Variant report

Variant	rs9843666
Chromosome Location	chr3:112018769-112018770
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	E2F4	chr3:112018428-112018908	MCF10A-Er-Src	breast:	n/a	n/a

Variant related genes	Relation type
ENSG00000239482	TF binding region

Extended variants
information (count: 31 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:29)

rs_ID	r²[population]
rs11923402	0.90[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs13090060	1.00[JPT][hapmap]
rs1317295	0.92[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs1317658	0.96[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs13316383	0.84[AFR][1000 genomes];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs2399422	1.00[JPT][hapmap];0.91[ASN][1000 genomes]
rs28615303	0.82[AFR][1000 genomes];0.94[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs4507229	0.89[AFR][1000 genomes];0.94[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs4682400	0.84[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs55947719	0.90[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs56008438	0.84[AFR][1000 genomes];0.94[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs56294743	0.94[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs59251107	0.90[ASN][1000 genomes]
rs59444768	0.90[ASN][1000 genomes]
rs62278765	0.94[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs62278768	0.94[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs62278769	0.94[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs62278770	0.94[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs62278771	0.94[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs62278843	0.84[AFR][1000 genomes];0.92[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs6766013	0.82[AFR][1000 genomes];0.96[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs6795820	0.94[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs72952417	0.81[ASN][1000 genomes]
rs7637088	1.00[JPT][hapmap];0.91[ASN][1000 genomes]
rs9810421	0.95[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs9816969	0.90[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs9829698	0.86[AFR][1000 genomes];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs9837134	0.89[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs9853669	0.89[AMR][1000 genomes];0.96[EUR][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
rs9843666	C6orf106	trans	lymphoblastoid	RTeQTL

Chromatin state (count:32 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:112013000-112021400	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
2	chr3:112013200-112020200	Weak transcription	iPS-20b Cell Line	embryonic stem cell
3	chr3:112013200-112021000	Weak transcription	Thymus	Thymus
4	chr3:112013200-112021400	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
5	chr3:112013400-112021000	Weak transcription	Breast Myoepithelial Primary Cells	Breast
6	chr3:112013400-112022200	Weak transcription	Monocytes-CD14+_RO01746	blood
7	chr3:112016400-112020800	Weak transcription	iPS-18 Cell Line	embryonic stem cell
8	chr3:112016600-112022000	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
9	chr3:112016600-112022400	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
10	chr3:112017000-112021600	Weak transcription	Fetal Brain Male	brain
11	chr3:112017000-112022200	Weak transcription	Primary T cells from cord blood	blood
12	chr3:112017200-112022000	Weak transcription	Pancreatic Islets	Pancreatic Islet
13	chr3:112017600-112022000	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
14	chr3:112017600-112022200	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
15	chr3:112017800-112020800	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
16	chr3:112017800-112021000	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
17	chr3:112017800-112021800	Weak transcription	Primary B cells from cord blood	blood
18	chr3:112017800-112022000	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
19	chr3:112017800-112022200	Weak transcription	Primary T killer memory cells from peripheral blood	blood
20	chr3:112018000-112019400	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
21	chr3:112018000-112020600	Weak transcription	Fetal Thymus	thymus
22	chr3:112018000-112021200	Weak transcription	Primary hematopoietic stem cells	blood
23	chr3:112018000-112021800	Weak transcription	Primary B cells from peripheral blood	blood
24	chr3:112018000-112021800	Weak transcription	Primary T cells fromperipheralblood	blood
25	chr3:112018000-112021800	Weak transcription	Primary T helper cells fromperipheralblood	blood
26	chr3:112018000-112022000	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
27	chr3:112018000-112022000	Weak transcription	Primary T helper naive cells from peripheral blood	blood
28	chr3:112018000-112022000	Weak transcription	Primary T helper cells PMA-I stimulated	--
29	chr3:112018000-112022000	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
30	chr3:112018000-112022200	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
31	chr3:112018400-112021000	Weak transcription	GM12878-XiMat	blood
32	chr3:112018600-112021000	Weak transcription	Esophagus	oesophagus

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