Variant report

Variant	rs6997589
Chromosome Location	chr8:19177772-19177773
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr8:19169455..19173162-chr8:19175391..19178341,5	MCF-7	breast:

Variant related genes	Relation type
ENSG00000104611	Chromatin interaction

Extended variants
information (count: 26 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:10)

rs_ID	r²[population]
rs1915417	0.88[EUR][1000 genomes]
rs2139767	0.89[AMR][1000 genomes];0.82[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs2683324	0.81[JPT][hapmap]
rs4921635	0.90[ASN][1000 genomes]
rs4922018	0.94[AMR][1000 genomes];0.83[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6997245	0.89[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7005125	0.92[AFR][1000 genomes];0.90[AMR][1000 genomes];0.83[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7005298	0.82[ASW][hapmap];0.90[CHB][hapmap];0.82[CHD][hapmap];0.91[GIH][hapmap];0.90[JPT][hapmap];0.90[ASN][1000 genomes]
rs7006741	0.90[ASN][1000 genomes]
rs7813165	0.86[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:16 , 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	nsv917232	chr8:18585309-19208665	Enhancers Weak transcription Flanking Active TSS Flanking Bivalent TSS/Enh Strong transcription Bivalent Enhancer Bivalent/Poised TSS Active TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	25 gene(s)	inside rSNPs	diseases
6	nsv890610	chr8:18749120-19260599	Enhancers Strong transcription Weak transcription ZNF genes & repeats Flanking Active TSS Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	20 gene(s)	inside rSNPs	diseases
7	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
8	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
9	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
10	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
11	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
12	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
13	nsv890615	chr8:18989735-19181921	Weak transcription Enhancers Active TSS Flanking Active TSS Bivalent Enhancer Bivalent/Poised TSS Genic enhancers Flanking Bivalent TSS/Enh Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases
14	nsv890616	chr8:18989735-19197809	Weak transcription Flanking Active TSS Active TSS Enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Strong transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases
15	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
16	nsv890621	chr8:19173379-19211220	Genic enhancers Weak transcription Strong transcription Flanking Active TSS Enhancers ZNF genes & repeats Bivalent Enhancer Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region	3 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs6997589	CSGALNACT1	cis	parietal	SCAN

Chromatin state (count:56 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr8:19172000-19179600	Weak transcription	Spleen	Spleen
2	chr8:19172200-19179800	Weak transcription	Left Ventricle	heart
3	chr8:19172200-19182600	Weak transcription	Esophagus	oesophagus
4	chr8:19172400-19180600	Weak transcription	Fetal Stomach	stomach
5	chr8:19172400-19184800	Weak transcription	Stomach Smooth Muscle	stomach
6	chr8:19172400-19187800	Weak transcription	Fetal Heart	heart
7	chr8:19172400-19188000	Weak transcription	Right Ventricle	heart
8	chr8:19172400-19202400	Weak transcription	ES-I3 Cell Line	embryonic stem cell
9	chr8:19172600-19181200	Weak transcription	NH-A	brain
10	chr8:19172600-19202800	Weak transcription	Pancreatic Islets	Pancreatic Islet
11	chr8:19172800-19181600	Weak transcription	Placenta	Placenta
12	chr8:19173600-19178800	Weak transcription	NHLF	lung
13	chr8:19173600-19180600	Weak transcription	Rectal Mucosa Donor 29	rectum
14	chr8:19173600-19254800	Weak transcription	Colonic Mucosa	Colon
15	chr8:19173800-19185200	Weak transcription	Sigmoid Colon	Sigmoid Colon
16	chr8:19173800-19205400	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
17	chr8:19174000-19178200	Weak transcription	NHEK	skin
18	chr8:19174000-19223600	Weak transcription	Duodenum Smooth Muscle	Duodenum
19	chr8:19174200-19177800	Weak transcription	Fetal Intestine Small	intestine
20	chr8:19174200-19178200	Weak transcription	Duodenum Mucosa	Duodenum
21	chr8:19174200-19179200	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
22	chr8:19174200-19179600	Weak transcription	Lung	lung
23	chr8:19174200-19183400	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
24	chr8:19174200-19183400	Weak transcription	HMEC	breast
25	chr8:19174200-19184000	Weak transcription	Aorta	Aorta
26	chr8:19174200-19191400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
27	chr8:19174200-19220400	Weak transcription	HSMM	muscle
28	chr8:19174400-19178200	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
29	chr8:19174400-19183400	Weak transcription	Small Intestine	intestine
30	chr8:19174400-19205200	Weak transcription	Muscle Satellite Cultured Cells	--
31	chr8:19175200-19179600	Weak transcription	Gastric	stomach
32	chr8:19175600-19179800	Enhancers	Ovary	ovary
33	chr8:19176200-19178600	Strong transcription	NHDF-Ad	bronchial
34	chr8:19176600-19187000	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
35	chr8:19176800-19178000	Flanking Active TSS	Liver	Liver
36	chr8:19176800-19178000	Flanking Active TSS	HepG2	liver
37	chr8:19176800-19178600	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
38	chr8:19176800-19183600	Strong transcription	Hela-S3	cervix
39	chr8:19176800-19185600	Strong transcription	Osteobl	bone
40	chr8:19177000-19177800	Strong transcription	Adipose Nuclei	Adipose
41	chr8:19177000-19178200	Weak transcription	Cortex derived primary cultured neurospheres	brain
42	chr8:19177000-19179200	Weak transcription	Rectal Mucosa Donor 31	rectum
43	chr8:19177000-19185400	Strong transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
44	chr8:19177000-19188800	Strong transcription	A549	lung
45	chr8:19177000-19189600	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
46	chr8:19177200-19177800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
47	chr8:19177200-19179200	Weak transcription	Placenta Amnion	Placenta Amnion
48	chr8:19177200-19179200	Weak transcription	GM12878-XiMat	blood
49	chr8:19177200-19180000	Strong transcription	Fetal Intestine Large	intestine
50	chr8:19177200-19189400	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow

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