Variant report

Variant	rs4922029
Chromosome Location	chr8:19304533-19304534
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 78 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:65)

rs_ID	r²[population]
rs10107348	0.85[JPT][hapmap]
rs10107416	1.00[JPT][hapmap];0.82[ASN][1000 genomes]
rs11204039	0.81[CHB][hapmap];0.81[GIH][hapmap];0.85[JPT][hapmap];0.81[MEX][hapmap]
rs11204040	1.00[JPT][hapmap];0.84[YRI][hapmap];0.85[ASN][1000 genomes]
rs11204041	0.81[CHB][hapmap];0.87[ASN][1000 genomes]
rs11780343	0.81[CHB][hapmap];0.81[CHD][hapmap];0.85[GIH][hapmap];0.81[MEX][hapmap];0.82[MKK][hapmap];0.84[YRI][hapmap];0.84[ASN][1000 genomes]
rs11782540	0.83[YRI][hapmap]
rs11784873	0.85[JPT][hapmap]
rs11787230	0.81[GIH][hapmap];0.85[JPT][hapmap];0.81[MEX][hapmap]
rs11991105	0.81[CHB][hapmap];0.81[ASN][1000 genomes]
rs12542575	1.00[JPT][hapmap];0.96[YRI][hapmap];0.85[ASN][1000 genomes]
rs12543061	0.82[CHD][hapmap];0.81[MEX][hapmap];0.84[YRI][hapmap]
rs12674938	0.81[CHB][hapmap];1.00[JPT][hapmap];0.88[YRI][hapmap];0.81[AFR][1000 genomes];0.88[ASN][1000 genomes]
rs12675717	0.84[YRI][hapmap];0.82[ASN][1000 genomes]
rs12677088	1.00[CHB][hapmap];0.88[CHD][hapmap];1.00[JPT][hapmap];0.81[ASN][1000 genomes]
rs12679712	0.81[MEX][hapmap]
rs13255677	1.00[JPT][hapmap];0.87[ASN][1000 genomes]
rs13255946	0.81[GIH][hapmap];0.81[MEX][hapmap]
rs13258090	0.82[CHD][hapmap];0.83[GIH][hapmap];0.81[MEX][hapmap]
rs13278459	1.00[JPT][hapmap];0.88[YRI][hapmap];0.81[AFR][1000 genomes];0.87[ASN][1000 genomes]
rs17407149	0.84[YRI][hapmap]
rs34156560	0.81[ASN][1000 genomes]
rs35029660	0.90[ASN][1000 genomes]
rs3802328	0.81[CHB][hapmap];1.00[JPT][hapmap];0.87[ASN][1000 genomes]
rs4307360	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.97[ASN][1000 genomes]
rs4333618	0.85[JPT][hapmap]
rs4379462	0.86[JPT][hapmap]
rs4391454	0.88[YRI][hapmap]
rs4392915	1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[YRI][hapmap];0.90[ASN][1000 genomes]
rs4392916	0.90[ASN][1000 genomes]
rs4409408	0.86[JPT][hapmap]
rs4412390	0.81[MEX][hapmap]
rs4430112	0.87[ASN][1000 genomes]
rs4431609	0.80[YRI][hapmap]
rs4481612	0.85[JPT][hapmap]
rs4541947	0.85[JPT][hapmap]
rs4618712	0.81[AFR][1000 genomes];0.96[ASN][1000 genomes]
rs4921638	0.81[GIH][hapmap];0.81[MEX][hapmap]
rs4921642	0.87[ASN][1000 genomes]
rs4921643	0.87[ASN][1000 genomes]
rs4921645	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.97[ASN][1000 genomes]
rs4922028	0.91[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.96[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.80[LWK][hapmap];1.00[MEX][hapmap];0.85[MKK][hapmap];1.00[TSI][hapmap];0.92[YRI][hapmap];0.89[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs56298301	0.96[ASN][1000 genomes]
rs6586833	1.00[CHB][hapmap];0.96[CHD][hapmap];1.00[JPT][hapmap];0.94[ASN][1000 genomes]
rs6981898	1.00[CHB][hapmap];0.96[CHD][hapmap];0.85[GIH][hapmap];1.00[JPT][hapmap];0.83[LWK][hapmap];0.81[MEX][hapmap];0.92[MKK][hapmap];0.88[YRI][hapmap];0.85[AFR][1000 genomes];0.94[ASN][1000 genomes]
rs6983973	0.81[CHB][hapmap];1.00[JPT][hapmap];0.84[YRI][hapmap];0.87[ASN][1000 genomes]
rs6984145	0.87[ASN][1000 genomes]
rs6990357	0.81[GIH][hapmap];0.81[MEX][hapmap]
rs6992893	1.00[JPT][hapmap];0.84[YRI][hapmap];0.87[ASN][1000 genomes]
rs6997164	0.87[ASN][1000 genomes]
rs6999786	0.81[GIH][hapmap];0.80[MEX][hapmap]
rs7008916	0.90[ASN][1000 genomes]
rs7011602	0.88[ASN][1000 genomes]
rs7012529	0.85[ASN][1000 genomes]
rs7814793	1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[ASN][1000 genomes]
rs7818345	0.82[AFR][1000 genomes];0.94[ASN][1000 genomes]
rs7820698	0.81[CHB][hapmap];1.00[JPT][hapmap];0.88[ASN][1000 genomes]
rs7822046	0.81[CHD][hapmap];0.87[ASN][1000 genomes]
rs7823194	0.87[ASN][1000 genomes]
rs7830251	1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[ASN][1000 genomes]
rs7833166	0.81[ASN][1000 genomes]
rs7835461	1.00[CHB][hapmap];0.96[CHD][hapmap];0.85[GIH][hapmap];1.00[JPT][hapmap];0.81[MEX][hapmap];0.85[MKK][hapmap];0.96[ASN][1000 genomes]
rs7835945	1.00[JPT][hapmap];0.88[ASN][1000 genomes]
rs7844175	0.87[ASN][1000 genomes]
rs9720249	0.84[AFR][1000 genomes];0.84[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:13 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1015395	chr8:18489538-19370258	Weak transcription Enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Flanking Active TSS Active TSS Strong transcription Genic enhancers Bivalent/Poised TSS ZNF genes & repeats 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	nsv429907	chr8:18578720-19398220	Active TSS Weak transcription Enhancers Strong transcription Genic enhancers Bivalent/Poised TSS Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	26 gene(s)	inside rSNPs	diseases
3	nsv949745	chr8:18826830-19363963	Flanking Active TSS Enhancers Weak transcription Strong transcription Active TSS Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	20 gene(s)	inside rSNPs	diseases
4	nsv1016482	chr8:18834807-19339487	Enhancers Weak transcription Active TSS Flanking Active TSS Strong transcription ZNF genes & repeats Bivalent/Poised TSS Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	20 gene(s)	inside rSNPs	diseases
5	nsv533109	chr8:18845845-19456780	Weak transcription Flanking Active TSS Enhancers Strong transcription Active TSS ZNF genes & repeats Genic enhancers Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	20 gene(s)	inside rSNPs	diseases
6	nsv1016993	chr8:18855623-19311731	Enhancers Weak transcription Strong transcription Genic enhancers Flanking Active TSS Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	18 gene(s)	inside rSNPs	diseases
7	nsv949636	chr8:18957705-19664732	Enhancers Weak transcription Active TSS Strong transcription Flanking Active TSS Genic enhancers Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	18 gene(s)	inside rSNPs	diseases
8	nsv948861	chr8:19199688-19609029	Strong transcription Enhancers Weak transcription Bivalent/Poised TSS ZNF genes & repeats Genic enhancers Active TSS Flanking Bivalent TSS/Enh Flanking Active TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	10 gene(s)	inside rSNPs	diseases
9	nsv949304	chr8:19199688-19625912	Enhancers Weak transcription Flanking Active TSS Active TSS ZNF genes & repeats Genic enhancers Strong transcription Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	11 gene(s)	inside rSNPs	diseases
10	esv3693374	chr8:19241970-19359184	Enhancers Weak transcription Strong transcription Flanking Active TSS Genic enhancers Active TSS ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region miRNA target site	2 gene(s)	inside rSNPs	diseases
11	esv34007	chr8:19252602-19482098	Enhancers Weak transcription ZNF genes & repeats Genic enhancers Strong transcription Flanking Active TSS Transcr. at gene 5' and 3' Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	3 gene(s)	inside rSNPs	diseases
12	nsv610752	chr8:19254816-19311496	Enhancers Weak transcription Genic enhancers Strong transcription Flanking Active TSS ZNF genes & repeats Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	Chromatin interactive region miRNA target site	2 gene(s)	inside rSNPs	diseases
13	nsv1022344	chr8:19270143-19324083	Weak transcription ZNF genes & repeats Enhancers Genic enhancers Flanking Active TSS Strong transcription Bivalent Enhancer Active TSS Transcr. at gene 5' and 3'	Chromatin interactive region	2 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs4922029	CSGALNACT1	cis	cerebellum	SCAN
rs4922029	CSGALNACT1	cis	parietal	SCAN
rs4922029	CSGALNACT1	cis	Thyroid	GTEx

Chromatin state (count:48 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr8:19271800-19305200	Weak transcription	Pancreas	Pancrea
2	chr8:19277600-19307800	Weak transcription	Fetal Stomach	stomach
3	chr8:19278000-19304800	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
4	chr8:19283800-19307800	Weak transcription	Ovary	ovary
5	chr8:19291600-19308000	Weak transcription	Right Ventricle	heart
6	chr8:19295000-19318800	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
7	chr8:19296600-19309400	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
8	chr8:19296600-19317400	Weak transcription	Hela-S3	cervix
9	chr8:19297200-19309200	Weak transcription	ES-I3 Cell Line	embryonic stem cell
10	chr8:19297400-19313400	Weak transcription	Brain Cingulate Gyrus	brain
11	chr8:19297600-19307800	Weak transcription	Left Ventricle	heart
12	chr8:19297600-19308000	Weak transcription	Monocytes-CD14+_RO01746	blood
13	chr8:19297600-19319000	Weak transcription	Spleen	Spleen
14	chr8:19300000-19313800	Weak transcription	Fetal Heart	heart
15	chr8:19300400-19305800	Strong transcription	Placenta	Placenta
16	chr8:19300600-19319200	Weak transcription	Gastric	stomach
17	chr8:19301600-19317200	Weak transcription	Skeletal Muscle Male	skeletal muscle
18	chr8:19301800-19307800	Weak transcription	Right Atrium	heart
19	chr8:19302200-19304800	Enhancers	Primary T cells fromperipheralblood	blood
20	chr8:19302400-19305200	Enhancers	Fetal Thymus	thymus
21	chr8:19302800-19304600	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
22	chr8:19302800-19317800	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
23	chr8:19303000-19307800	Weak transcription	Primary monocytes fromperipheralblood	blood
24	chr8:19303200-19307800	Weak transcription	Adipose Nuclei	Adipose
25	chr8:19303200-19307800	Weak transcription	Thymus	Thymus
26	chr8:19303200-19307800	Weak transcription	Dnd41	blood
27	chr8:19303200-19308000	Weak transcription	Primary B cells from cord blood	blood
28	chr8:19303200-19308000	Weak transcription	HepG2	liver
29	chr8:19303200-19309200	Weak transcription	Brain Angular Gyrus	brain
30	chr8:19303200-19309800	Weak transcription	Primary hematopoietic stem cells	blood
31	chr8:19303200-19313800	Weak transcription	HUVEC	blood vessel
32	chr8:19303400-19305000	Enhancers	Primary T cells from cord blood	blood
33	chr8:19303400-19305800	Strong transcription	A549	lung
34	chr8:19303400-19306200	Enhancers	Primary T helper naive cells fromperipheralblood	blood
35	chr8:19303400-19306800	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
36	chr8:19303400-19307800	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
37	chr8:19303400-19315200	Enhancers	Primary T helper cells PMA-I stimulated	--
38	chr8:19303600-19306400	Strong transcription	Primary neutrophils fromperipheralblood	blood
39	chr8:19303800-19306800	Weak transcription	Primary T killer memory cells from peripheral blood	blood
40	chr8:19303800-19307400	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
41	chr8:19304000-19305600	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
42	chr8:19304000-19306800	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
43	chr8:19304000-19306800	Weak transcription	Primary T helper cells fromperipheralblood	blood
44	chr8:19304200-19304600	Weak transcription	Primary T helper naive cells from peripheral blood	blood
45	chr8:19304200-19310200	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
46	chr8:19304400-19305600	Enhancers	Placenta Amnion	Placenta Amnion
47	chr8:19304400-19306000	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
48	chr8:19304400-19308800	Weak transcription	Pancreatic Islets	Pancreatic Islet

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