Variant report

Variant	rs12780491
Chromosome Location	chr10:96121022-96121023
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr10:96120934..96124258-chr10:96160439..96165957,6	MCF-7	breast:
2	chr10:96120995..96123181-chr10:96304440..96307322,3	MCF-7	breast:
3	chr10:96121005..96123981-chr10:96160609..96162843,2	K562	blood:

Variant related genes	Relation type
ENSG00000119969	Chromatin interaction
ENSG00000108239	Chromatin interaction

Extended variants
information (count: 53 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:49)

rs_ID	r²[population]
rs10509670	0.93[MEX][hapmap]
rs10509671	0.81[CEU][hapmap];0.87[GIH][hapmap];0.93[MEX][hapmap]
rs10509672	1.00[CHB][hapmap];1.00[JPT][hapmap];0.97[ASN][1000 genomes]
rs10786161	0.85[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs10882416	0.83[TSI][hapmap]
rs10882422	0.93[MEX][hapmap]
rs10882424	0.81[CEU][hapmap];0.82[GIH][hapmap];0.93[MEX][hapmap];0.88[TSI][hapmap];0.83[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs10882430	0.83[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs10882435	1.00[CEU][hapmap];0.87[YRI][hapmap];0.83[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs10882436	1.00[CEU][hapmap];0.86[YRI][hapmap];0.85[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs10882437	0.81[CEU][hapmap];0.82[GIH][hapmap];1.00[MEX][hapmap];0.93[TSI][hapmap];0.85[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs11187850	0.93[MEX][hapmap]
rs11187851	0.81[CEU][hapmap]
rs11187853	0.81[EUR][1000 genomes]
rs11187869	0.89[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs11187876	0.83[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs11187881	0.81[CEU][hapmap];0.83[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs11187893	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[GIH][hapmap];0.93[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];0.95[TSI][hapmap];1.00[YRI][hapmap];0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs11187894	0.95[CEU][hapmap];1.00[YRI][hapmap];0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs11187899	0.85[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs11187900	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs11187901	0.81[CEU][hapmap];0.82[GIH][hapmap];1.00[MEX][hapmap];0.93[TSI][hapmap];0.85[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs11187906	0.95[ASN][1000 genomes]
rs11187907	1.00[CHB][hapmap];0.95[ASN][1000 genomes]
rs11558740	0.89[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs12217597	0.89[CEU][hapmap];1.00[GIH][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.96[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs12219063	0.88[AMR][1000 genomes];0.94[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12220125	0.81[CEU][hapmap];0.81[EUR][1000 genomes]
rs12263737	0.93[MEX][hapmap];0.83[TSI][hapmap]
rs12773229	0.83[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs12781451	1.00[CEU][hapmap];0.89[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs2274223	0.93[MEX][hapmap]
rs3765524	0.81[CEU][hapmap];0.93[MEX][hapmap];0.83[TSI][hapmap]
rs3781264	0.81[CEU][hapmap];0.90[GIH][hapmap];0.93[MEX][hapmap];0.81[TSI][hapmap];0.81[AMR][1000 genomes]
rs3818432	0.81[CEU][hapmap];0.93[MEX][hapmap];0.83[TSI][hapmap];0.80[EUR][1000 genomes]
rs6583937	0.81[CEU][hapmap];0.83[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs7074125	0.83[EUR][1000 genomes]
rs7077192	0.86[AMR][1000 genomes];0.93[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7081265	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.82[JPT][hapmap];0.93[MEX][hapmap];0.97[TSI][hapmap];0.88[AMR][1000 genomes];0.94[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7084339	0.93[MEX][hapmap]
rs7084988	0.81[CEU][hapmap];0.85[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs7085378	0.81[CEU][hapmap];0.85[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs7092226	0.93[MEX][hapmap];0.83[TSI][hapmap]
rs7094783	0.81[EUR][1000 genomes]
rs7096037	0.83[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs7100430	0.80[CEU][hapmap];0.82[GIH][hapmap];1.00[MEX][hapmap];0.93[TSI][hapmap];0.85[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs7100870	0.87[AFR][1000 genomes];0.90[AMR][1000 genomes];0.90[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7101207	0.97[ASN][1000 genomes]
rs7908638	0.81[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	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
2	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
3	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
4	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:2)

SNP	Gene	Cis/trans	Tissue	Source
rs12780491	NOC3L	cis	Heart Left Ventricle	GTEx
rs12780491	NOC3L	cis	parietal	SCAN

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr10:96078200-96121600	Weak transcription	Fetal Brain Male	brain
2	chr10:96085000-96122200	Weak transcription	Gastric	stomach
3	chr10:96086200-96121200	Strong transcription	HUES48 Cell Line	embryonic stem cell
4	chr10:96087600-96121200	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
5	chr10:96088200-96121800	Weak transcription	Aorta	Aorta
6	chr10:96100000-96121800	Weak transcription	Colonic Mucosa	Colon
7	chr10:96108400-96121800	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
8	chr10:96110400-96121800	Weak transcription	Spleen	Spleen
9	chr10:96110400-96122000	Weak transcription	Pancreas	Pancrea
10	chr10:96111600-96121200	Weak transcription	iPS-15b Cell Line	embryonic stem cell
11	chr10:96111600-96121800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
12	chr10:96111600-96121800	Weak transcription	Lung	lung
13	chr10:96112800-96121400	Weak transcription	Right Ventricle	heart
14	chr10:96113400-96122000	Weak transcription	Esophagus	oesophagus
15	chr10:96114600-96121600	Weak transcription	Placenta Amnion	Placenta Amnion
16	chr10:96117400-96121600	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
17	chr10:96117600-96121400	Weak transcription	Stomach Smooth Muscle	stomach
18	chr10:96117800-96121400	Weak transcription	Fetal Kidney	kidney
19	chr10:96118000-96121200	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
20	chr10:96118200-96121800	Weak transcription	Fetal Thymus	thymus
21	chr10:96118600-96121400	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
22	chr10:96118800-96121200	Weak transcription	Monocytes-CD14+_RO01746	blood
23	chr10:96118800-96121400	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
24	chr10:96118800-96121800	Weak transcription	Placenta	Placenta
25	chr10:96118800-96122000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
26	chr10:96119000-96121800	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
27	chr10:96119200-96122000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
28	chr10:96119200-96122200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
29	chr10:96119400-96121400	Weak transcription	H1 Cell Line	embryonic stem cell
30	chr10:96119400-96121400	Weak transcription	Primary monocytes fromperipheralblood	blood
31	chr10:96119400-96121800	Enhancers	Ovary	ovary
32	chr10:96119800-96121800	Weak transcription	Fetal Muscle Trunk	muscle
33	chr10:96120400-96121400	Enhancers	Primary T regulatory cells fromperipheralblood	blood
34	chr10:96120600-96121200	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
35	chr10:96120600-96121200	Enhancers	Primary T cells fromperipheralblood	blood
36	chr10:96120600-96121200	Genic enhancers	Fetal Muscle Leg	muscle
37	chr10:96120600-96121200	Enhancers	Left Ventricle	heart
38	chr10:96120600-96121400	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
39	chr10:96120600-96121400	Enhancers	Primary T cells from cord blood	blood
40	chr10:96120600-96121400	Enhancers	Small Intestine	intestine
41	chr10:96120600-96121800	Enhancers	Fetal Adrenal Gland	Adrenal Gland
42	chr10:96120800-96121200	Enhancers	Primary T helper cells fromperipheralblood	blood
43	chr10:96120800-96121200	Transcr. at gene 5' and 3'	Foreskin Keratinocyte Primary Cells skin03	Skin
44	chr10:96120800-96121200	Flanking Active TSS	NHEK	skin
45	chr10:96120800-96121400	Transcr. at gene 5' and 3'	NH-A	brain
46	chr10:96120800-96121600	Enhancers	Primary T helper naive cells fromperipheralblood	blood
47	chr10:96120800-96121800	Enhancers	Primary hematopoietic stem cells	blood
48	chr10:96120800-96121800	Flanking Active TSS	HMEC	breast
49	chr10:96121000-96121200	Genic enhancers	ES-I3 Cell Line	embryonic stem cell
50	chr10:96121000-96121200	Flanking Active TSS	H9 Cell Line	embryonic stem cell

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