Variant report

Variant	rs41298781
Chromosome Location	chr10:43650915-43650916
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr10:43649271..43651758-chr10:43657631..43659326,2	K562	blood:
2	chr10:43649752..43652450-chr10:43654182..43655742,2	K562	blood:

Extended variants
information (count: 20 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:12)

rs_ID	r²[population]
rs11238472	0.90[AFR][1000 genomes];0.80[AMR][1000 genomes]
rs12244413	0.84[AMR][1000 genomes]
rs12570625	0.89[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs1800862	1.00[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs1955355	0.84[AMR][1000 genomes]
rs3026768	1.00[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs3026771	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs3026775	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs3026785	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs35718664	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs41301581	0.89[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs41301585	0.89[AMR][1000 genomes];0.98[EUR][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	nsv534548	chr10:42890664-43729688	Weak transcription Strong transcription Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh Enhancers Flanking Active TSS Active TSS ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	56 gene(s)	inside rSNPs	diseases
2	nsv430159	chr10:43291894-43946294	Flanking Active TSS Enhancers Active TSS Strong transcription Weak transcription ZNF genes & repeats Bivalent Enhancer Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	92 gene(s)	inside rSNPs	diseases
3	nsv895082	chr10:43530071-43755506	Strong transcription ZNF genes & repeats Enhancers Genic enhancers Flanking Active TSS Weak transcription Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	12 gene(s)	inside rSNPs	diseases
4	nsv895083	chr10:43549708-43765485	Weak transcription Strong transcription Active TSS Enhancers Flanking Active TSS Bivalent Enhancer Genic enhancers ZNF genes & repeats 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	13 gene(s)	inside rSNPs	diseases
5	nsv916378	chr10:43622151-43868356	Weak transcription Enhancers Active TSS Flanking Active TSS Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	16 gene(s)	inside rSNPs	diseases
6	nsv1042310	chr10:43623060-43688505	Weak transcription Active TSS Enhancers Genic enhancers Strong transcription ZNF genes & repeats Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	7 gene(s)	inside rSNPs	diseases
7	nsv1043661	chr10:43626619-43890162	Bivalent Enhancer Active TSS Enhancers Weak transcription Bivalent/Poised TSS Flanking Active TSS Genic enhancers Strong transcription Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	17 gene(s)	inside rSNPs	diseases
8	nsv540574	chr10:43626619-43890162	Enhancers Bivalent Enhancer Flanking Active TSS Active TSS Weak transcription Genic enhancers Strong transcription Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	17 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs41298781	GALNACT-2	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:88 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr10:43634800-43652200	Weak transcription	Gastric	stomach
2	chr10:43635400-43655600	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
3	chr10:43635600-43689000	Weak transcription	Esophagus	oesophagus
4	chr10:43636600-43654800	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
5	chr10:43636600-43655600	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
6	chr10:43637400-43655200	Weak transcription	HSMM	muscle
7	chr10:43637600-43651200	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
8	chr10:43637600-43652200	Weak transcription	Fetal Thymus	thymus
9	chr10:43641400-43657400	Weak transcription	A549	lung
10	chr10:43644800-43652200	Weak transcription	Primary hematopoietic stem cells short term culture	blood
11	chr10:43645600-43651600	Enhancers	Primary T helper cells fromperipheralblood	blood
12	chr10:43645600-43656800	Weak transcription	Cortex derived primary cultured neurospheres	brain
13	chr10:43646600-43658400	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
14	chr10:43647000-43652200	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
15	chr10:43647000-43655600	Weak transcription	Primary B cells from peripheral blood	blood
16	chr10:43647200-43651000	Weak transcription	Primary hematopoietic stem cells	blood
17	chr10:43647200-43652000	Weak transcription	Pancreas	Pancrea
18	chr10:43647200-43652200	Weak transcription	Ovary	ovary
19	chr10:43647200-43652200	Weak transcription	Thymus	Thymus
20	chr10:43647200-43656200	Weak transcription	Spleen	Spleen
21	chr10:43647200-43656400	Weak transcription	Fetal Muscle Leg	muscle
22	chr10:43647200-43667800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
23	chr10:43647400-43652000	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
24	chr10:43647400-43652200	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
25	chr10:43647400-43652200	Weak transcription	Skeletal Muscle Female	skeletal muscle
26	chr10:43647400-43652400	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
27	chr10:43647400-43654800	Weak transcription	Psoas Muscle	Psoas
28	chr10:43647400-43655200	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
29	chr10:43647400-43655400	Weak transcription	Rectal Smooth Muscle	rectum
30	chr10:43647400-43655600	Weak transcription	Breast Myoepithelial Primary Cells	Breast
31	chr10:43647400-43656200	Weak transcription	Duodenum Mucosa	Duodenum
32	chr10:43647400-43656400	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
33	chr10:43647400-43656800	Weak transcription	Sigmoid Colon	Sigmoid Colon
34	chr10:43647400-43657200	Weak transcription	Left Ventricle	heart
35	chr10:43647400-43667800	Weak transcription	HUES6 Cell Line	embryonic stem cell
36	chr10:43647600-43652400	Weak transcription	Primary T cells from cord blood	blood
37	chr10:43647600-43654800	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
38	chr10:43647600-43654800	Weak transcription	Adipose Nuclei	Adipose
39	chr10:43647600-43654800	Weak transcription	HSMMtube	muscle
40	chr10:43647600-43654800	Weak transcription	NHLF	lung
41	chr10:43647600-43655600	Weak transcription	Brain Anterior Caudate	brain
42	chr10:43647600-43655600	Weak transcription	GM12878-XiMat	blood
43	chr10:43647600-43659600	Weak transcription	Rectal Mucosa Donor 31	rectum
44	chr10:43647600-43664000	Weak transcription	Fetal Brain Male	brain
45	chr10:43647600-43667000	Weak transcription	iPS-15b Cell Line	embryonic stem cell
46	chr10:43648200-43652200	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
47	chr10:43648400-43653200	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
48	chr10:43648600-43653000	Enhancers	Primary T killer naive cells fromperipheralblood	blood
49	chr10:43648800-43652000	Weak transcription	Dnd41	blood
50	chr10:43648800-43653200	Enhancers	Fetal Lung	lung

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