Variant report

Variant	rs17438706
Chromosome Location	chr10:96087056-96087057
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 53 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:48)

rs_ID	r²[population]
rs11814451	0.81[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11817642	0.82[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12217597	0.84[ASW][hapmap]
rs12255683	0.85[CEU][hapmap];0.80[GIH][hapmap];0.85[MEX][hapmap];0.93[TSI][hapmap];0.92[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12766693	1.00[MEX][hapmap];0.88[TSI][hapmap];0.83[EUR][1000 genomes]
rs12773803	0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12774398	1.00[CEU][hapmap];0.87[YRI][hapmap];0.89[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12778016	0.81[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs12780240	1.00[ASN][1000 genomes]
rs12781422	0.84[EUR][1000 genomes]
rs12781481	0.92[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12781628	0.92[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12782263	1.00[ASW][hapmap];1.00[CEU][hapmap];0.96[GIH][hapmap];1.00[MEX][hapmap];0.97[TSI][hapmap];0.89[YRI][hapmap];0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12783744	0.84[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12783751	0.84[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12785155	0.85[MEX][hapmap]
rs1334596	0.85[MEX][hapmap]
rs1678	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]
rs17438643	1.00[CEU][hapmap];1.00[YRI][hapmap];0.88[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17439123	1.00[CEU][hapmap];0.96[GIH][hapmap];1.00[MEX][hapmap];0.97[TSI][hapmap];0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17516758	1.00[ASW][hapmap];1.00[CEU][hapmap];0.88[GIH][hapmap];0.97[TSI][hapmap];0.89[YRI][hapmap];0.89[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17516904	0.84[ASW][hapmap];1.00[CEU][hapmap];0.88[GIH][hapmap];1.00[MEX][hapmap];0.97[TSI][hapmap];0.84[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17517368	0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17517515	1.00[ASW][hapmap];1.00[CEU][hapmap];0.96[GIH][hapmap];1.00[MEX][hapmap];0.81[MKK][hapmap];0.97[TSI][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]
rs17517578	0.85[CEU][hapmap];0.96[GIH][hapmap];0.85[MEX][hapmap];0.97[TSI][hapmap];0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17517669	1.00[CEU][hapmap];0.89[YRI][hapmap];0.86[AFR][1000 genomes];0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3203713	0.91[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34032820	0.85[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34053022	0.84[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34156870	1.00[ASN][1000 genomes]
rs34573359	0.80[AFR][1000 genomes];0.91[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34818536	1.00[ASN][1000 genomes]
rs34999028	0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35058175	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35084709	0.86[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35247409	0.84[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs35258481	0.85[AFR][1000 genomes];0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35348430	0.82[AFR][1000 genomes];0.92[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs35446195	0.84[EUR][1000 genomes]
rs35658839	1.00[ASN][1000 genomes]
rs4394764	0.84[GIH][hapmap];1.00[MEX][hapmap];1.00[ASN][1000 genomes]
rs57178050	0.89[AMR][1000 genomes];0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs71480900	0.80[AFR][1000 genomes];0.91[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs71482303	0.84[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs71482304	0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs71482305	0.92[AMR][1000 genomes];0.96[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:3)

SNP	Gene	Cis/trans	Tissue	Source
rs17438706	NOC3L	cis	parietal	SCAN
rs17438706	NOC3L	cis	Heart Left Ventricle	GTEx
rs17438706	C10orf62	cis	cerebellum	SCAN

Chromatin state (count:123 , 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	chr10:96069200-96089800	Weak transcription	HUVEC	blood vessel
4	chr10:96072800-96093800	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
5	chr10:96075200-96091000	Weak transcription	Right Ventricle	heart
6	chr10:96075200-96112200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
7	chr10:96075800-96087200	Weak transcription	Small Intestine	intestine
8	chr10:96076000-96089000	Weak transcription	Fetal Heart	heart
9	chr10:96076000-96095800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
10	chr10:96076400-96093600	Weak transcription	HepG2	liver
11	chr10:96076600-96090400	Weak transcription	NHDF-Ad	bronchial
12	chr10:96076600-96091000	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
13	chr10:96076600-96097000	Weak transcription	Colon Smooth Muscle	Colon
14	chr10:96077600-96100200	Strong transcription	Rectal Mucosa Donor 31	rectum
15	chr10:96078200-96121600	Weak transcription	Fetal Brain Male	brain
16	chr10:96078800-96087600	Weak transcription	Hela-S3	cervix
17	chr10:96079400-96087200	Weak transcription	Primary hematopoietic stem cells	blood
18	chr10:96079800-96090400	Weak transcription	Fetal Thymus	thymus
19	chr10:96080200-96090600	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
20	chr10:96080200-96092400	Strong transcription	Fetal Muscle Leg	muscle
21	chr10:96080200-96095000	Weak transcription	Brain Cingulate Gyrus	brain
22	chr10:96080200-96095800	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
23	chr10:96080400-96088000	Strong transcription	Sigmoid Colon	Sigmoid Colon
24	chr10:96080400-96088200	Strong transcription	A549	lung
25	chr10:96080400-96089800	Weak transcription	H1 Cell Line	embryonic stem cell
26	chr10:96080400-96090800	Weak transcription	Dnd41	blood
27	chr10:96080400-96094600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
28	chr10:96080400-96096000	Strong transcription	HMEC	breast
29	chr10:96080400-96100200	Strong transcription	Rectal Mucosa Donor 29	rectum
30	chr10:96080400-96105200	Weak transcription	iPS-15b Cell Line	embryonic stem cell
31	chr10:96080400-96121000	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
32	chr10:96080600-96088000	Strong transcription	Osteobl	bone
33	chr10:96080600-96088200	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
34	chr10:96080600-96088800	Strong transcription	Cortex derived primary cultured neurospheres	brain
35	chr10:96080600-96092400	Weak transcription	Placenta Amnion	Placenta Amnion
36	chr10:96080600-96101800	Weak transcription	Thymus	Thymus
37	chr10:96080800-96102600	Strong transcription	Primary B cells from peripheral blood	blood
38	chr10:96081000-96088400	Strong transcription	Fetal Muscle Trunk	muscle
39	chr10:96081000-96105600	Strong transcription	Duodenum Mucosa	Duodenum
40	chr10:96081000-96118200	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
41	chr10:96081200-96118400	Strong transcription	Breast Myoepithelial Primary Cells	Breast
42	chr10:96081400-96087400	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
43	chr10:96081400-96091800	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
44	chr10:96081400-96091800	Weak transcription	Primary T helper naive cells from peripheral blood	blood
45	chr10:96081600-96087200	Strong transcription	Adipose Nuclei	Adipose
46	chr10:96081600-96087400	Strong transcription	Primary hematopoietic stem cells short term culture	blood
47	chr10:96081600-96087400	Strong transcription	HSMMtube	muscle
48	chr10:96081600-96088200	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
49	chr10:96081600-96088400	Strong transcription	Ganglion Eminence derived primary cultured neurospheres	brain
50	chr10:96081600-96088400	Strong transcription	Duodenum Smooth Muscle	Duodenum

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