Variant report

Variant	rs3777140
Chromosome Location	chr5:147494831-147494832
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 78 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:76)

rs_ID	r²[population]
rs10038991	0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10060214	0.89[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs10064815	0.81[AFR][1000 genomes]
rs10065129	0.84[AMR][1000 genomes];0.89[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs10069070	0.89[CEU][hapmap];0.92[JPT][hapmap];1.00[YRI][hapmap];0.82[AFR][1000 genomes];0.86[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs10069697	0.96[ASN][1000 genomes]
rs10073775	0.85[CEU][hapmap];1.00[YRI][hapmap];0.88[AFR][1000 genomes];0.82[AMR][1000 genomes];0.90[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs1007977	0.89[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs1007978	0.85[CEU][hapmap];0.89[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs1017222	0.88[CEU][hapmap];0.91[JPT][hapmap];0.90[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs10213857	0.85[EUR][1000 genomes]
rs11745768	1.00[YRI][hapmap]
rs12108690	0.88[CEU][hapmap];0.91[JPT][hapmap];1.00[YRI][hapmap];0.88[AFR][1000 genomes];0.82[AMR][1000 genomes];0.90[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs12519144	0.85[CEU][hapmap];0.89[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs12519499	0.81[AMR][1000 genomes];0.85[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs12521759	0.88[AFR][1000 genomes];0.85[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs12521761	0.89[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs1363729	0.89[CEU][hapmap];0.92[JPT][hapmap];1.00[YRI][hapmap];0.88[AFR][1000 genomes];0.86[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs1422993	1.00[CHB][hapmap];0.83[JPT][hapmap];0.96[ASN][1000 genomes]
rs1422995	0.90[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1422996	0.84[AMR][1000 genomes];0.91[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1423000	0.88[CEU][hapmap];0.83[JPT][hapmap];1.00[YRI][hapmap];0.88[AFR][1000 genomes];0.82[AMR][1000 genomes];0.90[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs1423001	0.88[CEU][hapmap];0.91[JPT][hapmap];1.00[YRI][hapmap];0.88[AFR][1000 genomes];0.82[AMR][1000 genomes];0.90[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs1423002	0.85[CEU][hapmap];0.89[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs1423003	0.89[CEU][hapmap];0.91[JPT][hapmap];1.00[YRI][hapmap];0.89[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs1423004	0.89[CEU][hapmap];0.91[JPT][hapmap];0.89[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs1423005	0.89[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs1423006	0.85[CEU][hapmap];0.87[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs1423007	0.88[CEU][hapmap];0.91[JPT][hapmap];0.87[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs1423008	0.81[AFR][1000 genomes]
rs1609851	0.89[CEU][hapmap];0.91[JPT][hapmap];0.89[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs1833768	0.88[AFR][1000 genomes];0.82[AMR][1000 genomes];0.89[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs1862439	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][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]
rs1862445	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.94[AFR][1000 genomes];0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1862446	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.94[AFR][1000 genomes];0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2287772	0.82[CEU][hapmap]
rs3752676	0.88[CEU][hapmap];0.81[JPT][hapmap];0.90[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs3756688	0.88[CEU][hapmap];0.91[JPT][hapmap];1.00[YRI][hapmap];0.88[AFR][1000 genomes];0.82[AMR][1000 genomes];0.87[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs3777143	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.94[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3815735	1.00[CEU][hapmap];1.00[CHB][hapmap];0.89[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs3815737	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3822744	0.85[CEU][hapmap];1.00[YRI][hapmap];0.88[AFR][1000 genomes];0.82[AMR][1000 genomes];0.87[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs4354025	0.86[ASN][1000 genomes]
rs4357026	0.89[CEU][hapmap];0.91[JPT][hapmap];1.00[YRI][hapmap];0.82[AMR][1000 genomes];0.89[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4472254	0.82[CEU][hapmap]
rs4519912	0.85[CEU][hapmap];0.88[AFR][1000 genomes];0.82[AMR][1000 genomes];0.90[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs4529181	0.82[CEU][hapmap]
rs4610447	0.90[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4705223	1.00[CEU][hapmap];1.00[YRI][hapmap];0.95[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs57930479	0.92[ASN][1000 genomes]
rs62388364	0.82[AFR][1000 genomes];0.91[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6580517	0.84[AMR][1000 genomes];0.91[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6580519	0.85[CEU][hapmap]
rs6580520	0.85[CEU][hapmap]
rs6864920	0.86[CEU][hapmap]
rs6872218	1.00[CHB][hapmap];0.91[JPT][hapmap];0.94[ASN][1000 genomes]
rs6872326	0.92[ASN][1000 genomes]
rs6876628	0.90[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs6886271	0.96[ASN][1000 genomes]
rs6891892	1.00[CHB][hapmap];0.96[ASN][1000 genomes]
rs6895078	0.96[ASN][1000 genomes]
rs6896914	0.94[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7707841	0.84[EUR][1000 genomes]
rs7728739	0.96[ASN][1000 genomes]
rs9325061	0.88[CEU][hapmap];0.91[JPT][hapmap];0.89[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs9325064	0.88[CEU][hapmap];0.91[JPT][hapmap];0.89[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs9325066	0.89[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs9325068	0.88[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs9325069	0.90[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs9325073	1.00[CHB][hapmap];0.83[JPT][hapmap];0.92[ASN][1000 genomes]
rs9325074	0.92[ASN][1000 genomes]
rs9325075	0.92[ASN][1000 genomes]
rs986493	0.89[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs986494	0.91[JPT][hapmap]
rs986495	0.89[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs988885	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];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	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
2	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:2)

SNP	Gene	Cis/trans	Tissue	Source
rs3777140	SPINK5	cis	Heart Left Ventricle	GTEx
rs3777140	SPINK5	cis	Thyroid	GTEx

Chromatin state (count:22 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:147470400-147518400	Weak transcription	iPS-18 Cell Line	embryonic stem cell
2	chr5:147470600-147508400	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
3	chr5:147470600-147509000	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
4	chr5:147471600-147514800	Weak transcription	iPS-15b Cell Line	embryonic stem cell
5	chr5:147472000-147505000	Weak transcription	ES-I3 Cell Line	embryonic stem cell
6	chr5:147472600-147497200	Weak transcription	H1 Cell Line	embryonic stem cell
7	chr5:147474200-147513400	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
8	chr5:147479000-147500600	Strong transcription	HUES64 Cell Line	embryonic stem cell
9	chr5:147480800-147498200	Weak transcription	Rectal Mucosa Donor 31	rectum
10	chr5:147481400-147513200	Weak transcription	Sigmoid Colon	Sigmoid Colon
11	chr5:147481600-147505000	Weak transcription	Esophagus	oesophagus
12	chr5:147482200-147509000	Weak transcription	iPS-20b Cell Line	embryonic stem cell
13	chr5:147486800-147515000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
14	chr5:147487400-147505000	Weak transcription	Breast Myoepithelial Primary Cells	Breast
15	chr5:147487800-147525800	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
16	chr5:147491800-147495000	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
17	chr5:147493600-147495400	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
18	chr5:147493600-147496800	Strong transcription	HUES48 Cell Line	embryonic stem cell
19	chr5:147493800-147497200	Strong transcription	Hela-S3	cervix
20	chr5:147494000-147500400	Strong transcription	HUES6 Cell Line	embryonic stem cell
21	chr5:147494200-147497800	Weak transcription	H9 Cell Line	embryonic stem cell
22	chr5:147494800-147495200	Enhancers	Fetal Adrenal Gland	Adrenal Gland

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