Variant report

Variant	rs13278459
Chromosome Location	chr8:19297583-19297584
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr8:19271639..19274356-chr8:19296369..19298218,2	MCF-7	breast:
2	chr8:19294799..19297740-chr8:19300863..19302648,2	MCF-7	breast:
3	chr8:19280974..19282712-chr8:19296114..19297888,2	MCF-7	breast:

Extended variants
information (count: 104 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:91)

rs_ID	r²[population]
rs10107348	1.00[CHB][hapmap];0.85[JPT][hapmap]
rs10107416	1.00[JPT][hapmap];0.90[AMR][1000 genomes];0.93[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs11204039	0.85[JPT][hapmap];0.89[AMR][1000 genomes];0.93[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs11204040	1.00[JPT][hapmap];0.96[YRI][hapmap];0.86[AFR][1000 genomes];0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs11204041	0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs11204046	0.89[CHB][hapmap]
rs11204047	0.89[CHB][hapmap]
rs11780343	0.95[YRI][hapmap];0.87[AFR][1000 genomes];0.94[AMR][1000 genomes];0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs11780388	0.88[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs11784873	0.85[JPT][hapmap];0.91[AMR][1000 genomes];0.93[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs11785649	0.82[YRI][hapmap]
rs11786847	0.91[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs11787230	0.85[JPT][hapmap];0.87[YRI][hapmap];0.82[AFR][1000 genomes];0.94[AMR][1000 genomes];0.93[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs11991105	0.83[AMR][1000 genomes];0.97[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs12542575	1.00[JPT][hapmap];0.84[YRI][hapmap];0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs12543061	0.95[YRI][hapmap];0.87[AFR][1000 genomes];0.94[AMR][1000 genomes];0.93[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs12674938	1.00[JPT][hapmap];1.00[YRI][hapmap];0.92[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12675717	0.96[YRI][hapmap];0.87[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs12677088	1.00[JPT][hapmap]
rs12678336	0.82[AFR][1000 genomes];0.94[AMR][1000 genomes];0.93[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs12679671	0.92[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs12679712	0.87[YRI][hapmap];0.92[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs13255677	1.00[JPT][hapmap];0.91[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs13255946	0.91[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs13258090	0.93[AMR][1000 genomes];0.95[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs13265751	0.89[CHB][hapmap]
rs17407149	0.95[YRI][hapmap]
rs17479099	0.91[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs34156560	0.91[ASN][1000 genomes]
rs35029660	0.86[AFR][1000 genomes];0.84[AMR][1000 genomes];0.88[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs3802328	1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs4307360	1.00[JPT][hapmap];0.89[ASN][1000 genomes]
rs4333618	0.85[JPT][hapmap];0.88[YRI][hapmap];0.82[AFR][1000 genomes];0.94[AMR][1000 genomes];0.93[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs4379462	0.86[JPT][hapmap];0.81[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs4391454	0.94[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs4392915	1.00[JPT][hapmap];1.00[YRI][hapmap];0.82[AFR][1000 genomes];0.83[AMR][1000 genomes];0.89[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs4392916	0.83[AFR][1000 genomes];0.84[AMR][1000 genomes];0.88[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs4409408	0.86[JPT][hapmap];0.83[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs4412390	0.87[YRI][hapmap];0.92[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs4413788	0.89[CHB][hapmap]
rs4430112	0.87[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4431609	0.91[YRI][hapmap];0.81[AFR][1000 genomes]
rs4433156	0.91[AMR][1000 genomes];0.93[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs4481612	0.85[JPT][hapmap];0.88[ASN][1000 genomes]
rs4541947	0.89[CHB][hapmap];0.85[JPT][hapmap]
rs4546679	0.82[AFR][1000 genomes];0.94[AMR][1000 genomes];0.93[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs4549789	0.82[AFR][1000 genomes];0.94[AMR][1000 genomes];0.93[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs4554480	0.87[YRI][hapmap];0.82[AFR][1000 genomes];0.94[AMR][1000 genomes];0.92[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs4617172	0.88[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs4618712	0.92[AFR][1000 genomes];0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs4633071	0.81[AFR][1000 genomes];0.94[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs4921638	0.87[YRI][hapmap];0.81[AFR][1000 genomes];0.92[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs4921642	0.83[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4921643	0.97[ASN][1000 genomes]
rs4921644	0.84[ASN][1000 genomes]
rs4921645	1.00[JPT][hapmap];0.89[ASN][1000 genomes]
rs4921651	0.89[CHB][hapmap]
rs4922028	1.00[JPT][hapmap];1.00[YRI][hapmap];0.83[AFR][1000 genomes];0.87[ASN][1000 genomes]
rs4922029	1.00[JPT][hapmap];0.88[YRI][hapmap];0.81[AFR][1000 genomes];0.87[ASN][1000 genomes]
rs56298301	0.85[AFR][1000 genomes];0.83[AMR][1000 genomes];0.88[ASN][1000 genomes]
rs6586830	0.89[CHB][hapmap]
rs6586833	1.00[JPT][hapmap];0.87[ASN][1000 genomes]
rs6981898	1.00[JPT][hapmap];1.00[YRI][hapmap];0.82[AFR][1000 genomes];0.94[AMR][1000 genomes];0.95[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs6983973	1.00[JPT][hapmap];0.96[YRI][hapmap];0.87[AFR][1000 genomes];0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6984145	0.87[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6990217	0.91[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs6990357	0.90[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs6991212	0.91[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs6992893	1.00[JPT][hapmap];0.96[YRI][hapmap];0.87[AFR][1000 genomes];0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6997164	0.97[ASN][1000 genomes]
rs6999786	0.87[YRI][hapmap];0.81[AFR][1000 genomes];0.94[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs7004435	0.90[AMR][1000 genomes];0.93[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs7006702	0.88[YRI][hapmap];0.82[AFR][1000 genomes];0.92[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs7008916	0.96[ASN][1000 genomes]
rs7011602	0.88[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs7012529	0.95[ASN][1000 genomes]
rs7015440	0.91[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs7016259	0.91[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs7016592	0.91[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs7814793	1.00[JPT][hapmap];0.88[ASN][1000 genomes]
rs7818345	0.89[AFR][1000 genomes];0.94[AMR][1000 genomes];0.95[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs7820698	1.00[JPT][hapmap];0.99[ASN][1000 genomes]
rs7821446	0.87[YRI][hapmap];0.84[AMR][1000 genomes]
rs7822046	0.97[ASN][1000 genomes]
rs7823194	0.87[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7830251	1.00[JPT][hapmap];0.87[ASN][1000 genomes]
rs7833166	0.83[AFR][1000 genomes];0.90[AMR][1000 genomes];0.99[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs7835461	1.00[JPT][hapmap];0.80[YRI][hapmap];0.93[AMR][1000 genomes];0.94[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs7835945	1.00[JPT][hapmap];0.99[ASN][1000 genomes]
rs7844175	0.97[ASN][1000 genomes]
rs9720249	0.97[AFR][1000 genomes];0.99[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[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:2)

SNP	Gene	Cis/trans	Tissue	Source
rs13278459	CSGALNACT1	cis	Thyroid	GTEx
rs13278459	CSGALNACT1	cis	Skin Sun Exposed Lower leg	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	chr8:19277800-19300200	Weak transcription	Primary B cells from peripheral blood	blood
4	chr8:19278000-19304800	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
5	chr8:19283800-19302200	Weak transcription	Primary T cells fromperipheralblood	blood
6	chr8:19283800-19307800	Weak transcription	Ovary	ovary
7	chr8:19284000-19302400	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
8	chr8:19284200-19300000	Weak transcription	Primary hematopoietic stem cells	blood
9	chr8:19290400-19297600	Strong transcription	Primary neutrophils fromperipheralblood	blood
10	chr8:19291200-19297600	Strong transcription	Primary B cells from cord blood	blood
11	chr8:19291600-19308000	Weak transcription	Right Ventricle	heart
12	chr8:19292600-19301400	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
13	chr8:19294400-19297600	Strong transcription	Primary T cells from cord blood	blood
14	chr8:19294600-19297600	Enhancers	H9 Cell Line	embryonic stem cell
15	chr8:19294600-19297600	Enhancers	HUES48 Cell Line	embryonic stem cell
16	chr8:19294600-19297600	Enhancers	HUES6 Cell Line	embryonic stem cell
17	chr8:19294600-19297600	Enhancers	iPS-15b Cell Line	embryonic stem cell
18	chr8:19294600-19297600	Transcr. at gene 5' and 3'	A549	lung
19	chr8:19294600-19297800	Strong transcription	Placenta	Placenta
20	chr8:19294600-19302000	Weak transcription	Primary T killer memory cells from peripheral blood	blood
21	chr8:19294800-19297600	Enhancers	H1 Cell Line	embryonic stem cell
22	chr8:19294800-19297600	Enhancers	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
23	chr8:19294800-19297600	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
24	chr8:19294800-19297600	Strong transcription	Left Ventricle	heart
25	chr8:19295000-19318800	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
26	chr8:19295200-19297600	Enhancers	HSMMtube	muscle
27	chr8:19295800-19302800	Weak transcription	Thymus	Thymus
28	chr8:19296000-19297600	Enhancers	Brain Inferior Temporal Lobe	brain
29	chr8:19296400-19297600	Strong transcription	Primary T helper cells fromperipheralblood	blood
30	chr8:19296400-19297600	Enhancers	Brain Hippocampus Middle	brain
31	chr8:19296600-19302000	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
32	chr8:19296600-19302000	Weak transcription	Cortex derived primary cultured neurospheres	brain
33	chr8:19296600-19302200	Weak transcription	HepG2	liver
34	chr8:19296600-19309400	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
35	chr8:19296600-19317400	Weak transcription	Hela-S3	cervix
36	chr8:19296800-19297600	Genic enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
37	chr8:19296800-19297600	Enhancers	iPS DF 6.9 Cell Line	embryonic stem cell
38	chr8:19296800-19300400	Weak transcription	Primary T helper cells PMA-I stimulated	--
39	chr8:19297000-19297600	Strong transcription	Primary T helper naive cells from peripheral blood	blood
40	chr8:19297000-19297600	Strong transcription	Monocytes-CD14+_RO01746	blood
41	chr8:19297000-19297800	Enhancers	iPS-20b Cell Line	embryonic stem cell
42	chr8:19297000-19302400	Weak transcription	Fetal Thymus	thymus
43	chr8:19297200-19297600	Flanking Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
44	chr8:19297200-19309200	Weak transcription	ES-I3 Cell Line	embryonic stem cell
45	chr8:19297400-19297600	Genic enhancers	Primary T regulatory cells fromperipheralblood	blood
46	chr8:19297400-19297600	ZNF genes & repeats	Spleen	Spleen
47	chr8:19297400-19302000	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
48	chr8:19297400-19313400	Weak transcription	Brain Cingulate Gyrus	brain

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