Variant report

Variant	rs62278769
Chromosome Location	chr3:112027201-112027202
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 71 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:68)

rs_ID	r²[population]
rs10804498	1.00[ASN][1000 genomes]
rs10934163	1.00[ASN][1000 genomes]
rs10934164	1.00[ASN][1000 genomes]
rs10934165	1.00[ASN][1000 genomes]
rs11709101	1.00[ASN][1000 genomes]
rs11717777	1.00[ASN][1000 genomes]
rs11720514	1.00[ASN][1000 genomes]
rs11923402	0.83[AFR][1000 genomes];0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12497979	1.00[ASN][1000 genomes]
rs13084103	1.00[ASN][1000 genomes]
rs1317295	0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1317658	0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13316383	0.87[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1492479	1.00[ASN][1000 genomes]
rs17513880	1.00[ASN][1000 genomes]
rs2399419	0.80[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2633546	1.00[ASN][1000 genomes]
rs2683891	1.00[ASN][1000 genomes]
rs2683892	1.00[ASN][1000 genomes]
rs28615303	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4507229	0.87[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4622877	1.00[ASN][1000 genomes]
rs4682393	1.00[ASN][1000 genomes]
rs4682400	0.86[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs55748364	1.00[ASN][1000 genomes]
rs55947719	0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs56008438	0.87[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs56065326	1.00[ASN][1000 genomes]
rs56294743	0.93[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs56364691	1.00[ASN][1000 genomes]
rs56404254	1.00[ASN][1000 genomes]
rs57998879	1.00[ASN][1000 genomes]
rs60949597	1.00[ASN][1000 genomes]
rs62262366	1.00[ASN][1000 genomes]
rs62262408	1.00[ASN][1000 genomes]
rs62262411	1.00[ASN][1000 genomes]
rs62264125	0.81[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62264128	1.00[ASN][1000 genomes]
rs62276848	1.00[ASN][1000 genomes]
rs62278760	1.00[ASN][1000 genomes]
rs62278765	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62278768	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62278770	0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62278771	0.83[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62278843	0.87[AFR][1000 genomes];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6438072	1.00[ASN][1000 genomes]
rs6766013	0.81[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs6775536	1.00[ASN][1000 genomes]
rs6795820	0.83[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73223638	1.00[ASN][1000 genomes]
rs7609904	1.00[ASN][1000 genomes]
rs7612748	1.00[ASN][1000 genomes]
rs7621431	1.00[ASN][1000 genomes]
rs7631673	1.00[ASN][1000 genomes]
rs7636107	1.00[ASN][1000 genomes]
rs7650962	1.00[ASN][1000 genomes]
rs7651121	1.00[ASN][1000 genomes]
rs9810421	0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9816969	0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9818407	0.80[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9823824	1.00[ASN][1000 genomes]
rs9829698	0.90[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9837134	0.92[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs9843666	0.94[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs9851760	1.00[ASN][1000 genomes]
rs9853669	0.83[AFR][1000 genomes];0.92[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9855755	1.00[ASN][1000 genomes]
rs9871088	1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv10307	chr3:111903974-112087686	Enhancers Active TSS Weak transcription Flanking Active TSS Strong transcription Genic enhancers Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
2	nsv3949	chr3:111998512-112044060	Enhancers Weak transcription Active TSS Flanking Active TSS ZNF genes & repeats Strong transcription Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
3	nsv967052	chr3:112020436-112027937	Flanking Active TSS Active TSS Enhancers Weak transcription Transcr. at gene 5' and 3' ZNF genes & repeats Genic enhancers	TF binding region CpG island lncRNA	2 gene(s)	inside rSNPs	n/a

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs62278769	C6orf106	trans	lymphoblastoid	RTeQTL

Chromatin state (count:36 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:112024000-112028800	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
2	chr3:112025200-112034600	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
3	chr3:112026200-112027600	Enhancers	Breast Myoepithelial Primary Cells	Breast
4	chr3:112026400-112027400	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
5	chr3:112026400-112027600	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
6	chr3:112026400-112027600	Enhancers	Cortex derived primary cultured neurospheres	brain
7	chr3:112026400-112027600	Enhancers	Fetal Adrenal Gland	Adrenal Gland
8	chr3:112026600-112027400	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
9	chr3:112026600-112028400	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
10	chr3:112026800-112027400	Enhancers	Placenta	Placenta
11	chr3:112026800-112027600	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
12	chr3:112027000-112027400	Enhancers	ES-WA7 Cell Line	embryonic stem cell
13	chr3:112027000-112027400	Enhancers	H1 Cell Line	embryonic stem cell
14	chr3:112027000-112027400	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
15	chr3:112027000-112027400	Enhancers	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
16	chr3:112027000-112027400	Enhancers	H9 Cell Line	embryonic stem cell
17	chr3:112027000-112027400	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
18	chr3:112027000-112027400	Enhancers	HUES48 Cell Line	embryonic stem cell
19	chr3:112027000-112027400	Enhancers	HUES6 Cell Line	embryonic stem cell
20	chr3:112027000-112027400	Flanking Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
21	chr3:112027000-112027400	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
22	chr3:112027000-112027400	Enhancers	Brain Substantia Nigra	brain
23	chr3:112027000-112027400	Enhancers	Fetal Thymus	thymus
24	chr3:112027000-112027400	Enhancers	Ovary	ovary
25	chr3:112027000-112027400	Enhancers	Right Atrium	heart
26	chr3:112027000-112027400	Enhancers	HMEC	breast
27	chr3:112027000-112027600	Enhancers	ES-I3 Cell Line	embryonic stem cell
28	chr3:112027000-112027600	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
29	chr3:112027000-112027600	Enhancers	iPS-15b Cell Line	embryonic stem cell
30	chr3:112027000-112027600	Enhancers	iPS-18 Cell Line	embryonic stem cell
31	chr3:112027000-112027600	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
32	chr3:112027000-112028000	Weak transcription	Pancreatic Islets	Pancreatic Islet
33	chr3:112027200-112027400	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
34	chr3:112027200-112027400	Flanking Active TSS	IMR90 fetal lung fibroblasts Cell Line	lung
35	chr3:112027200-112027400	Enhancers	NH-A	brain
36	chr3:112027200-112027600	Enhancers	iPS-20b Cell Line	embryonic stem cell

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