Variant report

Variant	rs4778858
Chromosome Location	chr15:79172011-79172012
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr15:79152585..79154428-chr15:79171888..79174495,2	K562	blood:
2	chr15:79152585..79155864-chr15:79171888..79174971,4	K562	blood:
3	chr15:79099510..79101479-chr15:79170931..79173380,2	K562	blood:
4	chr15:79164114..79167612-chr15:79169909..79172320,4	MCF-7	breast:

Variant related genes	Relation type
ENSG00000185787	Chromatin interaction

Extended variants
information (count: 35 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:32)

rs_ID	r²[population]
rs10519214	1.00[CHB][hapmap];1.00[JPT][hapmap];0.97[AMR][1000 genomes];0.99[ASN][1000 genomes]
rs1075965	0.95[CHB][hapmap];1.00[JPT][hapmap];0.97[AMR][1000 genomes];0.94[ASN][1000 genomes]
rs16970190	1.00[CHB][hapmap];0.94[JPT][hapmap];1.00[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs16970207	1.00[CHB][hapmap];1.00[JPT][hapmap];0.97[AMR][1000 genomes];0.96[ASN][1000 genomes]
rs16970215	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AMR][1000 genomes];0.94[ASN][1000 genomes]
rs16970216	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AMR][1000 genomes];0.94[ASN][1000 genomes]
rs16970248	1.00[CHB][hapmap];1.00[JPT][hapmap];0.97[AMR][1000 genomes];0.94[ASN][1000 genomes]
rs1808757	0.80[AMR][1000 genomes]
rs3803545	1.00[AMR][1000 genomes];0.96[ASN][1000 genomes]
rs3825930	0.85[AMR][1000 genomes]
rs4778627	0.95[CHB][hapmap];1.00[JPT][hapmap];0.97[AMR][1000 genomes];0.99[ASN][1000 genomes]
rs4778645	1.00[CHB][hapmap];1.00[JPT][hapmap];0.87[AMR][1000 genomes];0.99[ASN][1000 genomes]
rs4778659	1.00[CHB][hapmap];1.00[JPT][hapmap];0.97[AMR][1000 genomes];0.97[ASN][1000 genomes]
rs4778952	0.97[AMR][1000 genomes];0.97[ASN][1000 genomes]
rs4779081	1.00[AMR][1000 genomes];0.91[ASN][1000 genomes]
rs4779082	1.00[CHB][hapmap];0.89[JPT][hapmap];0.97[AMR][1000 genomes];0.91[ASN][1000 genomes]
rs56963875	0.97[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs58105551	1.00[AMR][1000 genomes];0.94[ASN][1000 genomes]
rs58257692	0.83[AMR][1000 genomes];0.91[ASN][1000 genomes]
rs58807257	0.97[AMR][1000 genomes];0.94[ASN][1000 genomes]
rs58858460	0.84[ASN][1000 genomes]
rs59238093	0.85[AMR][1000 genomes]
rs60009001	1.00[AMR][1000 genomes];0.91[ASN][1000 genomes]
rs61009187	0.97[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs61504829	0.85[AMR][1000 genomes]
rs6495342	0.84[ASN][1000 genomes]
rs7171615	1.00[ASN][1000 genomes]
rs73470371	0.93[AMR][1000 genomes];0.91[ASN][1000 genomes]
rs73470375	0.93[AMR][1000 genomes];0.91[ASN][1000 genomes]
rs73470383	1.00[AMR][1000 genomes];0.88[ASN][1000 genomes]
rs7402463	1.00[CHB][hapmap];1.00[JPT][hapmap];0.97[AMR][1000 genomes];0.94[ASN][1000 genomes]
rs7402487	0.95[CHB][hapmap];0.94[JPT][hapmap];0.83[AMR][1000 genomes];0.94[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv917303	chr15:78491050-79205255	Enhancers Genic enhancers Weak transcription Flanking Active TSS Strong transcription Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	122 gene(s)	inside rSNPs	diseases
2	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
3	nsv904432	chr15:79066932-79175813	Active TSS Enhancers Weak transcription Bivalent/Poised TSS Bivalent Enhancer Flanking Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Genic enhancers Strong transcription ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	17 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs4778858	CTSH	cis	multi-tissue	Pritchard

Chromatin state (count:127 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:79166800-79173400	Enhancers	Fetal Heart	heart
2	chr15:79167000-79179200	Weak transcription	Esophagus	oesophagus
3	chr15:79167200-79172200	Enhancers	Cortex derived primary cultured neurospheres	brain
4	chr15:79167200-79178200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
5	chr15:79167600-79172200	Enhancers	Fetal Muscle Leg	muscle
6	chr15:79167800-79172400	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
7	chr15:79167800-79173200	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
8	chr15:79167800-79183800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
9	chr15:79168000-79172400	Enhancers	Brain Substantia Nigra	brain
10	chr15:79168000-79172400	Enhancers	Fetal Lung	lung
11	chr15:79168000-79173000	Enhancers	Brain Hippocampus Middle	brain
12	chr15:79168000-79173600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
13	chr15:79168000-79174000	Weak transcription	H9 Cell Line	embryonic stem cell
14	chr15:79168000-79174800	Enhancers	Primary T killer memory cells from peripheral blood	blood
15	chr15:79168800-79172800	Enhancers	Brain Angular Gyrus	brain
16	chr15:79169000-79172800	Enhancers	NHEK	skin
17	chr15:79169200-79172400	Enhancers	Duodenum Mucosa	Duodenum
18	chr15:79169200-79172600	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
19	chr15:79169200-79172800	Enhancers	Primary T killer naive cells fromperipheralblood	blood
20	chr15:79169200-79173000	Enhancers	Adipose Nuclei	Adipose
21	chr15:79169200-79173200	Enhancers	Primary T helper naive cells fromperipheralblood	blood
22	chr15:79169200-79173400	Enhancers	Fetal Adrenal Gland	Adrenal Gland
23	chr15:79169200-79173600	Weak transcription	Thymus	Thymus
24	chr15:79169400-79176400	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
25	chr15:79169600-79172800	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
26	chr15:79169800-79172600	Enhancers	HMEC	breast
27	chr15:79169800-79180000	Weak transcription	Gastric	stomach
28	chr15:79170000-79172200	Genic enhancers	Primary B cells from peripheral blood	blood
29	chr15:79170000-79174400	Genic enhancers	Hela-S3	cervix
30	chr15:79170000-79174600	Genic enhancers	HSMM	muscle
31	chr15:79170200-79172200	Enhancers	Fetal Brain Male	brain
32	chr15:79170200-79172600	Enhancers	Primary T cells from cord blood	blood
33	chr15:79170200-79187000	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
34	chr15:79170400-79172200	Enhancers	HUES6 Cell Line	embryonic stem cell
35	chr15:79170400-79172200	Enhancers	Breast Myoepithelial Primary Cells	Breast
36	chr15:79170400-79172200	Enhancers	Foreskin Fibroblast Primary Cells skin02	Skin
37	chr15:79170400-79172400	Weak transcription	Fetal Intestine Large	intestine
38	chr15:79170400-79172800	Enhancers	Brain Inferior Temporal Lobe	brain
39	chr15:79170400-79172800	Enhancers	Osteobl	bone
40	chr15:79170400-79173000	Enhancers	Primary T helper naive cells from peripheral blood	blood
41	chr15:79170400-79174000	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
42	chr15:79170400-79177200	Weak transcription	Colonic Mucosa	Colon
43	chr15:79170400-79198600	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
44	chr15:79170600-79172200	Genic enhancers	HUES48 Cell Line	embryonic stem cell
45	chr15:79170600-79173200	Genic enhancers	HUES64 Cell Line	embryonic stem cell
46	chr15:79170600-79173200	Transcr. at gene 5' and 3'	GM12878-XiMat	blood
47	chr15:79170600-79173400	Genic enhancers	HepG2	liver
48	chr15:79170600-79173600	Weak transcription	Sigmoid Colon	Sigmoid Colon
49	chr15:79170600-79176000	Genic enhancers	Primary T regulatory cells fromperipheralblood	blood
50	chr15:79170600-79182400	Weak transcription	Aorta	Aorta

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