Variant report

Variant	rs9956809
Chromosome Location	chr18:44655843-44655844
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 60 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:55)

rs_ID	r²[population]
rs12953864	1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[YRI][hapmap];0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs12960378	0.86[GIH][hapmap]
rs12968552	0.94[AFR][1000 genomes];0.96[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs13381713	1.00[ASW][hapmap];0.96[CEU][hapmap];0.86[CHB][hapmap];0.97[GIH][hapmap];0.86[JPT][hapmap];0.98[LWK][hapmap];0.96[MEX][hapmap];1.00[MKK][hapmap];0.98[TSI][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1434529	0.81[AFR][1000 genomes];0.91[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs16954921	1.00[ASW][hapmap];0.96[CEU][hapmap];0.90[CHB][hapmap];0.94[CHD][hapmap];1.00[GIH][hapmap];0.95[JPT][hapmap];1.00[LWK][hapmap];0.96[MEX][hapmap];0.99[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs16954999	1.00[ASW][hapmap];1.00[CEU][hapmap];0.95[CHB][hapmap];0.94[CHD][hapmap];1.00[GIH][hapmap];0.95[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.91[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs1836259	0.90[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs2289036	0.88[ASW][hapmap]
rs2289133	0.94[ASW][hapmap];1.00[CEU][hapmap];0.90[CHB][hapmap];0.91[CHD][hapmap];0.95[GIH][hapmap];0.90[JPT][hapmap];0.96[LWK][hapmap];0.90[MKK][hapmap];0.93[TSI][hapmap];1.00[YRI][hapmap];0.90[AFR][1000 genomes];0.97[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2317324	0.92[CEU][hapmap]
rs2461247	0.81[GIH][hapmap]
rs2571002	0.96[AFR][1000 genomes];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2571004	1.00[CEU][hapmap];0.90[CHB][hapmap];0.81[JPT][hapmap];0.90[YRI][hapmap];0.80[AFR][1000 genomes];0.91[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs2571005	0.92[CEU][hapmap];0.89[TSI][hapmap];0.86[EUR][1000 genomes]
rs2571006	1.00[CEU][hapmap];0.90[CHB][hapmap];0.81[JPT][hapmap];0.86[YRI][hapmap];0.93[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs2571007	0.82[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs2571008	0.96[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2571009	0.83[YRI][hapmap]
rs2571010	0.93[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2571014	0.88[CEU][hapmap];0.83[EUR][1000 genomes]
rs2571016	0.86[GIH][hapmap]
rs2571017	0.83[AFR][1000 genomes];0.97[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs2576052	0.92[CEU][hapmap];0.95[TSI][hapmap];0.83[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs2576057	0.92[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2576058	0.96[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2576060	0.86[GIH][hapmap]
rs2635049	0.86[GIH][hapmap]
rs2635051	0.96[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2635052	0.96[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2635054	0.96[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2635056	0.83[AFR][1000 genomes];0.93[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs2668758	1.00[CEU][hapmap];0.95[CHB][hapmap];0.85[JPT][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];0.96[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs2668759	0.97[AFR][1000 genomes];0.97[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs2668761	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];0.98[TSI][hapmap];1.00[YRI][hapmap];0.93[AFR][1000 genomes];0.98[AMR][1000 genomes];0.95[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2668762	0.88[EUR][1000 genomes]
rs2668763	0.96[AFR][1000 genomes];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2668784	0.83[AFR][1000 genomes];0.93[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs2684819	1.00[CEU][hapmap];0.90[CHB][hapmap];0.81[JPT][hapmap];0.90[YRI][hapmap];0.83[AFR][1000 genomes];0.93[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs2684833	0.92[CEU][hapmap];0.89[TSI][hapmap];0.86[EUR][1000 genomes]
rs2684851	0.82[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs28718304	0.96[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2932126	0.81[GIH][hapmap]
rs3816125	0.81[GIH][hapmap]
rs4986228	0.82[TSI][hapmap]
rs55730206	0.90[AFR][1000 genomes];0.98[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs7239323	0.83[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs7242978	0.83[GIH][hapmap]
rs7504798	0.86[GIH][hapmap]
rs8085634	0.92[CEU][hapmap];1.00[TSI][hapmap];0.94[EUR][1000 genomes]
rs9951617	0.81[EUR][1000 genomes]
rs9953157	0.97[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs9960264	0.81[GIH][hapmap]
rs9961383	1.00[CEU][hapmap];0.95[CHB][hapmap];0.90[JPT][hapmap];1.00[YRI][hapmap];0.90[AFR][1000 genomes];0.97[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs9962436	0.81[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:5 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv9629	chr18:44264693-44757511	Enhancers Weak transcription Active TSS Flanking Active TSS Strong transcription Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	28 gene(s)	inside rSNPs	diseases
2	nsv833640	chr18:44552276-44714872	Enhancers Weak transcription Strong transcription Flanking Active TSS Active TSS ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	17 gene(s)	inside rSNPs	diseases
3	nsv909612	chr18:44560875-44681485	Weak transcription Strong transcription Enhancers Flanking Active TSS Active TSS Genic enhancers Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	15 gene(s)	inside rSNPs	diseases
4	nsv576819	chr18:44602249-44677627	Strong transcription Weak transcription Flanking Active TSS Enhancers Active TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	12 gene(s)	inside rSNPs	diseases
5	nsv909613	chr18:44644530-44690107	Enhancers Strong transcription Weak transcription Flanking Active TSS Active TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	10 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs9956809	IER3IP1	cis	cerebellum	SCAN

Chromatin state (count:122 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr18:44620800-44675400	Weak transcription	A549	lung
2	chr18:44621600-44674400	Weak transcription	Small Intestine	intestine
3	chr18:44626600-44664800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
4	chr18:44629200-44675800	Weak transcription	HUVEC	blood vessel
5	chr18:44630600-44660400	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
6	chr18:44632400-44675800	Weak transcription	Stomach Mucosa	stomach
7	chr18:44636200-44670600	Weak transcription	Pancreas	Pancrea
8	chr18:44636600-44661000	Weak transcription	Psoas Muscle	Psoas
9	chr18:44638400-44660800	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
10	chr18:44639200-44662400	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
11	chr18:44639600-44660600	Weak transcription	NHLF	lung
12	chr18:44639600-44665000	Weak transcription	Colonic Mucosa	Colon
13	chr18:44639600-44666400	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
14	chr18:44639800-44660600	Weak transcription	NH-A	brain
15	chr18:44639800-44660800	Weak transcription	Rectal Smooth Muscle	rectum
16	chr18:44640400-44662000	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
17	chr18:44640600-44675600	Weak transcription	Placenta Amnion	Placenta Amnion
18	chr18:44640800-44662000	Weak transcription	Primary T killer memory cells from peripheral blood	blood
19	chr18:44641200-44659600	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
20	chr18:44641600-44660400	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
21	chr18:44641600-44670400	Weak transcription	HepG2	liver
22	chr18:44641600-44674000	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
23	chr18:44641600-44675800	Weak transcription	Lung	lung
24	chr18:44641800-44656200	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
25	chr18:44641800-44660400	Weak transcription	Skeletal Muscle Female	skeletal muscle
26	chr18:44641800-44660800	Weak transcription	Brain Substantia Nigra	brain
27	chr18:44641800-44661400	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
28	chr18:44641800-44662000	Weak transcription	K562	blood
29	chr18:44641800-44662600	Weak transcription	Brain Angular Gyrus	brain
30	chr18:44641800-44663200	Weak transcription	Esophagus	oesophagus
31	chr18:44641800-44664400	Weak transcription	H9 Cell Line	embryonic stem cell
32	chr18:44641800-44665600	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
33	chr18:44641800-44674400	Weak transcription	Aorta	Aorta
34	chr18:44641800-44675200	Weak transcription	Primary T helper naive cells from peripheral blood	blood
35	chr18:44641800-44675400	Weak transcription	Fetal Intestine Small	intestine
36	chr18:44641800-44675800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
37	chr18:44641800-44675800	Weak transcription	Brain Inferior Temporal Lobe	brain
38	chr18:44642000-44656000	Weak transcription	Colon Smooth Muscle	Colon
39	chr18:44642000-44660600	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
40	chr18:44642000-44660800	Weak transcription	Brain Germinal Matrix	brain
41	chr18:44642000-44664600	Weak transcription	ES-I3 Cell Line	embryonic stem cell
42	chr18:44642000-44675200	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
43	chr18:44642200-44674600	Weak transcription	NHEK	skin
44	chr18:44644800-44656800	Strong transcription	Monocytes-CD14+_RO01746	blood
45	chr18:44645400-44660000	Weak transcription	Muscle Satellite Cultured Cells	--
46	chr18:44645600-44660400	Weak transcription	Cortex derived primary cultured neurospheres	brain
47	chr18:44645600-44660800	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
48	chr18:44645600-44665200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
49	chr18:44645600-44667600	Weak transcription	HSMMtube	muscle
50	chr18:44645800-44660800	Weak transcription	Fetal Kidney	kidney

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