Variant report

Variant	rs17317763
Chromosome Location	chr3:42857757-42857758
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	STAT3	chr3:42857475-42857784	MCF10A-Er-Src	breast:	n/a	n/a
2	KAP1	chr3:42856326-42857806	U2OS	brain:	n/a	n/a
3	KAP1	chr3:42856175-42857851	HEK293	kidney:	n/a	n/a
4	STAT3	chr3:42857466-42857849	MCF10A-Er-Src	breast:	n/a	n/a
5	ARID3A	chr3:42857753-42857998	HepG2	liver:	n/a	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr3:42842006..42848504-chr3:42854036..42858354,7	K562	blood:
2	chr3:42841845..42845236-chr3:42855285..42858253,3	K562	blood:

Variant related genes	Relation type
ACKR2	TF binding region
ENSG00000144648	Chromatin interaction
ENSG00000181061	Chromatin interaction

Extended variants
information (count: 28 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:27)

rs_ID	r²[population]
rs12488174	0.91[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs12490743	0.85[CEU][hapmap]
rs12492886	0.85[CEU][hapmap]
rs12495805	0.85[CEU][hapmap]
rs13061576	1.00[CEU][hapmap];0.91[AMR][1000 genomes];0.98[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs13064320	0.91[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs13085272	0.85[CEU][hapmap]
rs13090185	1.00[CEU][hapmap];0.91[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs13095730	0.85[CEU][hapmap]
rs1871121	0.88[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs2372111	0.90[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs339681	0.93[CEU][hapmap];0.87[EUR][1000 genomes]
rs34336220	0.91[AMR][1000 genomes];0.98[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs34648075	0.88[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs34974363	0.91[AMR][1000 genomes];0.98[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs35488977	0.88[AMR][1000 genomes];0.98[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs35647815	0.91[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs35766391	0.91[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs35919797	0.95[AFR][1000 genomes];0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs3912102	0.85[CEU][hapmap]
rs4488806	1.00[CEU][hapmap];0.91[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs62246631	0.91[AMR][1000 genomes];0.98[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs62246641	1.00[AFR][1000 genomes];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6765740	1.00[CEU][hapmap];0.91[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs6799524	0.91[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs7429327	0.88[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs7617368	0.85[CEU][hapmap]

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:2)

SNP	Gene	Cis/trans	Tissue	Source
rs17317763	CCDC13-AS1	cis	Thyroid	GTEx
rs17317763	CCDC13	cis	Thyroid	GTEx

Chromatin state (count:26 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:42853200-42858600	Enhancers	Rectal Mucosa Donor 31	rectum
2	chr3:42853800-42861000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
3	chr3:42853800-42861200	Weak transcription	Fetal Intestine Large	intestine
4	chr3:42853800-42862200	Weak transcription	Fetal Intestine Small	intestine
5	chr3:42854200-42861200	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
6	chr3:42854800-42858000	Enhancers	Fetal Heart	heart
7	chr3:42855800-42857800	Enhancers	HepG2	liver
8	chr3:42856000-42857800	Enhancers	Hela-S3	cervix
9	chr3:42856200-42858000	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
10	chr3:42856400-42857800	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
11	chr3:42856400-42857800	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
12	chr3:42856400-42858200	Enhancers	Sigmoid Colon	Sigmoid Colon
13	chr3:42856800-42857800	Enhancers	Pancreatic Islets	Pancreatic Islet
14	chr3:42856800-42861000	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
15	chr3:42857000-42858600	Weak transcription	Placenta	Placenta
16	chr3:42857000-42861000	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
17	chr3:42857000-42869800	Weak transcription	Colonic Mucosa	Colon
18	chr3:42857200-42860600	Weak transcription	Fetal Kidney	kidney
19	chr3:42857200-42861000	Weak transcription	Cortex derived primary cultured neurospheres	brain
20	chr3:42857400-42860800	Weak transcription	Rectal Mucosa Donor 29	rectum
21	chr3:42857400-42861000	Weak transcription	Liver	Liver
22	chr3:42857400-42861200	Weak transcription	HMEC	breast
23	chr3:42857400-42861200	Weak transcription	NHEK	skin
24	chr3:42857600-42861000	Weak transcription	Duodenum Mucosa	Duodenum
25	chr3:42857600-42861000	Weak transcription	Stomach Mucosa	stomach
26	chr3:42857600-42861400	Weak transcription	Placenta Amnion	Placenta Amnion

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