Variant report

Variant	rs4510567
Chromosome Location	chr5:147470096-147470097
allele	A/C
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	MAX	chr5:147469541-147470862	Hela-S3	cervix:	n/a	n/a
2	POLR2A	chr5:147469534-147470879	Hela-S3	cervix:	n/a	n/a
3	GTF3C2	chr5:147469728-147470691	Hela-S3	cervix:	n/a	n/a
4	TBP	chr5:147469747-147470968	Hela-S3	cervix:	n/a	n/a
5	ELK4	chr5:147469836-147470685	Hela-S3	cervix:	n/a	n/a
6	CEBPB	chr5:147469495-147470904	Hela-S3	cervix:	n/a	n/a
7	MAFK	chr5:147469609-147471157	Hela-S3	cervix:	n/a	chr5:147470367-147470382 chr5:147470797-147470807
8	MXI1	chr5:147469611-147470848	Hela-S3	cervix:	n/a	n/a
9	JUND	chr5:147469555-147470986	Hela-S3	cervix:	n/a	chr5:147470686-147470698 chr5:147470797-147470804 chr5:147470795-147470806 chr5:147470689-147470696 chr5:147470797-147470806 chr5:147470456-147470466 chr5:147470455-147470467 chr5:147470688-147470696 chr5:147470456-147470466 chr5:147470457-147470465
10	BRCA1	chr5:147468993-147470890	Hela-S3	cervix:	n/a	n/a
11	STAT3	chr5:147469998-147470974	MCF10A-Er-Src	breast:	n/a	chr5:147470860-147470868 chr5:147470796-147470805 chr5:147470516-147470527
12	POLR2A	chr5:147469833-147471329	MCF10A-Er-Src	breast:	n/a	n/a
13	TCF7L2	chr5:147469587-147470346	Hela-S3	cervix:	n/a	chr5:147469887-147469894
14	MAX	chr5:147469539-147470784	Hela-S3	cervix:	n/a	n/a
15	RAD21	chr5:147469654-147470895	Hela-S3	cervix:	n/a	n/a
16	STAT3	chr5:147469800-147471015	MCF10A-Er-Src	breast:	n/a	chr5:147470860-147470868 chr5:147470796-147470805 chr5:147470516-147470527
17	STAT3	chr5:147469306-147470884	Hela-S3	cervix:	n/a	chr5:147470860-147470868 chr5:147470796-147470805 chr5:147470516-147470527
18	EP300	chr5:147469484-147470908	Hela-S3	cervix:	n/a	chr5:147470053-147470067 chr5:147470709-147470719 chr5:147470797-147470806
19	RFX5	chr5:147468763-147470934	Hela-S3	cervix:	n/a	n/a
20	STAT3	chr5:147469871-147471251	MCF10A-Er-Src	breast:	n/a	chr5:147470860-147470868 chr5:147470796-147470805 chr5:147470516-147470527
21	TCF7L2	chr5:147469485-147470846	Hela-S3	cervix:	n/a	chr5:147470797-147470806 chr5:147469887-147469894 chr5:147470796-147470805
22	RCOR1	chr5:147469628-147470856	Hela-S3	cervix:	n/a	n/a
23	MYC	chr5:147469504-147470131	Hela-S3	cervix:	n/a	n/a

Variant related genes	Relation type
SPINK5	TF binding region

Extended variants
information (count: 61 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:57)

rs_ID	r²[population]
rs10038561	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10059850	0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10060214	0.83[EUR][1000 genomes]
rs10065129	0.86[EUR][1000 genomes]
rs10069070	0.81[EUR][1000 genomes]
rs10073775	0.85[EUR][1000 genomes]
rs1007977	0.83[EUR][1000 genomes]
rs1007978	0.83[EUR][1000 genomes]
rs1017222	0.86[AFR][1000 genomes];0.85[EUR][1000 genomes]
rs10213857	0.80[EUR][1000 genomes]
rs12108690	0.85[EUR][1000 genomes]
rs12519144	0.83[EUR][1000 genomes]
rs12521761	0.83[EUR][1000 genomes]
rs1363729	0.81[EUR][1000 genomes]
rs1422995	0.96[AFR][1000 genomes];0.85[EUR][1000 genomes]
rs1422996	0.87[EUR][1000 genomes]
rs1423000	0.85[EUR][1000 genomes]
rs1423001	0.85[EUR][1000 genomes]
rs1423002	0.86[AFR][1000 genomes];0.83[EUR][1000 genomes]
rs1423003	0.83[EUR][1000 genomes]
rs1423004	0.83[EUR][1000 genomes]
rs1423005	0.83[EUR][1000 genomes]
rs1423006	0.82[EUR][1000 genomes]
rs1423007	0.82[EUR][1000 genomes]
rs1609851	0.83[EUR][1000 genomes]
rs1833768	0.83[EUR][1000 genomes]
rs1862445	0.80[EUR][1000 genomes]
rs1862446	0.80[EUR][1000 genomes]
rs2287772	0.87[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs3752676	0.86[AFR][1000 genomes];0.85[EUR][1000 genomes]
rs3756688	0.82[EUR][1000 genomes]
rs3822744	0.82[EUR][1000 genomes]
rs4333302	0.88[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4357026	0.86[EUR][1000 genomes]
rs4472254	0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4519912	0.85[EUR][1000 genomes]
rs4529181	0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4610447	0.86[AFR][1000 genomes];0.85[EUR][1000 genomes]
rs4705223	0.82[EUR][1000 genomes]
rs62388364	0.85[EUR][1000 genomes]
rs6580517	0.87[EUR][1000 genomes]
rs6580518	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6580519	0.84[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6580520	0.84[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6864564	0.87[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6864920	0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6876628	0.91[AFR][1000 genomes];0.85[EUR][1000 genomes]
rs6889688	0.88[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6894384	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7707841	0.91[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs9325061	0.83[EUR][1000 genomes]
rs9325064	0.83[EUR][1000 genomes]
rs9325066	0.83[EUR][1000 genomes]
rs9325068	0.82[EUR][1000 genomes]
rs9325069	0.86[AFR][1000 genomes];0.85[EUR][1000 genomes]
rs986493	0.83[AFR][1000 genomes];0.83[EUR][1000 genomes]
rs986495	0.83[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1033838	chr5:147360521-147484014	Flanking Active TSS Enhancers ZNF genes & repeats Weak transcription Active TSS Strong transcription Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
2	nsv933225	chr5:147395849-147486560	Flanking Active TSS Enhancers Weak transcription ZNF genes & repeats Strong transcription Active TSS Genic enhancers	TF binding region CpG island Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
3	nsv883015	chr5:147404281-147751035	Enhancers Weak transcription Strong transcription Active TSS Flanking Active TSS Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	17 gene(s)	inside rSNPs	diseases
4	nsv830515	chr5:147460852-147602247	Enhancers Weak transcription Active TSS Strong transcription Flanking Active TSS Genic enhancers ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs4510567	SPINK5	cis	Thyroid	GTEx
rs4510567	SPINK5	cis	Heart Left Ventricle	GTEx
rs4510567	SPINK5	cis	Adipose Subcutaneous	GTEx
rs4510567	SPINK5	cis	Muscle Skeletal	GTEx

Chromatin state (count:33 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:147450800-147474000	Weak transcription	HUES48 Cell Line	embryonic stem cell
2	chr5:147462600-147471600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
3	chr5:147464200-147491200	Weak transcription	H9 Cell Line	embryonic stem cell
4	chr5:147464400-147488800	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
5	chr5:147466200-147471600	Weak transcription	Breast Myoepithelial Primary Cells	Breast
6	chr5:147468600-147471000	Enhancers	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
7	chr5:147469000-147470200	Enhancers	HUES6 Cell Line	embryonic stem cell
8	chr5:147469000-147470400	Enhancers	Rectal Mucosa Donor 31	rectum
9	chr5:147469200-147471600	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
10	chr5:147469200-147471600	Weak transcription	Colon Smooth Muscle	Colon
11	chr5:147469200-147481400	Weak transcription	Esophagus	oesophagus
12	chr5:147469400-147470200	Enhancers	Brain Germinal Matrix	brain
13	chr5:147469400-147471600	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
14	chr5:147469600-147470200	Enhancers	iPS-20b Cell Line	embryonic stem cell
15	chr5:147469600-147470400	Enhancers	Fetal Intestine Small	intestine
16	chr5:147469600-147470800	Enhancers	HMEC	breast
17	chr5:147469600-147471000	Enhancers	iPS-15b Cell Line	embryonic stem cell
18	chr5:147469600-147471000	Enhancers	Fetal Adrenal Gland	Adrenal Gland
19	chr5:147469800-147470200	Enhancers	Fetal Intestine Large	intestine
20	chr5:147469800-147470200	Flanking Active TSS	Rectal Mucosa Donor 29	rectum
21	chr5:147469800-147470400	Enhancers	Fetal Lung	lung
22	chr5:147469800-147470400	Enhancers	HUVEC	blood vessel
23	chr5:147469800-147470600	Enhancers	ES-WA7 Cell Line	embryonic stem cell
24	chr5:147469800-147470600	Flanking Active TSS	Hela-S3	cervix
25	chr5:147469800-147472000	Enhancers	ES-I3 Cell Line	embryonic stem cell
26	chr5:147469800-147472200	Flanking Active TSS	NHEK	skin
27	chr5:147470000-147470200	Enhancers	Stomach Mucosa	stomach
28	chr5:147470000-147470400	Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
29	chr5:147470000-147470600	Flanking Active TSS	Foreskin Keratinocyte Primary Cells skin02	Skin
30	chr5:147470000-147470600	Flanking Active TSS	Foreskin Keratinocyte Primary Cells skin03	Skin
31	chr5:147470000-147470800	Enhancers	HUES64 Cell Line	embryonic stem cell
32	chr5:147470000-147470800	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
33	chr5:147470000-147473000	Weak transcription	Liver	Liver

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