Variant report

Variant	rs1998504
Chromosome Location	chr9:116111236-116111237
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:0)
CpG islands
(count:0)
Chromatin interactive
region (count:8)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

(count:8 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr9:116109902..116113383-chr9:116162345..116166968,8	MCF-7	breast:
2	chr9:116060077..116063011-chr9:116109868..116112387,2	MCF-7	breast:
3	chr9:116110213..116113414-chr9:116171126..116174421,5	MCF-7	breast:
4	chr9:116111218..116114895-chr9:116159419..116161993,4	MCF-7	breast:
5	chr9:116108846..116117047-chr9:116126327..116140994,30	MCF-7	breast:
6	chr9:116109912..116111859-chr9:116161206..116163943,2	K562	blood:
7	chr9:116101294..116104058-chr9:116110419..116112658,2	K562	blood:
8	chr9:116038056..116040048-chr9:116108621..116111534,2	MCF-7	breast:

No data

Variant related genes	Relation type
ENSG00000148225	Chromatin interaction
ENSG00000165188	Chromatin interaction
ENSG00000148218	Chromatin interaction
ENSG00000148229	Chromatin interaction
ENSG00000157653	Chromatin interaction
ENSG00000119431	Chromatin interaction

Extended variants
information (count: 34 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:31)

rs_ID	r²[population]
rs10114327	0.88[AMR][1000 genomes];0.93[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs10117906	0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs10118045	0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs10118275	0.85[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10759640	0.88[AMR][1000 genomes];0.94[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs10759641	0.92[EUR][1000 genomes]
rs10817481	0.85[AMR][1000 genomes];0.93[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs10817485	0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs10981762	0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs10981763	0.81[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs11787602	0.87[ASN][1000 genomes]
rs2093691	0.90[AMR][1000 genomes];0.93[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6478002	0.88[AMR][1000 genomes];0.92[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs6478003	0.92[AMR][1000 genomes];0.94[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6478004	0.88[ASN][1000 genomes]
rs6478005	0.88[ASN][1000 genomes]
rs6478006	0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7025188	0.94[AMR][1000 genomes];0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7025371	0.90[ASN][1000 genomes]
rs7025517	0.91[AMR][1000 genomes];0.93[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs7025770	0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7026076	0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7041572	0.88[AMR][1000 genomes];0.92[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs7048039	0.91[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7849513	0.88[AMR][1000 genomes];0.92[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs7850002	0.92[AMR][1000 genomes];0.94[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7850264	0.88[AMR][1000 genomes];0.92[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs7863921	0.90[AMR][1000 genomes];0.94[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7864788	0.88[AMR][1000 genomes];0.93[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs7868271	0.88[AMR][1000 genomes];0.93[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7873862	0.83[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	nsv530949	chr9:115821128-116487796	Flanking Active TSS Enhancers Active TSS Weak transcription Genic enhancers Strong transcription 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	71 gene(s)	inside rSNPs	diseases
2	nsv1042663	chr9:115920158-116167140	Weak transcription Active TSS Strong transcription Enhancers Flanking Active TSS Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	43 gene(s)	inside rSNPs	diseases
3	nsv893744	chr9:115934852-116170227	Active TSS Weak transcription Enhancers Strong transcription Flanking Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	40 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs1998504	PRPF4	cis	Esophagus Muscularis	GTEx
rs1998504	BSPRY	cis	Heart Left Ventricle	GTEx

Chromatin state (count:47 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr9:116103000-116111800	Weak transcription	Lung	lung
2	chr9:116103200-116111400	Weak transcription	Stomach Mucosa	stomach
3	chr9:116103200-116111400	Weak transcription	GM12878-XiMat	blood
4	chr9:116105800-116111400	Enhancers	Fetal Intestine Small	intestine
5	chr9:116105800-116111400	Weak transcription	Right Ventricle	heart
6	chr9:116106200-116111400	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
7	chr9:116106600-116111400	Weak transcription	Liver	Liver
8	chr9:116106600-116111400	Weak transcription	Esophagus	oesophagus
9	chr9:116106600-116111400	Weak transcription	Pancreas	Pancrea
10	chr9:116106600-116111800	Weak transcription	K562	blood
11	chr9:116107600-116111600	Weak transcription	Colon Smooth Muscle	Colon
12	chr9:116108000-116111400	Weak transcription	Brain Anterior Caudate	brain
13	chr9:116108000-116111600	Weak transcription	Brain Angular Gyrus	brain
14	chr9:116108000-116112000	Weak transcription	Brain Inferior Temporal Lobe	brain
15	chr9:116108200-116112000	Weak transcription	Brain Substantia Nigra	brain
16	chr9:116108600-116111400	Weak transcription	Sigmoid Colon	Sigmoid Colon
17	chr9:116108800-116111400	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
18	chr9:116108800-116111400	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
19	chr9:116108800-116111800	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
20	chr9:116109600-116111400	Enhancers	Rectal Mucosa Donor 29	rectum
21	chr9:116110000-116111400	Enhancers	Duodenum Mucosa	Duodenum
22	chr9:116110200-116111400	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
23	chr9:116110200-116111400	Bivalent Enhancer	Fetal Intestine Large	intestine
24	chr9:116110200-116112000	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
25	chr9:116110400-116111400	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
26	chr9:116110400-116111400	Weak transcription	Colonic Mucosa	Colon
27	chr9:116110400-116111600	Weak transcription	Right Atrium	heart
28	chr9:116110600-116111400	Enhancers	Rectal Mucosa Donor 31	rectum
29	chr9:116111000-116111400	Enhancers	Primary hematopoietic stem cells short term culture	blood
30	chr9:116111200-116111400	Flanking Bivalent TSS/Enh	ES-I3 Cell Line	embryonic stem cell
31	chr9:116111200-116111400	Flanking Bivalent TSS/Enh	HUES64 Cell Line	embryonic stem cell
32	chr9:116111200-116111400	Enhancers	Primary hematopoietic stem cells	blood
33	chr9:116111200-116111400	Active TSS	Brain Cingulate Gyrus	brain
34	chr9:116111200-116111600	Flanking Bivalent TSS/Enh	H1 Cell Line	embryonic stem cell
35	chr9:116111200-116111600	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
36	chr9:116111200-116111600	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Female	--
37	chr9:116111200-116112000	Bivalent/Poised TSS	Skeletal Muscle Male	skeletal muscle
38	chr9:116111200-116112400	Bivalent/Poised TSS	HUES6 Cell Line	embryonic stem cell
39	chr9:116111200-116112400	Bivalent/Poised TSS	Fetal Kidney	kidney
40	chr9:116111200-116112400	Active TSS	Rectal Smooth Muscle	rectum
41	chr9:116111200-116112600	Active TSS	H9 Cell Line	embryonic stem cell
42	chr9:116111200-116112600	Bivalent/Poised TSS	iPS-18 Cell Line	embryonic stem cell
43	chr9:116111200-116112600	Bivalent/Poised TSS	iPS-20b Cell Line	embryonic stem cell
44	chr9:116111200-116112800	Bivalent/Poised TSS	HUES48 Cell Line	embryonic stem cell
45	chr9:116111200-116113000	Bivalent/Poised TSS	ES-WA7 Cell Line	embryonic stem cell
46	chr9:116111200-116113000	Bivalent/Poised TSS	iPS-15b Cell Line	embryonic stem cell
47	chr9:116111200-116113000	Active TSS	Pancreatic Islets	Pancreatic Islet

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