Variant report

Variant	rs62246641
Chromosome Location	chr3:42859440-42859441
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr3:42843227..42846088-chr3:42858547..42861083,3	K562	blood:
2	chr3:42629985..42631739-chr3:42857764..42859472,2	MCF-7	breast:
3	chr3:42695556..42698208-chr3:42859174..42860846,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000230084	Chromatin interaction
ENSG00000181061	Chromatin interaction

Extended variants
information (count: 21 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:20)

rs_ID	r²[population]
rs12488174	0.88[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs13061576	0.88[AMR][1000 genomes];0.98[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs13064320	0.88[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs13090185	0.88[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs17317763	1.00[AFR][1000 genomes];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1871121	0.85[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs2372111	0.86[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs339681	0.86[EUR][1000 genomes]
rs34336220	0.88[AMR][1000 genomes];0.98[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs34648075	0.85[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs34974363	0.88[AMR][1000 genomes];0.98[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs35488977	0.85[AMR][1000 genomes];0.98[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs35647815	0.88[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs35766391	0.88[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs35919797	0.95[AFR][1000 genomes];0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs4488806	0.88[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs62246631	0.88[AMR][1000 genomes];0.98[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs6765740	0.88[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs6799524	0.88[AMR][1000 genomes];0.98[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs7429327	0.85[AMR][1000 genomes];0.91[EUR][1000 genomes]

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

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv1847016	chr3:42855765-42880490	Enhancers Bivalent Enhancer Weak transcription Flanking Active TSS Strong transcription Genic enhancers Active TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs62246641	LOC348817	cis	intralobular white matter	BrainEAC
rs62246641	CCDC13	cis	Thyroid	GTEx
rs62246641	CCDC13-AS1	cis	Thyroid	GTEx
rs62246641	LOC348817	cis	brain	BrainEAC

Chromatin state (count:21 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:42853800-42861000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
2	chr3:42853800-42861200	Weak transcription	Fetal Intestine Large	intestine
3	chr3:42853800-42862200	Weak transcription	Fetal Intestine Small	intestine
4	chr3:42854200-42861200	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
5	chr3:42856800-42861000	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
6	chr3:42857000-42861000	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
7	chr3:42857000-42869800	Weak transcription	Colonic Mucosa	Colon
8	chr3:42857200-42860600	Weak transcription	Fetal Kidney	kidney
9	chr3:42857200-42861000	Weak transcription	Cortex derived primary cultured neurospheres	brain
10	chr3:42857400-42860800	Weak transcription	Rectal Mucosa Donor 29	rectum
11	chr3:42857400-42861000	Weak transcription	Liver	Liver
12	chr3:42857400-42861200	Weak transcription	HMEC	breast
13	chr3:42857400-42861200	Weak transcription	NHEK	skin
14	chr3:42857600-42861000	Weak transcription	Duodenum Mucosa	Duodenum
15	chr3:42857600-42861000	Weak transcription	Stomach Mucosa	stomach
16	chr3:42857600-42861400	Weak transcription	Placenta Amnion	Placenta Amnion
17	chr3:42857800-42859600	Weak transcription	HepG2	liver
18	chr3:42857800-42860800	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
19	chr3:42857800-42861000	Weak transcription	Hela-S3	cervix
20	chr3:42858600-42859600	Weak transcription	Rectal Mucosa Donor 31	rectum
21	chr3:42858600-42861200	Strong transcription	Placenta	Placenta

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