Variant report

Variant	rs1678
Chromosome Location	chr10:96093632-96093633
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 50 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:45)

rs_ID	r²[population]
rs11814451	0.80[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11817642	0.82[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12255683	0.85[CEU][hapmap];0.95[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12766693	0.84[EUR][1000 genomes]
rs12773803	0.86[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12774398	1.00[CEU][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12778016	0.84[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs12780240	1.00[ASN][1000 genomes]
rs12781422	0.84[EUR][1000 genomes]
rs12781481	0.85[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12781628	0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12782263	1.00[CEU][hapmap];1.00[YRI][hapmap];0.86[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12783744	0.87[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12783751	0.87[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17438643	1.00[CEU][hapmap];0.93[YRI][hapmap];0.80[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17438706	1.00[CEU][hapmap];0.89[YRI][hapmap];0.91[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17439123	1.00[CEU][hapmap];0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17516758	1.00[CEU][hapmap];1.00[YRI][hapmap];0.81[AFR][1000 genomes];0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17516904	1.00[CEU][hapmap];0.84[YRI][hapmap];0.87[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17517368	0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17517515	1.00[CEU][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17517578	0.85[CEU][hapmap];0.84[YRI][hapmap];0.81[AFR][1000 genomes];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17517669	1.00[CEU][hapmap];1.00[YRI][hapmap];0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3203713	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34032820	0.87[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34053022	0.87[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34156870	1.00[ASN][1000 genomes]
rs34573359	0.89[AFR][1000 genomes];0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34818536	1.00[ASN][1000 genomes]
rs34999028	0.86[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35058175	0.91[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35084709	0.84[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35247409	0.87[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs35258481	0.83[AFR][1000 genomes];0.91[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35348430	0.91[AFR][1000 genomes];0.95[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs35446195	0.84[EUR][1000 genomes]
rs35658839	1.00[ASN][1000 genomes]
rs4394764	0.82[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs57178050	0.92[AMR][1000 genomes];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs71480900	0.89[AFR][1000 genomes];0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs71482303	0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs71482304	0.86[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs71482305	0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs71482306	1.00[ASN][1000 genomes]
rs72812701	1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:5 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1036676	chr10:95851376-96103876	Strong transcription Enhancers Weak transcription ZNF genes & repeats Bivalent Enhancer Active TSS Flanking Active TSS Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	12 gene(s)	inside rSNPs	diseases
2	esv2761616	chr10:95966768-96303701	Enhancers Strong transcription Flanking Active TSS ZNF genes & repeats Active TSS Genic enhancers Weak transcription Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	14 gene(s)	inside rSNPs	diseases
3	nsv831946	chr10:96055190-96226438	Weak transcription Flanking Active TSS ZNF genes & repeats Active TSS Bivalent/Poised TSS Bivalent Enhancer Strong transcription Enhancers Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	12 gene(s)	inside rSNPs	diseases
4	nsv497859	chr10:96058024-97027747	Strong transcription Weak transcription Active TSS Flanking Bivalent TSS/Enh Flanking Active TSS Enhancers ZNF genes & repeats Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	41 gene(s)	inside rSNPs	diseases
5	esv1819509	chr10:96064300-96361776	Weak transcription Strong transcription Enhancers Flanking Active TSS Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	24 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs1678	NOC3L	cis	Heart Left Ventricle	GTEx

Chromatin state (count:125 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr10:96031800-96121000	Weak transcription	Stomach Mucosa	stomach
2	chr10:96043600-96121000	Weak transcription	Psoas Muscle	Psoas
3	chr10:96072800-96093800	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
4	chr10:96075200-96112200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
5	chr10:96076000-96095800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
6	chr10:96076600-96097000	Weak transcription	Colon Smooth Muscle	Colon
7	chr10:96077600-96100200	Strong transcription	Rectal Mucosa Donor 31	rectum
8	chr10:96078200-96121600	Weak transcription	Fetal Brain Male	brain
9	chr10:96080200-96095000	Weak transcription	Brain Cingulate Gyrus	brain
10	chr10:96080200-96095800	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
11	chr10:96080400-96094600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
12	chr10:96080400-96096000	Strong transcription	HMEC	breast
13	chr10:96080400-96100200	Strong transcription	Rectal Mucosa Donor 29	rectum
14	chr10:96080400-96105200	Weak transcription	iPS-15b Cell Line	embryonic stem cell
15	chr10:96080400-96121000	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
16	chr10:96080600-96101800	Weak transcription	Thymus	Thymus
17	chr10:96080800-96102600	Strong transcription	Primary B cells from peripheral blood	blood
18	chr10:96081000-96105600	Strong transcription	Duodenum Mucosa	Duodenum
19	chr10:96081000-96118200	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
20	chr10:96081200-96118400	Strong transcription	Breast Myoepithelial Primary Cells	Breast
21	chr10:96081600-96100400	Strong transcription	Fetal Intestine Large	intestine
22	chr10:96081600-96117400	Strong transcription	NH-A	brain
23	chr10:96081600-96121000	Strong transcription	HUES6 Cell Line	embryonic stem cell
24	chr10:96081600-96121000	Strong transcription	HUES64 Cell Line	embryonic stem cell
25	chr10:96081800-96100400	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
26	chr10:96081800-96117400	Strong transcription	HSMM	muscle
27	chr10:96081800-96121000	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
28	chr10:96081800-96121000	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
29	chr10:96082000-96118400	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
30	chr10:96082200-96095600	Weak transcription	Brain Substantia Nigra	brain
31	chr10:96082200-96113000	Weak transcription	Esophagus	oesophagus
32	chr10:96082400-96099400	Weak transcription	Brain Angular Gyrus	brain
33	chr10:96082400-96121000	Strong transcription	iPS-18 Cell Line	embryonic stem cell
34	chr10:96082600-96109600	Weak transcription	Spleen	Spleen
35	chr10:96083000-96119800	Strong transcription	Primary T helper cells PMA-I stimulated	--
36	chr10:96083200-96118800	Strong transcription	Monocytes-CD14+_RO01746	blood
37	chr10:96084000-96099800	Strong transcription	Primary T cells from cord blood	blood
38	chr10:96084400-96118200	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
39	chr10:96084800-96098800	Weak transcription	Pancreas	Pancrea
40	chr10:96085000-96094000	Weak transcription	NHLF	lung
41	chr10:96085000-96097000	Weak transcription	Brain Inferior Temporal Lobe	brain
42	chr10:96085000-96121000	Weak transcription	Pancreatic Islets	Pancreatic Islet
43	chr10:96085000-96122200	Weak transcription	Gastric	stomach
44	chr10:96085400-96099400	Weak transcription	Colonic Mucosa	Colon
45	chr10:96085400-96109000	Weak transcription	Ovary	ovary
46	chr10:96086200-96121200	Strong transcription	HUES48 Cell Line	embryonic stem cell
47	chr10:96086800-96103400	Strong transcription	GM12878-XiMat	blood
48	chr10:96086800-96105400	Strong transcription	Primary T helper naive cells fromperipheralblood	blood
49	chr10:96087000-96093800	Weak transcription	Brain Hippocampus Middle	brain
50	chr10:96087200-96094000	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin

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