Variant report

Variant	rs3802329
Chromosome Location	chr8:19266727-19266728
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr8:19264741..19268726-chr8:19614195..19616222,3	MCF-7	breast:
2	chr8:19266166..19268628-chr8:19272265..19273861,2	MCF-7	breast:
3	chr8:19266168..19267872-chr8:19269454..19271041,2	MCF-7	breast:
4	chr8:19260819..19264347-chr8:19264477..19266949,3	MCF-7	breast:
5	chr8:19265111..19268034-chr8:19269778..19273718,6	MCF-7	breast:
6	chr8:19265734..19267679-chr8:19315325..19317057,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000147408	Chromatin interaction

Extended variants
information (count: 50 )
Associated
traits (count: 7 )

rSNPs within LD-proxies of this variant (count:32)

rs_ID	r²[population]
rs10102696	1.00[JPT][hapmap];0.86[ASN][1000 genomes]
rs10481426	0.81[CHD][hapmap];1.00[JPT][hapmap];0.85[ASN][1000 genomes]
rs10481427	1.00[JPT][hapmap];0.85[ASN][1000 genomes]
rs10481428	1.00[JPT][hapmap];0.85[ASN][1000 genomes]
rs11778175	1.00[JPT][hapmap];0.84[ASN][1000 genomes]
rs11780388	1.00[JPT][hapmap];0.88[ASN][1000 genomes]
rs11782540	1.00[JPT][hapmap];0.86[AMR][1000 genomes];0.90[ASN][1000 genomes]
rs11785649	0.84[CHD][hapmap];0.83[GIH][hapmap];1.00[JPT][hapmap];0.91[MEX][hapmap];0.86[AMR][1000 genomes];0.90[ASN][1000 genomes]
rs11786847	1.00[JPT][hapmap];0.88[ASN][1000 genomes]
rs12679671	0.88[ASN][1000 genomes]
rs12679712	0.84[CHD][hapmap];1.00[JPT][hapmap];0.90[ASN][1000 genomes]
rs13255946	0.84[CHD][hapmap];1.00[JPT][hapmap];0.89[ASN][1000 genomes]
rs17407039	0.86[AMR][1000 genomes];0.90[ASN][1000 genomes]
rs17479099	0.88[ASN][1000 genomes]
rs4256608	1.00[JPT][hapmap];0.83[AMR][1000 genomes];0.92[ASN][1000 genomes]
rs4391454	1.00[JPT][hapmap];0.89[ASN][1000 genomes]
rs4412390	0.87[CHD][hapmap];1.00[JPT][hapmap];0.90[ASN][1000 genomes]
rs4617172	1.00[JPT][hapmap];0.89[ASN][1000 genomes]
rs4633071	0.89[ASN][1000 genomes]
rs4642666	0.88[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.97[ASN][1000 genomes]
rs4921638	0.84[CHD][hapmap];1.00[JPT][hapmap];0.89[ASN][1000 genomes]
rs6990217	1.00[JPT][hapmap];0.88[ASN][1000 genomes]
rs6990357	0.84[CHD][hapmap];1.00[JPT][hapmap];0.88[ASN][1000 genomes]
rs6991212	0.88[ASN][1000 genomes]
rs6991231	0.86[ASN][1000 genomes]
rs6992950	1.00[JPT][hapmap];0.88[ASN][1000 genomes]
rs6999786	0.84[CHD][hapmap];1.00[JPT][hapmap];0.88[ASN][1000 genomes]
rs7006702	1.00[JPT][hapmap];0.88[ASN][1000 genomes]
rs7015440	0.88[ASN][1000 genomes]
rs7016259	1.00[JPT][hapmap];0.88[ASN][1000 genomes]
rs7016592	1.00[JPT][hapmap];0.88[ASN][1000 genomes]
rs7821446	0.84[CHD][hapmap];0.83[GIH][hapmap];1.00[JPT][hapmap];0.82[MEX][hapmap];0.83[AMR][1000 genomes];0.90[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:18 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1026466	chr8:18433493-19271274	Weak transcription Enhancers Strong transcription Active TSS Genic enhancers Bivalent Enhancer Flanking Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	29 gene(s)	inside rSNPs	diseases
2	nsv539520	chr8:18433493-19271274	Enhancers Weak transcription Strong transcription Active TSS Genic enhancers Flanking Active TSS ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	29 gene(s)	inside rSNPs	diseases
3	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
4	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
5	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
6	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
7	nsv890614	chr8:18838764-19274793	Weak transcription Enhancers Active TSS Bivalent/Poised TSS Flanking Active TSS Transcr. at gene 5' and 3' Genic enhancers Strong transcription Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	19 gene(s)	inside rSNPs	diseases
8	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
9	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
10	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
11	nsv1033229	chr8:19081684-19271274	Enhancers Weak transcription Strong transcription Flanking Active TSS Bivalent/Poised TSS Active TSS Genic enhancers ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	10 gene(s)	inside rSNPs	diseases
12	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
13	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
14	nsv890622	chr8:19224772-19275354	Weak transcription Flanking Active TSS Strong transcription Enhancers Active TSS ZNF genes & repeats Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer	Chromatin interactive region miRNA target site	2 gene(s)	inside rSNPs	diseases
15	nsv610751	chr8:19226335-19284889	Transcr. at gene 5' and 3' Weak transcription Enhancers Strong transcription Active TSS Flanking Active TSS Genic enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer	Chromatin interactive region miRNA target site	2 gene(s)	inside rSNPs	diseases
16	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
17	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
18	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

mRNA abundance (count:7)

SNP	Gene	Cis/trans	Tissue	Source
rs3802329	CSGALNACT1	cis	Thyroid	GTEx
rs3802329	CSGALNACT1	cis	parietal	SCAN
rs3802329	VPS37A	cis	parietal	SCAN
rs3802329	PIWIL2	cis	parietal	SCAN
rs3802329	CSGALNACT1	cis	cerebellum	SCAN
rs3802329	PPP3CC	cis	cerebellum	SCAN
rs3802329	CSGALNACT1	cis	Skin Sun Exposed Lower leg	GTEx

Chromatin state (count:98 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr8:19254000-19275000	Weak transcription	Gastric	stomach
2	chr8:19261800-19279600	Weak transcription	Pancreatic Islets	Pancreatic Islet
3	chr8:19263600-19266800	Weak transcription	Esophagus	oesophagus
4	chr8:19263800-19269600	Weak transcription	Lung	lung
5	chr8:19263800-19272600	Weak transcription	HUES48 Cell Line	embryonic stem cell
6	chr8:19265000-19267600	Enhancers	Fetal Brain Male	brain
7	chr8:19265400-19267400	Enhancers	Fetal Brain Female	brain
8	chr8:19265600-19267400	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
9	chr8:19265600-19267400	Enhancers	Placenta Amnion	Placenta Amnion
10	chr8:19265600-19267600	Enhancers	Primary T helper cells PMA-I stimulated	--
11	chr8:19265800-19266800	Enhancers	Hela-S3	cervix
12	chr8:19265800-19267000	Enhancers	Rectal Mucosa Donor 29	rectum
13	chr8:19265800-19267400	Enhancers	Primary T killer memory cells from peripheral blood	blood
14	chr8:19266000-19266800	Flanking Active TSS	Primary hematopoietic stem cells	blood
15	chr8:19266000-19266800	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
16	chr8:19266000-19266800	Active TSS	Ganglion Eminence derived primary cultured neurospheres	brain
17	chr8:19266000-19266800	Flanking Active TSS	HUVEC	blood vessel
18	chr8:19266000-19266800	Flanking Active TSS	Monocytes-CD14+_RO01746	blood
19	chr8:19266000-19267000	Flanking Active TSS	Primary T helper naive cells fromperipheralblood	blood
20	chr8:19266000-19267000	Flanking Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
21	chr8:19266000-19267400	Enhancers	Fetal Thymus	thymus
22	chr8:19266000-19267800	Enhancers	Primary B cells from peripheral blood	blood
23	chr8:19266000-19268800	Enhancers	Primary T helper cells fromperipheralblood	blood
24	chr8:19266200-19266800	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Female	--
25	chr8:19266200-19266800	Flanking Active TSS	Muscle Satellite Cultured Cells	--
26	chr8:19266200-19266800	Active TSS	Foreskin Fibroblast Primary Cells skin02	Skin
27	chr8:19266200-19266800	Flanking Active TSS	Brain Anterior Caudate	brain
28	chr8:19266200-19266800	Flanking Active TSS	Fetal Adrenal Gland	Adrenal Gland
29	chr8:19266200-19266800	Enhancers	Fetal Intestine Small	intestine
30	chr8:19266200-19266800	Flanking Active TSS	Fetal Lung	lung
31	chr8:19266200-19266800	Flanking Active TSS	Fetal Muscle Leg	muscle
32	chr8:19266200-19266800	Genic enhancers	Placenta	Placenta
33	chr8:19266200-19266800	Enhancers	Thymus	Thymus
34	chr8:19266200-19266800	Enhancers	Spleen	Spleen
35	chr8:19266200-19266800	Flanking Active TSS	HMEC	breast
36	chr8:19266200-19266800	Flanking Active TSS	NH-A	brain
37	chr8:19266200-19267000	Flanking Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
38	chr8:19266200-19267000	Flanking Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
39	chr8:19266200-19267000	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
40	chr8:19266200-19267000	Enhancers	Primary B cells from cord blood	blood
41	chr8:19266200-19267000	Flanking Active TSS	Primary T cells from cord blood	blood
42	chr8:19266200-19267000	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
43	chr8:19266200-19267000	Flanking Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
44	chr8:19266200-19267000	Enhancers	Primary mononuclear cells fromperipheralblood	Blood
45	chr8:19266200-19267000	Flanking Active TSS	Adipose Nuclei	Adipose
46	chr8:19266200-19267000	Active TSS	Aorta	Aorta
47	chr8:19266200-19267000	Enhancers	Brain Germinal Matrix	brain
48	chr8:19266200-19267000	Flanking Active TSS	Colon Smooth Muscle	Colon
49	chr8:19266200-19267000	Enhancers	Stomach Mucosa	stomach
50	chr8:19266200-19267000	Transcr. at gene 5' and 3'	A549	lung

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