Variant report

Variant	rs62278843
Chromosome Location	chr3:112041382-112041383
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 70 )
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	0.95[AFR][1000 genomes];0.96[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	0.92[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1317658	0.85[AFR][1000 genomes];0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13316383	1.00[AFR][1000 genomes];0.96[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	0.86[AFR][1000 genomes];0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4507229	0.95[AFR][1000 genomes];0.94[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	0.89[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs55748364	1.00[ASN][1000 genomes]
rs55947719	0.90[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs56008438	1.00[AFR][1000 genomes];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs56065326	1.00[ASN][1000 genomes]
rs56294743	0.94[AFR][1000 genomes];0.94[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	0.89[AFR][1000 genomes];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62278768	0.89[AFR][1000 genomes];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62278769	0.87[AFR][1000 genomes];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62278770	0.88[AFR][1000 genomes];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62278771	0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6438072	1.00[ASN][1000 genomes]
rs6766013	0.93[AFR][1000 genomes];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs6775536	1.00[ASN][1000 genomes]
rs6795820	0.83[AFR][1000 genomes];0.93[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	0.84[AFR][1000 genomes];0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9816969	0.90[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	0.97[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9837134	0.94[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs9843666	0.84[AFR][1000 genomes];0.92[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs9851760	1.00[ASN][1000 genomes]
rs9853669	0.95[AFR][1000 genomes];0.94[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:2 , 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

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs62278843	C6orf106	trans	lymphoblastoid	RTeQTL

Chromatin state (count:29 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:112037600-112041600	Enhancers	Breast Myoepithelial Primary Cells	Breast
2	chr3:112038400-112041400	Enhancers	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
3	chr3:112038400-112041400	Enhancers	Fetal Adrenal Gland	Adrenal Gland
4	chr3:112038400-112041400	Enhancers	Fetal Lung	lung
5	chr3:112038400-112045200	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
6	chr3:112040000-112041400	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
7	chr3:112040000-112041400	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
8	chr3:112040000-112041600	Enhancers	iPS-15b Cell Line	embryonic stem cell
9	chr3:112040200-112041400	Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
10	chr3:112040200-112041400	Enhancers	Cortex derived primary cultured neurospheres	brain
11	chr3:112040400-112041400	Enhancers	Primary hematopoietic stem cells	blood
12	chr3:112040400-112041600	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
13	chr3:112040400-112042000	Enhancers	HUES48 Cell Line	embryonic stem cell
14	chr3:112040600-112041400	Enhancers	H1 Cell Line	embryonic stem cell
15	chr3:112040600-112041400	Flanking Active TSS	HUES64 Cell Line	embryonic stem cell
16	chr3:112040600-112041400	Active TSS	Fetal Kidney	kidney
17	chr3:112040800-112041400	Enhancers	ES-WA7 Cell Line	embryonic stem cell
18	chr3:112040800-112041400	Enhancers	H9 Cell Line	embryonic stem cell
19	chr3:112040800-112041400	Enhancers	iPS DF 6.9 Cell Line	embryonic stem cell
20	chr3:112040800-112041400	Enhancers	Gastric	stomach
21	chr3:112041000-112041400	Enhancers	HUES6 Cell Line	embryonic stem cell
22	chr3:112041000-112042400	Weak transcription	Left Ventricle	heart
23	chr3:112041200-112041400	Enhancers	ES-I3 Cell Line	embryonic stem cell
24	chr3:112041200-112041400	Enhancers	iPS-18 Cell Line	embryonic stem cell
25	chr3:112041200-112041400	Enhancers	iPS-20b Cell Line	embryonic stem cell
26	chr3:112041200-112041400	Enhancers	Duodenum Mucosa	Duodenum
27	chr3:112041200-112041400	Enhancers	Fetal Intestine Small	intestine
28	chr3:112041200-112041400	Flanking Active TSS	Pancreatic Islets	Pancreatic Islet
29	chr3:112041200-112041400	Enhancers	Rectal Mucosa Donor 29	rectum

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