Variant report

Variant	rs6662416
Chromosome Location	chr1:184631037-184631038
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr1:184595979..184598591-chr1:184630812..184634151,3	MCF-7	breast:
2	chr1:184630885..184632795-chr1:184634591..184637459,2	MCF-7	breast:
3	chr1:184610419..184613412-chr1:184629459..184632397,2	MCF-7	breast:

Extended variants
information (count: 42 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:36)

rs_ID	r²[population]
rs1061508	0.84[GIH][hapmap]
rs1062994	0.81[AFR][1000 genomes];0.82[AMR][1000 genomes]
rs10752940	0.86[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs10911631	0.81[AFR][1000 genomes];0.86[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs10911633	0.81[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs10911634	0.81[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs10911636	0.82[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs10911644	0.82[ASW][hapmap];0.91[CEU][hapmap];0.81[CHD][hapmap];0.84[GIH][hapmap];0.83[LWK][hapmap]
rs10911645	0.83[CEU][hapmap]
rs12031028	0.81[AFR][1000 genomes]
rs12071631	0.80[GIH][hapmap]
rs12124929	1.00[ASW][hapmap];0.87[CEU][hapmap];0.82[CHD][hapmap];0.89[GIH][hapmap];0.81[MEX][hapmap];0.82[TSI][hapmap];0.81[AFR][1000 genomes]
rs12131285	1.00[ASW][hapmap];0.96[CEU][hapmap];0.89[CHD][hapmap];0.82[JPT][hapmap];1.00[LWK][hapmap];0.95[MEX][hapmap];0.95[TSI][hapmap];0.81[AFR][1000 genomes];0.86[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs12133128	0.81[AFR][1000 genomes]
rs12137438	0.82[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs12184284	0.81[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs12567225	1.00[ASW][hapmap];0.91[CEU][hapmap];0.82[CHD][hapmap];0.89[GIH][hapmap];1.00[LWK][hapmap];0.95[MEX][hapmap];0.84[TSI][hapmap];0.81[AFR][1000 genomes];0.80[EUR][1000 genomes]
rs12567226	1.00[ASW][hapmap];0.91[CEU][hapmap];0.82[CHD][hapmap];0.89[GIH][hapmap];1.00[LWK][hapmap];0.95[MEX][hapmap];0.84[TSI][hapmap];0.81[AFR][1000 genomes];0.80[EUR][1000 genomes]
rs2024767	0.81[GIH][hapmap]
rs2064605	0.91[CEU][hapmap]
rs2333715	1.00[ASW][hapmap];0.91[CEU][hapmap];0.89[GIH][hapmap];0.82[JPT][hapmap];1.00[LWK][hapmap];0.95[MEX][hapmap];0.84[TSI][hapmap]
rs2877994	0.81[AFR][1000 genomes];0.84[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs3736757	0.81[GIH][hapmap]
rs4233120	0.90[AFR][1000 genomes];0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs4651230	0.82[ASW][hapmap];0.91[CEU][hapmap];0.81[CHD][hapmap];0.86[GIH][hapmap];1.00[LWK][hapmap];0.85[MEX][hapmap];0.84[TSI][hapmap]
rs481215	0.82[ASW][hapmap]
rs484847	0.82[ASW][hapmap]
rs543912	1.00[ASW][hapmap]
rs549088	0.82[ASW][hapmap]
rs641337	1.00[ASW][hapmap]
rs861578	0.81[GIH][hapmap]
rs861581	0.80[GIH][hapmap]
rs9425338	0.81[AFR][1000 genomes];0.86[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs9425340	0.86[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs9425343	0.82[ASW][hapmap];0.91[CEU][hapmap];0.81[CHD][hapmap];0.89[GIH][hapmap];0.83[LWK][hapmap];0.90[MEX][hapmap];0.84[TSI][hapmap];0.81[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs9425632	0.81[AFR][1000 genomes];0.86[AMR][1000 genomes];0.89[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:6 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv530079	chr1:183797938-184639971	Enhancers Weak transcription Strong transcription Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	21 gene(s)	inside rSNPs	diseases
2	esv2756618	chr1:184393343-184674343	Flanking Active TSS Enhancers ZNF genes & repeats Strong transcription Weak transcription Active TSS Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	10 gene(s)	inside rSNPs	diseases
3	nsv1001323	chr1:184525419-185315876	Weak transcription Active TSS Enhancers Strong transcription ZNF genes & repeats Flanking Active TSS Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	69 gene(s)	inside rSNPs	diseases
4	nsv535222	chr1:184525419-185315876	Weak transcription Enhancers Strong transcription Genic enhancers Bivalent Enhancer Active TSS Flanking Active TSS Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	69 gene(s)	inside rSNPs	diseases
5	nsv832037	chr1:184568194-184756597	Enhancers Flanking Active TSS Weak transcription Strong transcription Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	14 gene(s)	inside rSNPs	diseases
6	nsv947339	chr1:184618714-184641256	Active TSS Enhancers Flanking Active TSS Bivalent Enhancer Weak transcription Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats	Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs6662416	EDEM3	Cis_1M	lymphoblastoid	RTeQTL
rs6662416	EDEM3	cis	Esophagus Muscularis	GTEx

Chromatin state (count:31 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:184625400-184633000	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
2	chr1:184625800-184632800	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
3	chr1:184626400-184632600	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
4	chr1:184626600-184632600	Weak transcription	Brain Substantia Nigra	brain
5	chr1:184626600-184632800	Weak transcription	H1 Cell Line	embryonic stem cell
6	chr1:184626800-184632800	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
7	chr1:184626800-184633000	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
8	chr1:184627400-184632600	Weak transcription	Skeletal Muscle Female	skeletal muscle
9	chr1:184629400-184631800	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
10	chr1:184629800-184631600	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
11	chr1:184629800-184633000	Weak transcription	H9 Cell Line	embryonic stem cell
12	chr1:184629800-184633000	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
13	chr1:184630000-184631600	Enhancers	Sigmoid Colon	Sigmoid Colon
14	chr1:184630000-184633000	Weak transcription	Ovary	ovary
15	chr1:184630200-184631800	Enhancers	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
16	chr1:184630200-184632800	Weak transcription	Spleen	Spleen
17	chr1:184630400-184632600	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
18	chr1:184630600-184631400	Enhancers	iPS-15b Cell Line	embryonic stem cell
19	chr1:184630800-184631600	Enhancers	HUES6 Cell Line	embryonic stem cell
20	chr1:184630800-184631600	Enhancers	Brain Cingulate Gyrus	brain
21	chr1:184630800-184631600	Enhancers	Rectal Mucosa Donor 31	rectum
22	chr1:184630800-184632800	Weak transcription	HUES48 Cell Line	embryonic stem cell
23	chr1:184630800-184633000	Weak transcription	Right Ventricle	heart
24	chr1:184631000-184631200	Enhancers	Rectal Mucosa Donor 29	rectum
25	chr1:184631000-184631400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
26	chr1:184631000-184631400	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
27	chr1:184631000-184631400	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
28	chr1:184631000-184631400	Enhancers	Cortex derived primary cultured neurospheres	brain
29	chr1:184631000-184631800	Enhancers	A549	lung
30	chr1:184631000-184632600	Weak transcription	Brain Angular Gyrus	brain
31	chr1:184631000-184632800	Weak transcription	Placenta	Placenta

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