Variant report

Variant	rs12781451
Chromosome Location	chr10:96083920-96083921
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	POLR2A	chr10:96083522-96084145	HepG2	liver:	n/a	n/a
2	POLR2A	chr10:96083840-96084204	A549	lung:	n/a	n/a

Variant related genes	Relation type
PLCE1	TF binding region

Extended variants
information (count: 75 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:70)

rs_ID	r²[population]
rs10509671	0.81[CEU][hapmap];0.86[CHB][hapmap];1.00[JPT][hapmap];0.88[AMR][1000 genomes];0.81[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs10786161	0.82[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs10882416	0.85[EUR][1000 genomes]
rs10882424	0.81[CEU][hapmap];0.86[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs10882430	0.86[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs10882435	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs10882436	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs10882437	0.81[CEU][hapmap];0.82[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs11187837	0.86[CHB][hapmap];1.00[JPT][hapmap];0.84[ASN][1000 genomes]
rs11187840	0.89[ASN][1000 genomes]
rs11187842	0.86[CHB][hapmap];1.00[JPT][hapmap];0.89[ASN][1000 genomes]
rs11187845	0.85[CHB][hapmap];1.00[JPT][hapmap];0.89[ASN][1000 genomes]
rs11187847	0.86[CHB][hapmap];1.00[JPT][hapmap];0.88[ASN][1000 genomes]
rs11187850	0.81[AMR][1000 genomes]
rs11187851	0.82[CEU][hapmap];0.85[CHB][hapmap];1.00[JPT][hapmap];0.90[AMR][1000 genomes];0.82[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs11187852	0.86[CHB][hapmap];1.00[JPT][hapmap];0.89[ASN][1000 genomes]
rs11187853	0.81[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs11187856	0.86[ASN][1000 genomes]
rs11187863	1.00[CHB][hapmap];1.00[JPT][hapmap];0.99[ASN][1000 genomes]
rs11187864	1.00[CHB][hapmap];0.91[JPT][hapmap];0.99[ASN][1000 genomes]
rs11187866	1.00[CHB][hapmap];1.00[JPT][hapmap];0.99[ASN][1000 genomes]
rs11187869	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs11187870	1.00[CHB][hapmap];1.00[JPT][hapmap];0.97[ASN][1000 genomes]
rs11187876	0.86[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs11187877	0.96[ASN][1000 genomes]
rs11187881	0.82[CEU][hapmap];0.86[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs11187882	0.93[ASN][1000 genomes]
rs11187883	1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[ASN][1000 genomes]
rs11187890	0.96[ASN][1000 genomes]
rs11187893	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs11187894	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs11187895	1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[ASN][1000 genomes]
rs11187897	1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[ASN][1000 genomes]
rs11187899	0.89[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs11187900	0.89[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs11187901	0.81[CEU][hapmap];0.82[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs11558740	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12217597	0.89[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[YRI][hapmap];0.93[AMR][1000 genomes];0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12217792	0.86[CHB][hapmap];1.00[JPT][hapmap];0.88[ASN][1000 genomes]
rs12219063	0.91[EUR][1000 genomes]
rs12220091	0.89[ASN][1000 genomes]
rs12220125	0.82[CEU][hapmap];0.85[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs12263737	0.85[EUR][1000 genomes]
rs12773229	0.80[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs12780491	1.00[CEU][hapmap];0.89[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs17109875	0.86[CHB][hapmap];1.00[JPT][hapmap];0.81[ASN][1000 genomes]
rs3740359	1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[ASN][1000 genomes]
rs3740360	0.85[CHB][hapmap];1.00[JPT][hapmap];0.84[ASN][1000 genomes]
rs3740365	0.86[CHB][hapmap];1.00[JPT][hapmap];0.88[ASN][1000 genomes]
rs3765524	0.81[CEU][hapmap];0.85[EUR][1000 genomes]
rs3781264	0.81[CEU][hapmap];0.86[CHB][hapmap];1.00[JPT][hapmap];0.89[YRI][hapmap];0.89[AFR][1000 genomes];0.91[AMR][1000 genomes];0.82[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs3781266	0.86[CHB][hapmap];1.00[JPT][hapmap];0.89[ASN][1000 genomes]
rs3818432	0.81[CEU][hapmap];0.86[EUR][1000 genomes]
rs6583935	0.83[JPT][hapmap]
rs6583937	0.81[CEU][hapmap];0.86[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs7074125	0.86[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs7077192	0.89[EUR][1000 genomes]
rs7081265	0.95[CEU][hapmap];0.91[EUR][1000 genomes]
rs7084988	0.82[CEU][hapmap];0.81[JPT][hapmap];0.82[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs7085378	0.82[CEU][hapmap];0.82[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs7094783	0.81[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs7096037	0.86[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs7096678	0.90[AMR][1000 genomes];0.81[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs7096883	0.89[ASN][1000 genomes]
rs7100430	0.80[CEU][hapmap];0.82[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs7100626	0.89[ASN][1000 genomes]
rs7100870	0.87[EUR][1000 genomes]
rs752140	0.89[ASN][1000 genomes]
rs753724	0.86[CHB][hapmap];1.00[JPT][hapmap];0.89[ASN][1000 genomes]
rs7908638	0.81[AMR][1000 genomes];0.86[EUR][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
rs12781451	NOC3L	cis	Heart Left Ventricle	GTEx

Chromatin state (count:121 , 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	chr10:96067400-96084400	Weak transcription	Pancreatic Islets	Pancreatic Islet
4	chr10:96069200-96089800	Weak transcription	HUVEC	blood vessel
5	chr10:96072800-96093800	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
6	chr10:96073200-96084200	Weak transcription	Brain Germinal Matrix	brain
7	chr10:96073800-96084000	Weak transcription	Ovary	ovary
8	chr10:96074000-96084200	Weak transcription	Gastric	stomach
9	chr10:96075200-96091000	Weak transcription	Right Ventricle	heart
10	chr10:96075200-96112200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
11	chr10:96075800-96087200	Weak transcription	Small Intestine	intestine
12	chr10:96076000-96089000	Weak transcription	Fetal Heart	heart
13	chr10:96076000-96095800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
14	chr10:96076400-96093600	Weak transcription	HepG2	liver
15	chr10:96076600-96084400	Weak transcription	NHLF	lung
16	chr10:96076600-96090400	Weak transcription	NHDF-Ad	bronchial
17	chr10:96076600-96091000	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
18	chr10:96076600-96097000	Weak transcription	Colon Smooth Muscle	Colon
19	chr10:96077600-96100200	Strong transcription	Rectal Mucosa Donor 31	rectum
20	chr10:96078200-96121600	Weak transcription	Fetal Brain Male	brain
21	chr10:96078800-96087600	Weak transcription	Hela-S3	cervix
22	chr10:96079400-96087200	Weak transcription	Primary hematopoietic stem cells	blood
23	chr10:96079800-96090400	Weak transcription	Fetal Thymus	thymus
24	chr10:96080200-96087000	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
25	chr10:96080200-96090600	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
26	chr10:96080200-96092400	Strong transcription	Fetal Muscle Leg	muscle
27	chr10:96080200-96095000	Weak transcription	Brain Cingulate Gyrus	brain
28	chr10:96080200-96095800	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
29	chr10:96080400-96084200	Weak transcription	Primary T cells fromperipheralblood	blood
30	chr10:96080400-96088000	Strong transcription	Sigmoid Colon	Sigmoid Colon
31	chr10:96080400-96088200	Strong transcription	A549	lung
32	chr10:96080400-96089800	Weak transcription	H1 Cell Line	embryonic stem cell
33	chr10:96080400-96090800	Weak transcription	Dnd41	blood
34	chr10:96080400-96094600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
35	chr10:96080400-96096000	Strong transcription	HMEC	breast
36	chr10:96080400-96100200	Strong transcription	Rectal Mucosa Donor 29	rectum
37	chr10:96080400-96105200	Weak transcription	iPS-15b Cell Line	embryonic stem cell
38	chr10:96080400-96121000	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
39	chr10:96080600-96084000	Weak transcription	Liver	Liver
40	chr10:96080600-96084600	Strong transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
41	chr10:96080600-96088000	Strong transcription	Osteobl	bone
42	chr10:96080600-96088200	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
43	chr10:96080600-96088800	Strong transcription	Cortex derived primary cultured neurospheres	brain
44	chr10:96080600-96092400	Weak transcription	Placenta Amnion	Placenta Amnion
45	chr10:96080600-96101800	Weak transcription	Thymus	Thymus
46	chr10:96080800-96085800	Strong transcription	GM12878-XiMat	blood
47	chr10:96080800-96102600	Strong transcription	Primary B cells from peripheral blood	blood
48	chr10:96081000-96085200	Strong transcription	Fetal Stomach	stomach
49	chr10:96081000-96086600	Strong transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
50	chr10:96081000-96088400	Strong transcription	Fetal Muscle Trunk	muscle

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