Variant report

Variant	rs7011602
Chromosome Location	chr8:19308915-19308916
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 87 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:72)

rs_ID	r²[population]
rs10107416	0.82[EUR][1000 genomes]
rs11204039	0.83[EUR][1000 genomes]
rs11204040	0.85[EUR][1000 genomes]
rs11204041	0.86[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs11780343	0.85[EUR][1000 genomes]
rs11784873	0.83[EUR][1000 genomes]
rs11786847	0.81[EUR][1000 genomes]
rs11787230	0.83[EUR][1000 genomes]
rs11991105	0.80[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs12542575	0.85[EUR][1000 genomes]
rs12543061	0.82[EUR][1000 genomes]
rs12674938	0.88[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs12675717	0.86[EUR][1000 genomes]
rs12677088	0.88[ASN][1000 genomes]
rs12678336	0.83[EUR][1000 genomes]
rs13255677	0.85[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs13255946	0.81[EUR][1000 genomes]
rs13258090	0.84[EUR][1000 genomes]
rs13278459	0.88[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs17479099	0.81[EUR][1000 genomes]
rs28517653	0.80[ASN][1000 genomes]
rs35029660	0.89[AMR][1000 genomes];0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs3802328	0.80[ASN][1000 genomes]
rs4307360	0.90[ASN][1000 genomes]
rs4333618	0.83[EUR][1000 genomes]
rs4379462	0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs4391454	0.81[EUR][1000 genomes]
rs4392915	0.90[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4392916	0.91[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4409408	0.90[AMR][1000 genomes];0.96[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs4430112	0.87[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs4433156	0.83[EUR][1000 genomes]
rs4546679	0.83[EUR][1000 genomes]
rs4549789	0.83[EUR][1000 genomes]
rs4554480	0.82[EUR][1000 genomes]
rs4617172	0.81[EUR][1000 genomes]
rs4618712	0.82[AMR][1000 genomes];0.90[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs4633071	0.81[EUR][1000 genomes]
rs4921638	0.81[EUR][1000 genomes]
rs4921642	0.87[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs4921643	0.80[ASN][1000 genomes]
rs4921645	0.90[ASN][1000 genomes]
rs4922028	0.88[ASN][1000 genomes]
rs4922029	0.88[ASN][1000 genomes]
rs56298301	0.91[ASN][1000 genomes]
rs6586833	0.90[ASN][1000 genomes]
rs6981898	0.81[AMR][1000 genomes];0.92[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs6983973	0.85[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs6984145	0.88[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs6990217	0.81[EUR][1000 genomes]
rs6990357	0.81[EUR][1000 genomes]
rs6991212	0.81[EUR][1000 genomes]
rs6992893	0.85[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs6997164	0.80[ASN][1000 genomes]
rs6999786	0.82[EUR][1000 genomes]
rs7004435	0.83[EUR][1000 genomes]
rs7006702	0.81[EUR][1000 genomes]
rs7008916	0.84[ASN][1000 genomes]
rs7015440	0.81[EUR][1000 genomes]
rs7016259	0.81[EUR][1000 genomes]
rs7016592	0.81[EUR][1000 genomes]
rs7814793	0.91[ASN][1000 genomes]
rs7818345	0.81[AMR][1000 genomes];0.92[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs7820698	0.82[ASN][1000 genomes]
rs7822046	0.80[ASN][1000 genomes]
rs7823194	0.86[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs7830251	0.90[ASN][1000 genomes]
rs7833166	0.87[EUR][1000 genomes]
rs7835461	0.91[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs7835945	0.82[ASN][1000 genomes]
rs7844175	0.80[ASN][1000 genomes]
rs9720249	0.85[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:15 , 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
14	esv3328637	chr8:19306497-19309045	Weak transcription Enhancers Bivalent Enhancer Genic enhancers	n/a	n/a	inside rSNPs	diseases
15	nsv890623	chr8:19307051-19383697	Weak transcription Enhancers Genic enhancers Flanking Active TSS Strong transcription Bivalent Enhancer Transcr. at gene 5' and 3' Active TSS Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs7011602	CSGALNACT1	cis	Skin Sun Exposed Lower leg	GTEx
rs7011602	CSGALNACT1	cis	Thyroid	GTEx

Chromatin state (count:65 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr8:19295000-19318800	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
2	chr8:19296600-19309400	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
3	chr8:19296600-19317400	Weak transcription	Hela-S3	cervix
4	chr8:19297200-19309200	Weak transcription	ES-I3 Cell Line	embryonic stem cell
5	chr8:19297400-19313400	Weak transcription	Brain Cingulate Gyrus	brain
6	chr8:19297600-19319000	Weak transcription	Spleen	Spleen
7	chr8:19300000-19313800	Weak transcription	Fetal Heart	heart
8	chr8:19300600-19319200	Weak transcription	Gastric	stomach
9	chr8:19301600-19317200	Weak transcription	Skeletal Muscle Male	skeletal muscle
10	chr8:19302800-19317800	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
11	chr8:19303200-19309200	Weak transcription	Brain Angular Gyrus	brain
12	chr8:19303200-19309800	Weak transcription	Primary hematopoietic stem cells	blood
13	chr8:19303200-19313800	Weak transcription	HUVEC	blood vessel
14	chr8:19303400-19315200	Enhancers	Primary T helper cells PMA-I stimulated	--
15	chr8:19304200-19310200	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
16	chr8:19305600-19313200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
17	chr8:19305600-19317600	Weak transcription	Placenta Amnion	Placenta Amnion
18	chr8:19305600-19318400	Weak transcription	Pancreas	Pancrea
19	chr8:19305800-19313000	Weak transcription	Placenta	Placenta
20	chr8:19306200-19309600	Weak transcription	HUES48 Cell Line	embryonic stem cell
21	chr8:19306400-19312000	Enhancers	Primary T cells from cord blood	blood
22	chr8:19306600-19312000	Enhancers	Primary T helper naive cells fromperipheralblood	blood
23	chr8:19306800-19311800	Enhancers	Primary T helper naive cells from peripheral blood	blood
24	chr8:19306800-19322400	Enhancers	Primary T helper cells fromperipheralblood	blood
25	chr8:19307000-19310000	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
26	chr8:19307200-19309400	Weak transcription	iPS-18 Cell Line	embryonic stem cell
27	chr8:19307200-19309400	Weak transcription	iPS-20b Cell Line	embryonic stem cell
28	chr8:19307400-19309400	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
29	chr8:19307400-19309600	Weak transcription	HUES64 Cell Line	embryonic stem cell
30	chr8:19307400-19309600	Weak transcription	Osteobl	bone
31	chr8:19307600-19309600	Weak transcription	Primary T killer memory cells from peripheral blood	blood
32	chr8:19307800-19312000	Enhancers	Primary T cells fromperipheralblood	blood
33	chr8:19307800-19312000	Enhancers	Dnd41	blood
34	chr8:19308000-19309400	Weak transcription	Fetal Brain Male	brain
35	chr8:19308000-19309400	Enhancers	HepG2	liver
36	chr8:19308000-19313000	Weak transcription	Duodenum Smooth Muscle	Duodenum
37	chr8:19308000-19313000	Weak transcription	Fetal Kidney	kidney
38	chr8:19308200-19309400	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
39	chr8:19308200-19309600	Weak transcription	Ovary	ovary
40	chr8:19308200-19310200	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
41	chr8:19308200-19310200	Weak transcription	Right Atrium	heart
42	chr8:19308200-19313000	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
43	chr8:19308200-19313800	Weak transcription	Adipose Nuclei	Adipose
44	chr8:19308200-19317000	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
45	chr8:19308200-19317000	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
46	chr8:19308200-19317400	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
47	chr8:19308200-19319000	Weak transcription	Lung	lung
48	chr8:19308400-19309400	Weak transcription	HUES6 Cell Line	embryonic stem cell
49	chr8:19308400-19309400	Weak transcription	iPS-15b Cell Line	embryonic stem cell
50	chr8:19308400-19309600	Weak transcription	Primary B cells from cord blood	blood

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links