Variant report

Variant	rs4778724
Chromosome Location	chr15:79238406-79238407
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr15:79164120..79166260-chr15:79235714..79238649,3	K562	blood:
2	chr15:79228914..79232769-chr15:79235901..79239047,4	MCF-7	breast:
3	chr15:79164120..79166028-chr15:79235714..79238649,2	K562	blood:
4	chr15:79224751..79228848-chr15:79235939..79238870,4	MCF-7	breast:
5	chr15:79219205..79223895-chr15:79234790..79239038,6	MCF-7	breast:
6	chr15:79229734..79233307-chr15:79235000..79238757,6	MCF-7	breast:
7	chr15:79236829..79239228-chr15:79240562..79242151,2	K562	blood:

Variant related genes	Relation type
ENSG00000185787	Chromatin interaction
ENSG00000103811	Chromatin interaction

Extended variants
information (count: 23 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:21)

rs_ID	r²[population]
rs10152587	0.87[AMR][1000 genomes];0.82[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs10152589	0.87[AMR][1000 genomes];0.83[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs1036937	0.91[AFR][1000 genomes];0.96[AMR][1000 genomes];0.92[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs1036938	0.90[AFR][1000 genomes];0.95[AMR][1000 genomes];0.93[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs1036939	0.96[AMR][1000 genomes];0.92[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs10400877	0.86[AMR][1000 genomes];0.84[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs10400881	0.88[AMR][1000 genomes];0.84[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs11072815	0.87[AMR][1000 genomes];0.83[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs11072817	0.91[AMR][1000 genomes];0.93[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs11072818	0.90[AFR][1000 genomes];0.94[AMR][1000 genomes];0.93[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs11855406	0.86[AMR][1000 genomes];0.84[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs11856301	0.87[AMR][1000 genomes];0.83[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs12913968	0.88[EUR][1000 genomes]
rs1369324	0.92[AMR][1000 genomes];0.94[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2289699	0.85[AMR][1000 genomes];0.85[ASN][1000 genomes]
rs28655102	0.85[AMR][1000 genomes];0.83[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2870085	0.87[AMR][1000 genomes];0.84[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs3825932	0.86[AMR][1000 genomes];0.83[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs4778716	0.87[AMR][1000 genomes];0.83[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs4779112	0.83[AMR][1000 genomes];0.81[ASN][1000 genomes]
rs7496812	0.85[AMR][1000 genomes];0.85[ASN][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:3)

SNP	Gene	Cis/trans	Tissue	Source
rs4778724	CTSH	cis	Muscle Skeletal	GTEx
rs4778724	CTSH	Cis_1M	lymphoblastoid	RTeQTL
rs4778724	CTSH	cis	multi-tissue	Pritchard

Chromatin state (count:29 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:79237400-79238800	Enhancers	Stomach Mucosa	stomach
2	chr15:79237600-79238800	Enhancers	Pancreas	Pancrea
3	chr15:79237800-79238600	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
4	chr15:79237800-79238600	Enhancers	iPS DF 6.9 Cell Line	embryonic stem cell
5	chr15:79237800-79238600	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
6	chr15:79237800-79238600	Weak transcription	HSMMtube	muscle
7	chr15:79237800-79238800	Enhancers	HepG2	liver
8	chr15:79237800-79239000	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
9	chr15:79237800-79241000	Weak transcription	Liver	Liver
10	chr15:79237800-79241800	Weak transcription	Fetal Intestine Large	intestine
11	chr15:79237800-79242200	Weak transcription	Esophagus	oesophagus
12	chr15:79237800-79242200	Weak transcription	Fetal Kidney	kidney
13	chr15:79237800-79242400	Weak transcription	Sigmoid Colon	Sigmoid Colon
14	chr15:79237800-79242600	Weak transcription	Rectal Mucosa Donor 31	rectum
15	chr15:79237800-79243600	Weak transcription	Right Atrium	heart
16	chr15:79237800-79243600	Weak transcription	Spleen	Spleen
17	chr15:79237800-79244200	Weak transcription	Psoas Muscle	Psoas
18	chr15:79238000-79238600	Enhancers	iPS DF 19.11 Cell Line	embryonic stem cell
19	chr15:79238000-79238600	Bivalent Enhancer	Primary hematopoietic stem cells G-CSF-mobilized Male	--
20	chr15:79238000-79239200	Enhancers	Primary hematopoietic stem cells short term culture	blood
21	chr15:79238000-79242000	Weak transcription	Breast Myoepithelial Primary Cells	Breast
22	chr15:79238000-79242000	Weak transcription	Duodenum Mucosa	Duodenum
23	chr15:79238000-79242200	Weak transcription	Lung	lung
24	chr15:79238000-79242400	Weak transcription	Adipose Nuclei	Adipose
25	chr15:79238000-79243200	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
26	chr15:79238000-79243400	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
27	chr15:79238400-79238600	Bivalent Enhancer	H1 Derived Mesenchymal Stem Cells	ES cell derived
28	chr15:79238400-79241600	Weak transcription	Gastric	stomach
29	chr15:79238400-79241800	Weak transcription	Fetal Intestine Small	intestine

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