Variant report

Variant	rs28655102
Chromosome Location	chr15:79232700-79232701
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:4)
CpG islands
(count:0)
Chromatin interactive
region (count:7)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:4 , 50 per page) page: 1

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	POLR2A	chr15:79231205-79232819	GM12878	blood:	n/a	n/a

No data

(count:7 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr15:79229734..79233307-chr15:79235000..79238757,6	MCF-7	breast:
2	chr15:79222510..79224898-chr15:79231355..79233391,2	K562	blood:
3	chr15:79226655..79228594-chr15:79231638..79234454,2	MCF-7	breast:
4	chr15:79164191..79167117-chr15:79232695..79235320,2	K562	blood:
5	chr15:79228950..79233188-chr15:79235013..79237607,6	K562	blood:
6	chr15:79228914..79232769-chr15:79235901..79239047,4	MCF-7	breast:
7	chr15:79228459..79231609-chr15:79232688..79237314,4	K562	blood:

No data

Variant related genes	Relation type
CTSH	TF binding region
ENSG00000103811	Chromatin interaction
ENSG00000185787	Chromatin interaction

Extended variants
information (count: 22 )
Associated
traits (count: 2 )

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

rs_ID	r²[population]
rs10152587	0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10152589	0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1036937	0.89[AMR][1000 genomes];0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1036938	0.88[AMR][1000 genomes];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1036939	0.89[AMR][1000 genomes];0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10400877	0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10400881	0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs10400902	0.97[EUR][1000 genomes]
rs11072815	0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11072817	0.96[AFR][1000 genomes];0.94[AMR][1000 genomes];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11072818	0.92[AMR][1000 genomes];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11855406	1.00[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11856301	0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1369324	0.89[AFR][1000 genomes];0.86[AMR][1000 genomes];0.85[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2289699	0.98[AMR][1000 genomes];0.94[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2870085	0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3825932	0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4778716	0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4778724	0.85[AMR][1000 genomes];0.83[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs4779112	0.95[AMR][1000 genomes];0.92[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7496812	0.97[AMR][1000 genomes];0.93[EUR][1000 genomes];0.98[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
rs28655102	CTSH	Cis_1M	lymphoblastoid	RTeQTL
rs28655102	CTSH	cis	multi-tissue	Pritchard

Chromatin state (count:70 , 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	chr15:79220200-79235200	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
6	chr15:79220600-79236200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
7	chr15:79220600-79236400	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
8	chr15:79222200-79233400	Weak transcription	Thymus	Thymus
9	chr15:79222400-79236400	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
10	chr15:79223800-79236000	Weak transcription	HSMMtube	muscle
11	chr15:79223800-79236200	Weak transcription	Brain Angular Gyrus	brain
12	chr15:79224200-79236400	Weak transcription	Colonic Mucosa	Colon
13	chr15:79224400-79236600	Weak transcription	HMEC	breast
14	chr15:79224600-79236200	Weak transcription	Psoas Muscle	Psoas
15	chr15:79225600-79236400	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
16	chr15:79226400-79236000	Weak transcription	Fetal Kidney	kidney
17	chr15:79226600-79236200	Weak transcription	Rectal Smooth Muscle	rectum
18	chr15:79227000-79236000	Weak transcription	Colon Smooth Muscle	Colon
19	chr15:79227200-79236000	Weak transcription	Duodenum Smooth Muscle	Duodenum
20	chr15:79227200-79236200	Weak transcription	Placenta	Placenta
21	chr15:79227400-79234800	Weak transcription	Rectal Mucosa Donor 29	rectum
22	chr15:79227400-79236400	Weak transcription	Aorta	Aorta
23	chr15:79227400-79236600	Weak transcription	Sigmoid Colon	Sigmoid Colon
24	chr15:79227600-79236200	Weak transcription	Right Ventricle	heart
25	chr15:79228000-79236000	Weak transcription	Stomach Smooth Muscle	stomach
26	chr15:79228200-79235400	Weak transcription	Brain Anterior Caudate	brain
27	chr15:79229000-79233200	Flanking Active TSS	Monocytes-CD14+_RO01746	blood
28	chr15:79229200-79232800	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
29	chr15:79229800-79236200	Weak transcription	Esophagus	oesophagus
30	chr15:79230000-79235000	Weak transcription	Brain Hippocampus Middle	brain
31	chr15:79230000-79235600	Weak transcription	Fetal Stomach	stomach
32	chr15:79230000-79235600	Weak transcription	Skeletal Muscle Female	skeletal muscle
33	chr15:79230000-79235600	Weak transcription	Stomach Mucosa	stomach
34	chr15:79230000-79236200	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
35	chr15:79230200-79236000	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
36	chr15:79230200-79236000	Weak transcription	Fetal Intestine Large	intestine
37	chr15:79230200-79236200	Weak transcription	Pancreas	Pancrea
38	chr15:79230200-79236200	Weak transcription	Spleen	Spleen
39	chr15:79230200-79236400	Weak transcription	Ovary	ovary
40	chr15:79230200-79236600	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
41	chr15:79230400-79235200	Weak transcription	Duodenum Mucosa	Duodenum
42	chr15:79231000-79236400	Weak transcription	Brain Substantia Nigra	brain
43	chr15:79231200-79235200	Weak transcription	Liver	Liver
44	chr15:79231400-79236000	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
45	chr15:79231800-79232800	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
46	chr15:79231800-79232800	Flanking Active TSS	Primary T helper 17 cells PMA-I stimulated	--
47	chr15:79231800-79232800	Strong transcription	Fetal Intestine Small	intestine
48	chr15:79231800-79236200	Weak transcription	Brain Cingulate Gyrus	brain
49	chr15:79232000-79233000	Active TSS	GM12878-XiMat	blood
50	chr15:79232000-79234800	Weak transcription	HepG2	liver

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