Variant report

Variant	rs62438243
Chromosome Location	chr6:73999246-73999247
allele	C/T
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	CTCF	chr6:73999237-73999309	GM10248	blood:	n/a	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr6:73997793..73999329-chr6:74000981..74003213,2	K562	blood:

Variant related genes	Relation type
EIF3EP1	TF binding region
RPSAP41	TF binding region
ENSG00000234882	Chromatin interaction

Extended variants
information (count: 35 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:33)

rs_ID	r²[population]
rs10455272	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10943084	0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10943085	1.00[AFR][1000 genomes];0.89[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10943088	0.82[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs11963438	0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12190274	0.95[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12197094	0.82[EUR][1000 genomes]
rs12199180	0.82[EUR][1000 genomes]
rs12199709	1.00[ASN][1000 genomes]
rs12199821	0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12203786	0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12207480	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12208950	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12210588	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12213765	0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12216244	0.82[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs12529651	0.93[AFR][1000 genomes];0.89[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs16883518	1.00[AFR][1000 genomes];0.89[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs16883564	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs16883571	0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35542640	0.89[AFR][1000 genomes];0.89[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs45491600	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs55810380	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs56159527	0.95[AMR][1000 genomes];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62411447	0.96[EUR][1000 genomes]
rs62411451	1.00[AFR][1000 genomes];0.89[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62438234	0.80[EUR][1000 genomes]
rs62438240	0.82[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs62438242	0.84[EUR][1000 genomes]
rs62438245	1.00[ASN][1000 genomes]
rs62440564	0.83[ASN][1000 genomes]
rs62440565	0.83[ASN][1000 genomes]
rs72947904	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	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	nsv970143	chr6:73998606-74001817	Weak transcription Strong transcription Enhancers Genic enhancers ZNF genes & repeats	TF binding region Chromatin interactive region lncRNA	14 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs62438243	EIF3EP1	cis	Skin Sun Exposed Lower leg	GTEx
rs62438243	KHDC1	cis	multi-tissue	Pritchard
rs62438243	C6orf148	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:70 , 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	chr6:73973800-74000400	Weak transcription	H9 Cell Line	embryonic stem cell
6	chr6:73974000-74000400	Weak transcription	Muscle Satellite Cultured Cells	--
7	chr6:73974000-74009000	Weak transcription	HSMM	muscle
8	chr6:73974000-74018400	Weak transcription	iPS-15b Cell Line	embryonic stem cell
9	chr6:73974400-74000400	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
10	chr6:73974400-74000400	Weak transcription	NHDF-Ad	bronchial
11	chr6:73974400-74008800	Weak transcription	NH-A	brain
12	chr6:73974400-74009400	Weak transcription	ES-I3 Cell Line	embryonic stem cell
13	chr6:73974600-74008600	Weak transcription	Brain Cingulate Gyrus	brain
14	chr6:73974800-74000400	Weak transcription	Brain Anterior Caudate	brain
15	chr6:73974800-74008600	Weak transcription	Brain Inferior Temporal Lobe	brain
16	chr6:73977400-74008800	Weak transcription	Fetal Brain Male	brain
17	chr6:73979200-74004400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
18	chr6:73983800-74018600	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
19	chr6:73984400-74000200	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
20	chr6:73984400-74018600	Weak transcription	iPS-18 Cell Line	embryonic stem cell
21	chr6:73984600-74002200	Weak transcription	Primary T cells from cord blood	blood
22	chr6:73984800-74000800	Weak transcription	HUES48 Cell Line	embryonic stem cell
23	chr6:73984800-74004400	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
24	chr6:73984800-74008600	Weak transcription	Stomach Smooth Muscle	stomach
25	chr6:73985200-74000400	Weak transcription	iPS-20b Cell Line	embryonic stem cell
26	chr6:73985200-74004600	Weak transcription	Cortex derived primary cultured neurospheres	brain
27	chr6:73985200-74008800	Weak transcription	Placenta Amnion	Placenta Amnion
28	chr6:73985400-74000000	Weak transcription	HMEC	breast
29	chr6:73985400-74000400	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
30	chr6:73985400-74000600	Weak transcription	Primary hematopoietic stem cells	blood
31	chr6:73985400-74009000	Weak transcription	H1 Cell Line	embryonic stem cell
32	chr6:73985600-74000400	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
33	chr6:73985600-74000400	Weak transcription	Brain Germinal Matrix	brain
34	chr6:73985600-74000400	Weak transcription	Fetal Muscle Leg	muscle
35	chr6:73985600-74004800	Weak transcription	HUES6 Cell Line	embryonic stem cell
36	chr6:73985600-74008800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
37	chr6:73985600-74008800	Weak transcription	Thymus	Thymus
38	chr6:73985800-74000200	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
39	chr6:73985800-74000400	Weak transcription	Fetal Muscle Trunk	muscle
40	chr6:73985800-74006800	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
41	chr6:73985800-74008800	Weak transcription	Ovary	ovary
42	chr6:73986000-74000400	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
43	chr6:73986400-74000000	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
44	chr6:73986400-74008600	Weak transcription	Fetal Brain Female	brain
45	chr6:73989000-74000000	Weak transcription	HUES64 Cell Line	embryonic stem cell
46	chr6:73989000-74017200	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
47	chr6:73989800-74008800	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
48	chr6:73990000-74003800	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
49	chr6:73991000-74000800	Weak transcription	Fetal Thymus	thymus
50	chr6:73991600-74000200	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links