	Weak transcription	Esophagus	oesophagus
5	chr15:79237800-79242200	Weak transcription	Fetal Kidney	kidney
6	chr15:79237800-79242400	Weak transcription	Sigmoid Colon	Sigmoid Colon
7	chr15:79237800-79242600	Weak transcription	Rectal Mucosa Donor 31	rectum
8	chr15:79237800-79243600	Weak transcription	Right Atrium	heart
9	chr15:79237800-79243600	Weak transcription	Spleen	Spleen
10	chr15:79237800-79244200	Weak transcription	Psoas Muscle	Psoas
11	chr15:79238000-79239200	Enhancers	Primary hematopoietic stem cells short term culture	blood
12	chr15:79238000-79242000	Weak transcription	Breast Myoepithelial Primary Cells	Breast
13	chr15:79238000-79242000	Weak transcription	Duodenum Mucosa	Duodenum
14	chr15:79238000-79242200	Weak transcription	Lung	lung
15	chr15:79238000-79242400	Weak transcription	Adipose Nuclei	Adipose
16	chr15:79238000-79243200	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
17	chr15:79238000-79243400	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
18	chr15:79238400-79241600	Weak transcription	Gastric	stomach
19	chr15:79238400-79241800	Weak transcription	Fetal Intestine Small	intestine
20	chr15:79238600-79239200	Enhancers	HSMMtube	muscle
21	chr15:79238600-79241800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
22	chr15:79238600-79244200	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
23	chr15:79238600-79252600	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
24	chr15:79238800-79239000	Bivalent Enhancer	Fetal Lung	lung
25	chr15:79238800-79239000	Bivalent Enhancer	HepG2	liver
26	chr15:79238800-79239400	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
27	chr15:79238800-79240800	Weak transcription	Stomach Mucosa	stomach
28	chr15:79238800-79241600	Weak transcription	Pancreas	Pancrea

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