Variant report

Variant	rs2840354
Chromosome Location	chr18:9545961-9545962
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr18:9544173..9546289-chr18:9553833..9556141,2	MCF-7	breast:
2	chr18:9544463..9548034-chr18:9553025..9555805,3	K562	blood:
3	chr18:9545353..9548087-chr18:9560070..9562835,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000154845	Chromatin interaction

Extended variants
information (count: 92 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:86)

rs_ID	r²[population]
rs1036930	0.93[ASN][1000 genomes]
rs11081487	0.83[ASN][1000 genomes]
rs12327541	0.93[ASN][1000 genomes]
rs16955297	0.93[ASN][1000 genomes]
rs1869737	0.92[ASW][hapmap];1.00[CHB][hapmap];0.88[GIH][hapmap];1.00[JPT][hapmap];0.82[YRI][hapmap];0.86[ASN][1000 genomes]
rs1869739	0.86[ASN][1000 genomes]
rs2028657	0.93[ASN][1000 genomes]
rs2277709	0.92[CHD][hapmap];1.00[JPT][hapmap]
rs3786174	0.90[ASN][1000 genomes]
rs55841197	0.93[ASN][1000 genomes]
rs56883068	0.93[ASN][1000 genomes]
rs57539299	1.00[ASN][1000 genomes]
rs58800301	0.86[ASN][1000 genomes]
rs58982927	1.00[ASN][1000 genomes]
rs59114729	0.90[ASN][1000 genomes]
rs59992205	0.90[ASN][1000 genomes]
rs60290408	0.97[ASN][1000 genomes]
rs61166388	0.90[ASN][1000 genomes]
rs61275183	0.86[ASN][1000 genomes]
rs62086114	0.83[ASN][1000 genomes]
rs62086115	0.83[ASN][1000 genomes]
rs62086118	0.83[ASN][1000 genomes]
rs62086119	0.83[ASN][1000 genomes]
rs62086120	0.83[ASN][1000 genomes]
rs62086121	0.83[ASN][1000 genomes]
rs62086146	0.90[ASN][1000 genomes]
rs62086147	0.90[ASN][1000 genomes]
rs62086151	0.90[ASN][1000 genomes]
rs62086152	0.90[ASN][1000 genomes]
rs62086155	0.90[ASN][1000 genomes]
rs62086156	0.90[ASN][1000 genomes]
rs62086158	0.90[ASN][1000 genomes]
rs62086159	0.90[ASN][1000 genomes]
rs62087363	0.90[ASN][1000 genomes]
rs62087368	0.90[ASN][1000 genomes]
rs62087370	0.90[ASN][1000 genomes]
rs62087371	0.90[ASN][1000 genomes]
rs62087372	0.84[ASN][1000 genomes]
rs62087378	0.90[ASN][1000 genomes]
rs62087402	0.90[ASN][1000 genomes]
rs62087403	0.90[ASN][1000 genomes]
rs62087404	0.90[ASN][1000 genomes]
rs62087406	0.90[ASN][1000 genomes]
rs62087407	0.90[ASN][1000 genomes]
rs62087411	0.90[ASN][1000 genomes]
rs62087412	0.90[ASN][1000 genomes]
rs62087414	0.90[ASN][1000 genomes]
rs62087415	0.90[ASN][1000 genomes]
rs62087416	0.90[ASN][1000 genomes]
rs62087417	0.86[ASN][1000 genomes]
rs62087427	0.97[ASN][1000 genomes]
rs62087456	0.93[ASN][1000 genomes]
rs62088860	0.93[ASN][1000 genomes]
rs62088870	0.93[ASN][1000 genomes]
rs62088872	0.93[ASN][1000 genomes]
rs62088873	0.93[ASN][1000 genomes]
rs62088875	0.93[ASN][1000 genomes]
rs62088876	0.93[ASN][1000 genomes]
rs62088880	0.86[ASN][1000 genomes]
rs62088881	0.86[ASN][1000 genomes]
rs62088884	0.86[ASN][1000 genomes]
rs62088885	0.86[ASN][1000 genomes]
rs62088904	0.86[ASN][1000 genomes]
rs62088906	0.86[ASN][1000 genomes]
rs62088908	0.81[ASN][1000 genomes]
rs6506674	1.00[CHD][hapmap]
rs6506677	0.92[ASW][hapmap];1.00[CHB][hapmap];0.84[GIH][hapmap];0.85[JPT][hapmap];0.93[YRI][hapmap];0.93[ASN][1000 genomes]
rs7228280	0.81[ASN][1000 genomes]
rs7231531	0.92[ASW][hapmap];1.00[CHB][hapmap];0.88[GIH][hapmap];1.00[JPT][hapmap];0.93[YRI][hapmap];0.86[ASN][1000 genomes]
rs7233308	1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[YRI][hapmap];0.93[ASN][1000 genomes]
rs7233649	0.86[ASN][1000 genomes]
rs7234355	0.93[ASN][1000 genomes]
rs7235935	0.86[ASN][1000 genomes]
rs7236274	0.86[ASN][1000 genomes]
rs7237018	1.00[ASW][hapmap];1.00[CHB][hapmap];0.91[CHD][hapmap];0.88[GIH][hapmap];1.00[JPT][hapmap];0.84[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs7238137	1.00[JPT][hapmap];0.93[ASN][1000 genomes]
rs7239083	0.92[ASW][hapmap];1.00[CHB][hapmap];0.88[GIH][hapmap];1.00[JPT][hapmap];0.96[YRI][hapmap];0.86[ASN][1000 genomes]
rs72636719	0.80[ASN][1000 genomes]
rs72945737	0.86[ASN][1000 genomes]
rs732698	0.86[ASN][1000 genomes]
rs73393877	0.83[ASN][1000 genomes]
rs73393880	0.90[ASN][1000 genomes]
rs73395717	0.90[ASN][1000 genomes]
rs73395719	0.90[ASN][1000 genomes]
rs8096551	0.86[ASN][1000 genomes]
rs894757	0.90[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:6 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv916373	chr18:9026803-9592201	Strong transcription Weak transcription Enhancers ZNF genes & repeats Flanking Active TSS Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	60 gene(s)	inside rSNPs	diseases
2	nsv1056407	chr18:9144345-9553764	Strong transcription Weak transcription Flanking Active TSS Enhancers Active TSS ZNF genes & repeats Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	42 gene(s)	inside rSNPs	diseases
3	nsv1062025	chr18:9287249-9552470	Flanking Active TSS Strong transcription Bivalent/Poised TSS Active TSS Enhancers Weak transcription ZNF genes & repeats Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	35 gene(s)	inside rSNPs	diseases
4	nsv543643	chr18:9287249-9552470	ZNF genes & repeats Weak transcription Strong transcription Enhancers Flanking Active TSS Active TSS Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	35 gene(s)	inside rSNPs	diseases
5	nsv833585	chr18:9401630-9597291	Weak transcription Enhancers ZNF genes & repeats Strong transcription Genic enhancers Active TSS Flanking Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	28 gene(s)	inside rSNPs	diseases
6	esv3693417	chr18:9512985-9693638	Genic enhancers Flanking Active TSS Strong transcription Transcr. at gene 5' and 3' Weak transcription Enhancers Active TSS ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	27 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs2840354	PPP4R1	cis	lymphoblastoid	seeQTL

Chromatin state (count:125 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr18:9525800-9547200	Weak transcription	Stomach Mucosa	stomach
2	chr18:9526800-9552600	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
3	chr18:9527600-9546200	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
4	chr18:9528000-9546600	Weak transcription	Fetal Kidney	kidney
5	chr18:9528600-9547200	Weak transcription	ES-I3 Cell Line	embryonic stem cell
6	chr18:9532200-9547600	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
7	chr18:9534600-9546400	Weak transcription	Aorta	Aorta
8	chr18:9534800-9546600	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
9	chr18:9534800-9547200	Weak transcription	Primary T helper naive cells from peripheral blood	blood
10	chr18:9535200-9547400	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
11	chr18:9535200-9556800	Weak transcription	Pancreatic Islets	Pancreatic Islet
12	chr18:9535800-9546000	Weak transcription	A549	lung
13	chr18:9535800-9547200	Weak transcription	Fetal Heart	heart
14	chr18:9536000-9546200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
15	chr18:9536000-9546200	Weak transcription	Brain Angular Gyrus	brain
16	chr18:9536200-9546400	Weak transcription	Psoas Muscle	Psoas
17	chr18:9536600-9546200	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
18	chr18:9536600-9547200	Weak transcription	Primary T killer memory cells from peripheral blood	blood
19	chr18:9536800-9546400	Weak transcription	H1 Cell Line	embryonic stem cell
20	chr18:9536800-9546400	Weak transcription	H9 Cell Line	embryonic stem cell
21	chr18:9536800-9546400	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
22	chr18:9536800-9547000	Weak transcription	iPS-18 Cell Line	embryonic stem cell
23	chr18:9536800-9547000	Weak transcription	Pancreas	Pancrea
24	chr18:9536800-9547000	Weak transcription	K562	blood
25	chr18:9536800-9547200	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
26	chr18:9536800-9549000	Weak transcription	Small Intestine	intestine
27	chr18:9538000-9546200	Weak transcription	HUES64 Cell Line	embryonic stem cell
28	chr18:9538200-9546200	Weak transcription	Primary T helper cells PMA-I stimulated	--
29	chr18:9538400-9546000	Weak transcription	Ovary	ovary
30	chr18:9538400-9547200	Weak transcription	Fetal Brain Male	brain
31	chr18:9538800-9546000	Weak transcription	Colon Smooth Muscle	Colon
32	chr18:9538800-9546200	Weak transcription	Rectal Smooth Muscle	rectum
33	chr18:9538800-9546200	Weak transcription	GM12878-XiMat	blood
34	chr18:9538800-9546800	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
35	chr18:9539000-9546000	Weak transcription	Colonic Mucosa	Colon
36	chr18:9539000-9546400	Weak transcription	Brain Inferior Temporal Lobe	brain
37	chr18:9539000-9546400	Weak transcription	Skeletal Muscle Female	skeletal muscle
38	chr18:9539000-9547000	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
39	chr18:9539800-9546400	Weak transcription	Placenta Amnion	Placenta Amnion
40	chr18:9540000-9546600	Weak transcription	Gastric	stomach
41	chr18:9540200-9546000	Weak transcription	HSMMtube	muscle
42	chr18:9540200-9546200	Weak transcription	HUVEC	blood vessel
43	chr18:9540400-9546000	Weak transcription	Rectal Mucosa Donor 29	rectum
44	chr18:9540400-9546000	Weak transcription	NHDF-Ad	bronchial
45	chr18:9540400-9546600	Weak transcription	Primary B cells from cord blood	blood
46	chr18:9540600-9546200	Weak transcription	Brain Substantia Nigra	brain
47	chr18:9540600-9546200	Weak transcription	Left Ventricle	heart
48	chr18:9540800-9546000	Weak transcription	NHEK	skin
49	chr18:9540800-9546200	Weak transcription	Primary B cells from peripheral blood	blood
50	chr18:9541200-9549200	Weak transcription	iPS-15b Cell Line	embryonic stem cell

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