Variant report

Variant	rs7240239
Chromosome Location	chr18:44460037-44460038
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 100 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:95)

rs_ID	r²[population]
rs10070	0.90[CHB][hapmap];0.94[JPT][hapmap];0.92[ASN][1000 genomes]
rs10853544	0.89[AFR][1000 genomes];0.88[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs10853545	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.96[MEX][hapmap];0.98[TSI][hapmap];0.85[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs10853547	0.88[ASW][hapmap];0.96[CEU][hapmap];0.91[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.96[LWK][hapmap];1.00[MEX][hapmap];0.92[MKK][hapmap];0.86[TSI][hapmap];0.93[YRI][hapmap];0.81[AFR][1000 genomes];0.86[EUR][1000 genomes]
rs11082562	0.89[EUR][1000 genomes]
rs11659693	0.96[ASN][1000 genomes]
rs11660085	0.85[CHB][hapmap];0.97[CHD][hapmap];1.00[GIH][hapmap];0.94[JPT][hapmap];0.83[MEX][hapmap]
rs1465722	0.85[CHB][hapmap];0.94[JPT][hapmap]
rs1539878	0.89[ASW][hapmap];0.96[CEU][hapmap];0.91[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.96[LWK][hapmap];1.00[MEX][hapmap];0.93[MKK][hapmap];0.98[TSI][hapmap];0.93[YRI][hapmap];0.89[EUR][1000 genomes]
rs1539881	0.92[ASN][1000 genomes]
rs1789152	0.87[AFR][1000 genomes];0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1893427	0.87[AFR][1000 genomes];0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1970668	0.80[CHB][hapmap];0.97[CHD][hapmap];0.98[GIH][hapmap];0.94[JPT][hapmap]
rs2010834	0.89[ASW][hapmap];0.96[CEU][hapmap];0.91[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.85[LWK][hapmap];0.96[MEX][hapmap];0.86[TSI][hapmap];0.93[YRI][hapmap];0.81[EUR][1000 genomes]
rs2032215	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.96[MEX][hapmap];0.98[TSI][hapmap];0.91[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2051292	0.92[CEU][hapmap];0.92[EUR][1000 genomes]
rs2156049	0.96[ASN][1000 genomes]
rs2156050	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.92[AFR][1000 genomes];0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2187090	0.82[AFR][1000 genomes];0.87[AMR][1000 genomes];0.97[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs2187092	0.89[ASW][hapmap];0.96[CEU][hapmap];0.86[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.96[LWK][hapmap];1.00[MEX][hapmap];0.93[MKK][hapmap];0.98[TSI][hapmap];0.93[YRI][hapmap];0.81[AFR][1000 genomes];0.89[EUR][1000 genomes]
rs2510444	0.83[AMR][1000 genomes];0.83[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs2571024	0.82[EUR][1000 genomes]
rs2571026	0.81[EUR][1000 genomes]
rs2571028	0.85[CHB][hapmap];0.94[JPT][hapmap];0.85[YRI][hapmap]
rs2576040	0.82[GIH][hapmap]
rs2576042	0.82[GIH][hapmap]
rs2576050	0.85[CHB][hapmap];0.97[CHD][hapmap];1.00[GIH][hapmap];0.94[JPT][hapmap]
rs2576051	0.80[EUR][1000 genomes]
rs2957007	0.90[AMR][1000 genomes];0.87[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs3744863	0.82[EUR][1000 genomes]
rs3892820	0.84[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs4258717	0.92[AFR][1000 genomes];0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4548968	0.89[EUR][1000 genomes]
rs477826	0.90[CHB][hapmap];0.94[JPT][hapmap];0.92[ASN][1000 genomes]
rs478820	0.92[ASN][1000 genomes]
rs4890341	1.00[ASW][hapmap];0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];0.96[MEX][hapmap];1.00[MKK][hapmap];0.91[TSI][hapmap];1.00[YRI][hapmap];0.89[AFR][1000 genomes];0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4890343	0.85[CHB][hapmap];0.97[CHD][hapmap];1.00[GIH][hapmap];0.94[JPT][hapmap]
rs4890347	0.82[ASN][1000 genomes]
rs4890698	0.95[CHB][hapmap];0.95[CHD][hapmap];1.00[GIH][hapmap];0.94[JPT][hapmap];0.89[ASN][1000 genomes]
rs4890699	0.96[CEU][hapmap];0.91[CHB][hapmap];1.00[JPT][hapmap];0.93[YRI][hapmap];0.86[EUR][1000 genomes]
rs4890703	0.84[EUR][1000 genomes]
rs4890707	0.96[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.83[AFR][1000 genomes];0.93[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs501062	0.90[CHB][hapmap];0.97[CHD][hapmap];1.00[GIH][hapmap];0.94[JPT][hapmap];0.92[ASN][1000 genomes]
rs501882	0.88[JPT][hapmap]
rs504668	0.90[CHB][hapmap];0.97[CHD][hapmap];1.00[GIH][hapmap];0.94[JPT][hapmap];0.92[ASN][1000 genomes]
rs509647	0.84[AMR][1000 genomes];0.87[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs513775	0.92[CHD][hapmap];0.98[GIH][hapmap];0.83[ASN][1000 genomes]
rs530205	1.00[GIH][hapmap];0.88[JPT][hapmap]
rs538221	0.83[AMR][1000 genomes];0.83[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs541634	0.94[ASN][1000 genomes]
rs553456	1.00[ASW][hapmap];1.00[CEU][hapmap];0.95[CHB][hapmap];0.97[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.91[LWK][hapmap];1.00[MEX][hapmap];0.92[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.81[AFR][1000 genomes];0.89[AMR][1000 genomes];0.90[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs557089	0.83[AMR][1000 genomes];0.83[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs557661	0.81[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs577200	0.92[CEU][hapmap];0.95[TSI][hapmap];0.92[EUR][1000 genomes]
rs578146	0.96[ASN][1000 genomes]
rs578451	0.88[JPT][hapmap]
rs58993513	0.92[ASN][1000 genomes]
rs590923	0.95[CHB][hapmap];0.94[JPT][hapmap];0.92[ASN][1000 genomes]
rs593340	0.95[CHB][hapmap];0.97[CHD][hapmap];1.00[GIH][hapmap];0.94[JPT][hapmap];0.92[ASN][1000 genomes]
rs605487	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.92[AFR][1000 genomes];0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs607780	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[YRI][hapmap];0.86[AFR][1000 genomes];0.90[AMR][1000 genomes];0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs616900	0.90[CHB][hapmap];0.94[JPT][hapmap];0.80[YRI][hapmap];0.92[ASN][1000 genomes]
rs620228	0.85[ASN][1000 genomes]
rs626217	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];1.00[GIH][hapmap];0.94[JPT][hapmap];0.89[LWK][hapmap];1.00[MEX][hapmap];0.92[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.87[AFR][1000 genomes];0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs641366	0.95[CHB][hapmap];0.90[CHD][hapmap];1.00[GIH][hapmap];0.94[JPT][hapmap];0.96[ASN][1000 genomes]
rs642897	1.00[ASW][hapmap];1.00[CEU][hapmap];0.95[CHB][hapmap];0.97[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.91[LWK][hapmap];0.96[MEX][hapmap];0.92[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.86[AFR][1000 genomes];0.90[AMR][1000 genomes];0.92[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs644731	0.95[CHB][hapmap];0.95[CHD][hapmap];0.98[GIH][hapmap];0.88[JPT][hapmap];0.95[ASN][1000 genomes]
rs646128	1.00[GIH][hapmap];0.88[JPT][hapmap]
rs649076	1.00[ASW][hapmap];0.96[CEU][hapmap];0.95[CHB][hapmap];0.97[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.91[LWK][hapmap];1.00[MEX][hapmap];0.90[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.80[AFR][1000 genomes];0.90[AMR][1000 genomes];0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs6507709	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.96[MEX][hapmap];0.98[TSI][hapmap];0.91[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6507714	0.84[EUR][1000 genomes]
rs658756	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.91[LWK][hapmap];1.00[MEX][hapmap];0.92[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.87[AFR][1000 genomes];0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs680018	0.88[JPT][hapmap]
rs693503	0.92[ASN][1000 genomes]
rs695001	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.80[AFR][1000 genomes];0.88[AMR][1000 genomes];0.93[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7227700	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.85[EUR][1000 genomes]
rs7234570	0.92[AFR][1000 genomes];0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7244013	0.81[AFR][1000 genomes];0.86[EUR][1000 genomes]
rs7244778	0.89[ASW][hapmap];0.96[CEU][hapmap];0.91[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.94[JPT][hapmap];0.85[LWK][hapmap];0.96[MEX][hapmap];0.87[TSI][hapmap];0.93[YRI][hapmap];0.85[EUR][1000 genomes]
rs7245049	0.81[AFR][1000 genomes];0.85[EUR][1000 genomes]
rs8086286	0.95[CHB][hapmap];0.97[CHD][hapmap];1.00[GIH][hapmap];0.94[JPT][hapmap];0.94[ASN][1000 genomes]
rs8089938	0.92[EUR][1000 genomes]
rs8091984	0.87[EUR][1000 genomes]
rs8094654	0.85[CHB][hapmap];0.97[CHD][hapmap];1.00[GIH][hapmap];0.94[JPT][hapmap]
rs8095373	0.89[ASW][hapmap];0.96[CEU][hapmap];0.91[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.95[LWK][hapmap];0.93[MKK][hapmap];0.89[TSI][hapmap];0.86[YRI][hapmap];0.86[EUR][1000 genomes]
rs892586	0.85[CHB][hapmap];0.97[CHD][hapmap];0.98[GIH][hapmap];0.94[JPT][hapmap]
rs9304336	0.95[CHB][hapmap];0.97[CHD][hapmap];1.00[GIH][hapmap];0.94[JPT][hapmap];0.94[ASN][1000 genomes]
rs9304337	0.92[CEU][hapmap];0.98[TSI][hapmap];0.90[EUR][1000 genomes]
rs9304338	0.88[EUR][1000 genomes]
rs9304340	0.96[CEU][hapmap];0.91[CHB][hapmap];1.00[JPT][hapmap];0.88[EUR][1000 genomes]
rs9945443	0.85[AMR][1000 genomes];0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs9948405	0.83[ASN][1000 genomes]
rs9954336	0.95[CHB][hapmap];0.94[JPT][hapmap];0.95[ASN][1000 genomes]
rs9962523	0.85[AMR][1000 genomes];0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs998819	0.91[CHB][hapmap];1.00[JPT][hapmap];0.93[YRI][hapmap];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	esv2763189	chr18:44415779-44515384	Flanking Active TSS Strong transcription ZNF genes & repeats Enhancers Active TSS Weak transcription 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	7 gene(s)	inside rSNPs	diseases
3	nsv833639	chr18:44426363-44552719	Strong transcription Enhancers Active TSS Weak transcription Flanking Active TSS ZNF genes & repeats Bivalent/Poised TSS Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
4	nsv1059378	chr18:44431832-44509052	Strong transcription Active TSS ZNF genes & repeats Weak transcription Flanking Active TSS Enhancers Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
5	nsv522397	chr18:44451644-44516088	Strong transcription Enhancers Flanking Active TSS Weak transcription Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Genic enhancers Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs7240239	ST8SIA5	cis	cerebellum	SCAN
rs7240239	ST8SIA5	cis	lymphoblastoid	seeQTL

Chromatin state (count:83 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr18:44437200-44461600	Weak transcription	Ovary	ovary
2	chr18:44440400-44468400	Weak transcription	Placenta Amnion	Placenta Amnion
3	chr18:44448000-44460600	ZNF genes & repeats	Primary hematopoietic stem cells G-CSF-mobilized Male	--
4	chr18:44449000-44468600	Weak transcription	Pancreas	Pancrea
5	chr18:44449000-44468600	Weak transcription	NHLF	lung
6	chr18:44449800-44468400	Weak transcription	Stomach Smooth Muscle	stomach
7	chr18:44450800-44468600	Weak transcription	Gastric	stomach
8	chr18:44451200-44468400	Weak transcription	Skeletal Muscle Female	skeletal muscle
9	chr18:44451800-44460400	ZNF genes & repeats	Fetal Muscle Leg	muscle
10	chr18:44452000-44460200	ZNF genes & repeats	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
11	chr18:44452800-44460200	ZNF genes & repeats	Monocytes-CD14+_RO01746	blood
12	chr18:44453400-44468400	Weak transcription	HSMM	muscle
13	chr18:44454000-44468600	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
14	chr18:44454400-44468400	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
15	chr18:44454600-44460800	ZNF genes & repeats	HUES6 Cell Line	embryonic stem cell
16	chr18:44454800-44460400	ZNF genes & repeats	Dnd41	blood
17	chr18:44454800-44460600	ZNF genes & repeats	Primary hematopoietic stem cells G-CSF-mobilized Female	--
18	chr18:44454800-44460600	Weak transcription	K562	blood
19	chr18:44455400-44460600	ZNF genes & repeats	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
20	chr18:44455600-44461200	ZNF genes & repeats	HUES64 Cell Line	embryonic stem cell
21	chr18:44456000-44460600	ZNF genes & repeats	iPS-20b Cell Line	embryonic stem cell
22	chr18:44456200-44466000	Weak transcription	Sigmoid Colon	Sigmoid Colon
23	chr18:44457200-44460400	ZNF genes & repeats	Ganglion Eminence derived primary cultured neurospheres	brain
24	chr18:44457400-44460600	ZNF genes & repeats	Primary hematopoietic stem cells short term culture	blood
25	chr18:44457600-44468400	Weak transcription	Small Intestine	intestine
26	chr18:44457800-44460200	ZNF genes & repeats	HUES48 Cell Line	embryonic stem cell
27	chr18:44457800-44468400	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
28	chr18:44457800-44468400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
29	chr18:44457800-44468400	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
30	chr18:44457800-44468400	Weak transcription	Adipose Nuclei	Adipose
31	chr18:44457800-44468400	Weak transcription	Lung	lung
32	chr18:44457800-44468400	Weak transcription	Psoas Muscle	Psoas
33	chr18:44457800-44468600	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
34	chr18:44457800-44468600	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
35	chr18:44457800-44468600	Weak transcription	Brain Hippocampus Middle	brain
36	chr18:44457800-44468600	Weak transcription	Left Ventricle	heart
37	chr18:44457800-44468600	Weak transcription	Right Ventricle	heart
38	chr18:44458000-44468200	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
39	chr18:44458000-44468400	Weak transcription	Primary T killer memory cells from peripheral blood	blood
40	chr18:44458000-44468400	Weak transcription	Fetal Thymus	thymus
41	chr18:44458200-44460400	ZNF genes & repeats	Primary hematopoietic stem cells	blood
42	chr18:44458200-44468400	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
43	chr18:44458200-44468400	Weak transcription	Liver	Liver
44	chr18:44458400-44467800	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
45	chr18:44458400-44468400	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
46	chr18:44458800-44460200	Strong transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
47	chr18:44458800-44460200	Strong transcription	Primary T helper cells PMA-I stimulated	--
48	chr18:44458800-44468400	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
49	chr18:44458800-44468400	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
50	chr18:44458800-44468400	Weak transcription	Fetal Stomach	stomach

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links