Variant report

Variant	rs9851548
Chromosome Location	chr3:137880695-137880696
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	chr3:137880343..137882012-chr3:137893517..137895073,2	K562	blood:
2	chr3:137876601..137878547-chr3:137880308..137882922,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000138231	Chromatin interaction

Extended variants
information (count: 66 )
Associated
traits (count: 6 )

rSNPs within LD-proxies of this variant (count:59)

rs_ID	r²[population]
rs1137760	0.81[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs11712078	0.92[ASN][1000 genomes]
rs12185936	0.80[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs12185998	0.84[ASN][1000 genomes]
rs1600697	0.83[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs2219936	0.82[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs2251550	0.82[EUR][1000 genomes]
rs2346744	0.89[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2346745	0.89[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2346747	0.80[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs2622694	0.81[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs2622696	0.81[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs2622699	0.81[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs2622700	0.90[AMR][1000 genomes];0.96[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2622732	0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2622733	0.99[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2622734	0.96[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2622735	0.93[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2622736	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2622737	0.89[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2622739	0.89[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2622740	0.89[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2622741	0.81[AMR][1000 genomes];0.92[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2622742	0.84[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs2622743	0.83[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs2622744	0.82[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs2724681	0.82[AMR][1000 genomes];0.91[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs2724690	0.82[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs2724691	0.81[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs2724692	0.81[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs2724710	0.97[AFR][1000 genomes];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2724711	0.82[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs2724712	0.92[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2724725	0.81[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2724726	0.97[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2724727	0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs329380	0.83[AFR][1000 genomes];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs3732839	0.81[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs608594	0.86[AMR][1000 genomes];0.94[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs7430414	0.88[AMR][1000 genomes];0.94[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7613041	0.91[AMR][1000 genomes];0.99[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7613558	0.81[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs7632402	0.83[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs774803	0.96[AFR][1000 genomes];0.91[AMR][1000 genomes];0.96[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs774804	0.85[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs774805	0.88[AMR][1000 genomes];0.92[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs774806	0.86[AMR][1000 genomes];0.92[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs774807	0.86[AMR][1000 genomes];0.95[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs774808	0.86[AMR][1000 genomes];0.93[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs774809	0.86[AMR][1000 genomes];0.95[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs774810	0.90[AFR][1000 genomes];0.91[AMR][1000 genomes];0.95[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs774811	0.86[AMR][1000 genomes];0.95[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs774812	0.90[AFR][1000 genomes];0.91[AMR][1000 genomes];0.93[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs774813	0.86[AMR][1000 genomes];0.94[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs774814	0.89[AMR][1000 genomes];0.94[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs811810	0.89[AMR][1000 genomes];0.96[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs811811	0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs9827617	0.89[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9840008	0.89[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:7 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv530056	chr3:137312356-138161861	Weak transcription Active TSS Enhancers Genic enhancers Strong transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Flanking Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	26 gene(s)	inside rSNPs	diseases
2	esv2757890	chr3:137611789-137933835	Weak transcription Enhancers Flanking Active TSS Active TSS Genic enhancers Bivalent/Poised TSS Strong transcription ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	16 gene(s)	inside rSNPs	diseases
3	esv2759180	chr3:137611789-137933835	Enhancers Active TSS Genic enhancers Weak transcription Flanking Active TSS Strong transcription 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	16 gene(s)	inside rSNPs	diseases
4	esv2751978	chr3:137715302-137890750	Weak transcription Strong transcription Enhancers Flanking Active TSS ZNF genes & repeats Active TSS 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	8 gene(s)	inside rSNPs	diseases
5	esv2762347	chr3:137851198-137910007	Active TSS Transcr. at gene 5' and 3' Enhancers Flanking Active TSS Weak transcription Strong transcription Genic enhancers Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region	10 gene(s)	inside rSNPs	diseases
6	nsv998106	chr3:137851198-137934610	Weak transcription Enhancers Flanking Active TSS Strong transcription Genic enhancers Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region	10 gene(s)	inside rSNPs	diseases
7	nsv877536	chr3:137870523-137970907	Enhancers Weak transcription Strong transcription Active TSS Genic enhancers Flanking Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region miRNA target site	9 gene(s)	inside rSNPs	diseases

mRNA abundance (count:6)

SNP	Gene	Cis/trans	Tissue	Source
rs9851548	A4GNT	cis	Nerve Tibial	GTEx
rs9851548	A4GNT	cis	Artery Tibial	GTEx
rs9851548	A4GNT	cis	Skin Sun Exposed Lower leg	GTEx
rs9851548	A4GNT	cis	Adipose Subcutaneous	GTEx
rs9851548	A4GNT	cis	Thyroid	GTEx
rs9851548	DBR1	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:124 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:137876000-137884800	Weak transcription	Colon Smooth Muscle	Colon
2	chr3:137876000-137892400	Weak transcription	iPS-15b Cell Line	embryonic stem cell
3	chr3:137876400-137892800	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
4	chr3:137877200-137882000	Weak transcription	NHDF-Ad	bronchial
5	chr3:137877200-137882800	Weak transcription	Primary T killer memory cells from peripheral blood	blood
6	chr3:137877400-137880800	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
7	chr3:137877600-137880800	Weak transcription	Ovary	ovary
8	chr3:137877600-137880800	Weak transcription	Osteobl	bone
9	chr3:137877800-137880800	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
10	chr3:137877800-137880800	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
11	chr3:137877800-137880800	Weak transcription	Placenta	Placenta
12	chr3:137877800-137880800	Weak transcription	NH-A	brain
13	chr3:137878000-137880800	Weak transcription	Primary T helper cells PMA-I stimulated	--
14	chr3:137878000-137880800	Weak transcription	HSMM	muscle
15	chr3:137878000-137885600	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
16	chr3:137878200-137880800	Weak transcription	Placenta Amnion	Placenta Amnion
17	chr3:137878800-137882400	Strong transcription	Thymus	Thymus
18	chr3:137878800-137892200	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
19	chr3:137879000-137880800	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
20	chr3:137879000-137880800	Weak transcription	Brain Anterior Caudate	brain
21	chr3:137879000-137880800	Weak transcription	Rectal Mucosa Donor 31	rectum
22	chr3:137879000-137885400	Weak transcription	Pancreatic Islets	Pancreatic Islet
23	chr3:137879000-137886800	Strong transcription	Primary T helper 17 cells PMA-I stimulated	--
24	chr3:137879000-137888200	Strong transcription	Fetal Brain Female	brain
25	chr3:137879000-137888400	Strong transcription	Primary T helper naive cells fromperipheralblood	blood
26	chr3:137879000-137888600	Strong transcription	Primary T cells fromperipheralblood	blood
27	chr3:137879000-137889600	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
28	chr3:137879000-137890000	Strong transcription	Primary neutrophils fromperipheralblood	blood
29	chr3:137879000-137891000	Strong transcription	Monocytes-CD14+_RO01746	blood
30	chr3:137879000-137891200	Weak transcription	Fetal Brain Male	brain
31	chr3:137879000-137891400	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
32	chr3:137879000-137891600	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
33	chr3:137879200-137880800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
34	chr3:137879200-137880800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
35	chr3:137879200-137880800	Weak transcription	Brain Hippocampus Middle	brain
36	chr3:137879200-137880800	Weak transcription	Brain Substantia Nigra	brain
37	chr3:137879200-137880800	Weak transcription	Fetal Kidney	kidney
38	chr3:137879200-137880800	Weak transcription	Skeletal Muscle Male	skeletal muscle
39	chr3:137879200-137880800	Weak transcription	GM12878-XiMat	blood
40	chr3:137879200-137881800	Weak transcription	Gastric	stomach
41	chr3:137879200-137884400	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
42	chr3:137879200-137885200	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
43	chr3:137879200-137887600	Weak transcription	Esophagus	oesophagus
44	chr3:137879200-137888800	Strong transcription	Fetal Intestine Large	intestine
45	chr3:137879200-137889000	Strong transcription	Breast Myoepithelial Primary Cells	Breast
46	chr3:137879200-137889000	Weak transcription	Hela-S3	cervix
47	chr3:137879200-137889200	Strong transcription	Ganglion Eminence derived primary cultured neurospheres	brain
48	chr3:137879200-137889600	Strong transcription	Primary T helper cells fromperipheralblood	blood
49	chr3:137879200-137889600	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
50	chr3:137879200-137889600	Strong transcription	Left Ventricle	heart

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