Variant report

Variant	rs12216244
Chromosome Location	chr6:73986783-73986784
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 31 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:28)

rs_ID	r²[population]
rs10455272	0.82[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs10943084	0.85[MEX][hapmap]
rs10943085	0.84[EUR][1000 genomes]
rs10943088	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10943089	1.00[CEU][hapmap]
rs12207480	0.82[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs12208950	0.82[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs12210588	0.82[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs12213765	0.84[EUR][1000 genomes]
rs12526214	0.90[EUR][1000 genomes]
rs12529651	0.84[EUR][1000 genomes]
rs12529864	0.90[EUR][1000 genomes]
rs16883489	1.00[CHB][hapmap]
rs16883518	0.83[EUR][1000 genomes]
rs16883564	0.82[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs16883571	0.85[MEX][hapmap];0.81[EUR][1000 genomes]
rs16883573	1.00[CEU][hapmap];1.00[GIH][hapmap];1.00[TSI][hapmap];0.89[EUR][1000 genomes]
rs35542640	0.84[EUR][1000 genomes]
rs45491600	0.82[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs4708044	0.90[EUR][1000 genomes]
rs55810380	0.82[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs56725125	0.90[EUR][1000 genomes]
rs62411447	0.81[EUR][1000 genomes]
rs62411451	0.84[EUR][1000 genomes]
rs62438234	0.92[AFR][1000 genomes];0.88[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62438240	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs62438242	0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs62438243	0.82[AMR][1000 genomes];0.84[EUR][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	esv3410973	chr6:73716033-74419545	Active TSS Bivalent Enhancer Flanking Active TSS Weak transcription Enhancers Strong transcription Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats Genic enhancers Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	191 gene(s)	inside rSNPs	diseases
2	nsv1022151	chr6:73876795-73996828	Weak transcription Active TSS Flanking Active TSS Enhancers Strong transcription Genic enhancers Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	23 gene(s)	inside rSNPs	diseases
3	nsv538304	chr6:73876795-73996828	Flanking Active TSS Weak transcription Genic enhancers Enhancers Strong transcription Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	23 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs12216244	EIF3EP1	cis	Skin Sun Exposed Lower leg	GTEx
rs12216244	C6orf148	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:79 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:73973400-74000400	Weak transcription	Aorta	Aorta
2	chr6:73973600-74018600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
3	chr6:73973600-74018600	Weak transcription	A549	lung
4	chr6:73973600-74018800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
5	chr6:73973800-73995600	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
6	chr6:73973800-73995600	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
7	chr6:73973800-74000400	Weak transcription	H9 Cell Line	embryonic stem cell
8	chr6:73974000-73995600	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
9	chr6:73974000-74000400	Weak transcription	Muscle Satellite Cultured Cells	--
10	chr6:73974000-74009000	Weak transcription	HSMM	muscle
11	chr6:73974000-74018400	Weak transcription	iPS-15b Cell Line	embryonic stem cell
12	chr6:73974200-73992600	Weak transcription	Colon Smooth Muscle	Colon
13	chr6:73974400-73986800	Weak transcription	Primary T helper cells fromperipheralblood	blood
14	chr6:73974400-73986800	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
15	chr6:73974400-73986800	Weak transcription	Spleen	Spleen
16	chr6:73974400-73987000	Weak transcription	Primary B cells from cord blood	blood
17	chr6:73974400-74000400	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
18	chr6:73974400-74000400	Weak transcription	NHDF-Ad	bronchial
19	chr6:73974400-74008800	Weak transcription	NH-A	brain
20	chr6:73974400-74009400	Weak transcription	ES-I3 Cell Line	embryonic stem cell
21	chr6:73974600-73987000	Weak transcription	Primary T helper cells PMA-I stimulated	--
22	chr6:73974600-73992600	Weak transcription	Brain Angular Gyrus	brain
23	chr6:73974600-74008600	Weak transcription	Brain Cingulate Gyrus	brain
24	chr6:73974800-73988400	Weak transcription	Brain Hippocampus Middle	brain
25	chr6:73974800-73992000	Weak transcription	GM12878-XiMat	blood
26	chr6:73974800-73994400	Weak transcription	NHLF	lung
27	chr6:73974800-73995600	Weak transcription	Hela-S3	cervix
28	chr6:73974800-74000400	Weak transcription	Brain Anterior Caudate	brain
29	chr6:73974800-74008600	Weak transcription	Brain Inferior Temporal Lobe	brain
30	chr6:73977400-74008800	Weak transcription	Fetal Brain Male	brain
31	chr6:73978000-73986800	Strong transcription	Breast Myoepithelial Primary Cells	Breast
32	chr6:73979000-73991800	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
33	chr6:73979200-74004400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
34	chr6:73980600-73991000	Strong transcription	Fetal Stomach	stomach
35	chr6:73982400-73987200	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
36	chr6:73982400-73988600	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
37	chr6:73983800-74018600	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
38	chr6:73984400-74000200	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
39	chr6:73984400-74018600	Weak transcription	iPS-18 Cell Line	embryonic stem cell
40	chr6:73984600-73992400	Weak transcription	K562	blood
41	chr6:73984600-74002200	Weak transcription	Primary T cells from cord blood	blood
42	chr6:73984800-73988800	Weak transcription	Fetal Lung	lung
43	chr6:73984800-73989400	Weak transcription	NHEK	skin
44	chr6:73984800-74000800	Weak transcription	HUES48 Cell Line	embryonic stem cell
45	chr6:73984800-74004400	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
46	chr6:73984800-74008600	Weak transcription	Stomach Smooth Muscle	stomach
47	chr6:73985200-73988400	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
48	chr6:73985200-74000400	Weak transcription	iPS-20b Cell Line	embryonic stem cell
49	chr6:73985200-74004600	Weak transcription	Cortex derived primary cultured neurospheres	brain
50	chr6:73985200-74008800	Weak transcription	Placenta Amnion	Placenta Amnion

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