Variant report

Variant	rs1021436
Chromosome Location	chr8:19576883-19576884
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 31 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:23)

rs_ID	r²[population]
rs10095445	0.85[ASN][1000 genomes]
rs10097017	0.80[AMR][1000 genomes]
rs10098471	0.91[ASN][1000 genomes]
rs10112417	0.94[AMR][1000 genomes];0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11992703	0.83[AMR][1000 genomes]
rs12056388	0.87[AMR][1000 genomes];0.91[ASN][1000 genomes]
rs13253689	0.90[CHB][hapmap];0.82[JPT][hapmap];0.88[AMR][1000 genomes];0.91[ASN][1000 genomes]
rs1492644	0.90[CHB][hapmap];0.91[CHD][hapmap];0.82[JPT][hapmap];0.88[ASN][1000 genomes]
rs1492645	0.90[CHB][hapmap];0.82[JPT][hapmap];0.88[ASN][1000 genomes]
rs1552782	0.88[AMR][1000 genomes];0.92[ASN][1000 genomes]
rs1845041	0.81[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs1994788	0.92[ASN][1000 genomes]
rs2006476	0.95[ASN][1000 genomes]
rs3735956	0.88[AMR][1000 genomes];0.91[ASN][1000 genomes]
rs4921669	0.87[AMR][1000 genomes];0.87[ASN][1000 genomes]
rs4922089	0.85[AMR][1000 genomes];0.85[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4922090	0.93[AMR][1000 genomes];0.85[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6586856	0.90[CHB][hapmap];0.85[ASN][1000 genomes]
rs6586857	0.85[ASN][1000 genomes]
rs6586860	0.86[AMR][1000 genomes];0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7815576	0.85[AMR][1000 genomes];0.85[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7833352	0.88[AMR][1000 genomes];0.89[ASN][1000 genomes]
rs7836255	0.93[AMR][1000 genomes];0.83[EUR][1000 genomes];0.94[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:8 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	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
2	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
3	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
4	nsv890625	chr8:19368697-19799641	Strong transcription Weak transcription Enhancers Bivalent Enhancer Genic enhancers Flanking Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	19 gene(s)	inside rSNPs	diseases
5	nsv1021575	chr8:19430653-19623452	Enhancers Active TSS Weak transcription Genic enhancers Strong transcription Flanking Bivalent TSS/Enh Flanking Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases
6	nsv1021731	chr8:19515149-19643313	Flanking Bivalent TSS/Enh Weak transcription Bivalent Enhancer Enhancers Bivalent/Poised TSS Flanking Active TSS Active TSS ZNF genes & repeats Genic enhancers Strong transcription Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
7	nsv1021225	chr8:19554860-19586580	Flanking Active TSS Weak transcription Enhancers Strong transcription ZNF genes & repeats Genic enhancers Bivalent Enhancer	Chromatin interactive region	n/a	inside rSNPs	diseases
8	nsv610759	chr8:19561997-20068842	Enhancers Strong transcription Bivalent Enhancer Weak transcription Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	21 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs1021436	CSGALNACT1	cis	Whole Blood	GTEx

Chromatin state (count:58 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr8:19563200-19578200	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
2	chr8:19569000-19577600	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
3	chr8:19571600-19577200	Weak transcription	Esophagus	oesophagus
4	chr8:19572000-19577600	Weak transcription	Fetal Muscle Leg	muscle
5	chr8:19573200-19577600	Enhancers	Primary T cells from cord blood	blood
6	chr8:19573200-19578400	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
7	chr8:19573200-19579000	Enhancers	Primary T helper cells PMA-I stimulated	--
8	chr8:19573200-19579000	Enhancers	Primary T helper cells fromperipheralblood	blood
9	chr8:19573400-19577600	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
10	chr8:19573800-19577200	Weak transcription	Brain Anterior Caudate	brain
11	chr8:19573800-19577600	Weak transcription	Gastric	stomach
12	chr8:19573800-19578800	Enhancers	Primary T helper naive cells fromperipheralblood	blood
13	chr8:19573800-19580000	Weak transcription	Pancreas	Pancrea
14	chr8:19574400-19578200	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
15	chr8:19574400-19578200	Enhancers	HMEC	breast
16	chr8:19574400-19578600	Enhancers	Primary T helper 17 cells PMA-I stimulated	--
17	chr8:19574800-19578400	Enhancers	Right Ventricle	heart
18	chr8:19574800-19578800	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
19	chr8:19574800-19578800	Enhancers	Placenta	Placenta
20	chr8:19575000-19578400	Enhancers	Left Ventricle	heart
21	chr8:19575000-19578400	Enhancers	Osteobl	bone
22	chr8:19575200-19577600	Enhancers	NH-A	brain
23	chr8:19575200-19578000	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
24	chr8:19575400-19577400	Enhancers	Primary B cells from peripheral blood	blood
25	chr8:19575400-19587200	Weak transcription	Brain Angular Gyrus	brain
26	chr8:19575400-19596800	Weak transcription	Monocytes-CD14+_RO01746	blood
27	chr8:19575600-19577800	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
28	chr8:19576000-19577000	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
29	chr8:19576000-19578200	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
30	chr8:19576000-19578800	Enhancers	A549	lung
31	chr8:19576200-19577000	Enhancers	Hela-S3	cervix
32	chr8:19576200-19577400	Enhancers	NHDF-Ad	bronchial
33	chr8:19576200-19577800	Enhancers	NHEK	skin
34	chr8:19576200-19578200	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
35	chr8:19576200-19578400	Enhancers	Breast Myoepithelial Primary Cells	Breast
36	chr8:19576200-19578800	Enhancers	Right Atrium	heart
37	chr8:19576400-19577000	Weak transcription	Fetal Brain Male	brain
38	chr8:19576400-19577000	Enhancers	Spleen	Spleen
39	chr8:19576400-19577200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
40	chr8:19576400-19577200	Weak transcription	Fetal Thymus	thymus
41	chr8:19576400-19577200	Enhancers	Placenta Amnion	Placenta Amnion
42	chr8:19576400-19577200	Enhancers	NHLF	lung
43	chr8:19576400-19577400	Enhancers	Primary T killer naive cells fromperipheralblood	blood
44	chr8:19576400-19577400	Enhancers	HSMMtube	muscle
45	chr8:19576400-19579000	Weak transcription	Thymus	Thymus
46	chr8:19576400-19580000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
47	chr8:19576400-19591800	Weak transcription	Primary B cells from cord blood	blood
48	chr8:19576600-19577200	Weak transcription	Brain Inferior Temporal Lobe	brain
49	chr8:19576600-19577800	Enhancers	Primary T cells effector/memory enriched fromperipheralblood	blood
50	chr8:19576600-19578400	Enhancers	Primary T helper naive cells from peripheral blood	blood

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