Variant report

Variant	rs1117213
Chromosome Location	chr8:51284360-51284361
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 103 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:99)

rs_ID	r²[population]
rs10086867	0.86[CHB][hapmap];0.84[ASN][1000 genomes]
rs10092399	0.92[JPT][hapmap]
rs10101137	0.91[EUR][1000 genomes]
rs10103047	0.92[JPT][hapmap]
rs10113812	0.92[JPT][hapmap]
rs10504100	1.00[CEU][hapmap];0.91[TSI][hapmap];0.92[EUR][1000 genomes]
rs10504103	1.00[CEU][hapmap]
rs10504106	0.83[CEU][hapmap]
rs1160764	0.92[JPT][hapmap]
rs1160795	0.92[JPT][hapmap]
rs11782140	1.00[CEU][hapmap];0.92[EUR][1000 genomes]
rs11783674	0.87[ASN][1000 genomes]
rs12156091	1.00[CEU][hapmap];0.92[EUR][1000 genomes]
rs12540980	1.00[CEU][hapmap];0.92[EUR][1000 genomes]
rs12541772	0.92[JPT][hapmap]
rs12544425	1.00[CEU][hapmap];0.92[TSI][hapmap];0.92[EUR][1000 genomes]
rs12545003	0.83[CEU][hapmap];0.82[CHD][hapmap];0.95[GIH][hapmap];0.92[JPT][hapmap];0.86[LWK][hapmap];0.84[MKK][hapmap];0.89[YRI][hapmap]
rs12545927	0.84[CHB][hapmap]
rs12546829	0.82[ASN][1000 genomes]
rs12547038	0.92[EUR][1000 genomes]
rs12547242	1.00[CEU][hapmap];0.92[EUR][1000 genomes]
rs12548399	1.00[CEU][hapmap];1.00[EUR][1000 genomes]
rs12675994	0.98[ASN][1000 genomes]
rs12679464	0.82[ASN][1000 genomes]
rs13248969	0.82[CHB][hapmap]
rs13251725	0.82[CHB][hapmap]
rs13257386	1.00[CEU][hapmap];0.92[EUR][1000 genomes]
rs13257851	0.83[CEU][hapmap];0.82[CHD][hapmap];0.98[GIH][hapmap];0.92[JPT][hapmap]
rs13260021	0.82[CHB][hapmap]
rs13260506	1.00[CEU][hapmap];0.92[EUR][1000 genomes]
rs13261341	1.00[CEU][hapmap];0.92[EUR][1000 genomes]
rs13275607	0.84[JPT][hapmap]
rs13278343	0.91[CHB][hapmap];0.81[YRI][hapmap];0.82[ASN][1000 genomes]
rs13282203	1.00[CEU][hapmap];0.97[TSI][hapmap];0.92[EUR][1000 genomes]
rs1375942	0.92[CHB][hapmap];0.85[CHD][hapmap];0.89[YRI][hapmap];0.85[ASN][1000 genomes]
rs1375944	0.82[JPT][hapmap]
rs1450124	0.92[JPT][hapmap]
rs1450131	1.00[CEU][hapmap];1.00[EUR][1000 genomes]
rs1460437	0.92[JPT][hapmap]
rs1466128	1.00[CEU][hapmap];1.00[EUR][1000 genomes]
rs1470680	1.00[CEU][hapmap];0.92[EUR][1000 genomes]
rs1481471	0.83[CEU][hapmap];0.82[CHD][hapmap];0.98[GIH][hapmap];0.92[JPT][hapmap]
rs1548073	1.00[CEU][hapmap];1.00[EUR][1000 genomes]
rs1597432	0.93[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1597433	0.94[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs16914780	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.92[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs16914781	0.86[CHB][hapmap];0.85[CHD][hapmap];0.84[ASN][1000 genomes]
rs17769846	1.00[CEU][hapmap]
rs17770910	0.90[CHB][hapmap]
rs1947254	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2044777	1.00[CEU][hapmap];1.00[TSI][hapmap];1.00[EUR][1000 genomes]
rs2044778	1.00[CEU][hapmap];0.97[EUR][1000 genomes]
rs2219574	0.92[JPT][hapmap]
rs28669842	0.92[EUR][1000 genomes]
rs2923059	0.92[CHB][hapmap];0.89[YRI][hapmap];0.86[ASN][1000 genomes]
rs2923062	0.87[ASW][hapmap];0.92[CHB][hapmap];0.85[CHD][hapmap];0.98[LWK][hapmap];0.96[YRI][hapmap];0.88[AFR][1000 genomes];0.86[ASN][1000 genomes]
rs2957598	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2957599	1.00[CEU][hapmap];1.00[EUR][1000 genomes]
rs2957600	0.80[ASW][hapmap];0.86[CHB][hapmap];0.85[CHD][hapmap];0.98[LWK][hapmap];0.96[YRI][hapmap];0.88[AFR][1000 genomes];0.84[ASN][1000 genomes]
rs2957601	0.80[ASW][hapmap];0.92[CHB][hapmap];0.85[CHD][hapmap];0.98[LWK][hapmap];0.96[YRI][hapmap];0.88[AFR][1000 genomes];0.86[ASN][1000 genomes]
rs34113623	0.92[EUR][1000 genomes]
rs34365466	0.98[EUR][1000 genomes]
rs34530560	0.92[EUR][1000 genomes]
rs35063719	0.98[ASN][1000 genomes]
rs35894781	1.00[EUR][1000 genomes]
rs4147344	0.92[CHB][hapmap];0.96[YRI][hapmap];0.87[AFR][1000 genomes];0.80[AMR][1000 genomes];0.86[ASN][1000 genomes]
rs4242460	0.92[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4256602	0.83[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[ASN][1000 genomes]
rs4263785	1.00[CEU][hapmap];0.92[EUR][1000 genomes]
rs4292700	0.92[CHB][hapmap];0.89[CHD][hapmap];0.83[MEX][hapmap];0.86[ASN][1000 genomes]
rs4339654	0.83[CEU][hapmap];1.00[CHB][hapmap];0.96[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];0.95[LWK][hapmap];0.81[MKK][hapmap];0.89[YRI][hapmap];0.98[ASN][1000 genomes]
rs4364645	0.86[CHB][hapmap];0.85[CHD][hapmap];0.93[LWK][hapmap];0.86[YRI][hapmap];0.82[ASN][1000 genomes]
rs4379460	1.00[CEU][hapmap];0.92[EUR][1000 genomes]
rs4410921	0.83[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[YRI][hapmap];0.98[ASN][1000 genomes]
rs4529480	0.86[CHB][hapmap];0.85[CHD][hapmap];0.88[LWK][hapmap];0.86[YRI][hapmap];0.82[ASN][1000 genomes]
rs4534138	0.93[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.97[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4604450	1.00[CHB][hapmap];1.00[JPT][hapmap];0.98[ASN][1000 genomes]
rs4639524	0.92[CHB][hapmap];0.86[YRI][hapmap];0.84[ASN][1000 genomes]
rs4873141	0.92[JPT][hapmap]
rs4873143	0.92[JPT][hapmap]
rs4873438	0.92[JPT][hapmap]
rs4873439	0.92[JPT][hapmap]
rs4873443	0.92[JPT][hapmap]
rs4873453	0.82[AFR][1000 genomes];0.83[AMR][1000 genomes];0.91[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs62517613	0.92[EUR][1000 genomes]
rs62517614	0.92[EUR][1000 genomes]
rs6473114	0.98[ASN][1000 genomes]
rs6994415	0.84[ASN][1000 genomes]
rs6995334	0.85[YRI][hapmap]
rs7003725	0.92[JPT][hapmap]
rs7005672	0.83[CEU][hapmap];1.00[CHB][hapmap];0.96[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];0.96[ASN][1000 genomes]
rs7015950	0.83[CEU][hapmap];1.00[CHB][hapmap];0.96[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];0.98[LWK][hapmap];0.81[MKK][hapmap];0.89[YRI][hapmap];0.98[ASN][1000 genomes]
rs7816983	0.84[ASN][1000 genomes]
rs7820992	0.83[CEU][hapmap]
rs7839253	0.83[CEU][hapmap];1.00[CHB][hapmap];0.96[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];0.95[LWK][hapmap];0.81[MKK][hapmap];0.83[YRI][hapmap];0.98[ASN][1000 genomes]
rs7845433	0.85[ASN][1000 genomes]
rs896023	1.00[CEU][hapmap];1.00[EUR][1000 genomes]
rs930671	1.00[CEU][hapmap];1.00[TSI][hapmap];1.00[EUR][1000 genomes]
rs9643720	0.92[JPT][hapmap]

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	nsv916392	chr8:50827638-51395140	Enhancers Weak transcription Strong transcription Active TSS ZNF genes & repeats Flanking Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
2	nsv948436	chr8:51115028-51917504	Enhancers Weak transcription Flanking Active TSS ZNF genes & repeats Active TSS Bivalent Enhancer Strong transcription Genic enhancers Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
3	nsv831312	chr8:51239772-51422844	Weak transcription Enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats Active TSS Flanking Active TSS Genic enhancers Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
4	nsv525765	chr8:51269514-51284501	Active TSS Enhancers Weak transcription Flanking Active TSS ZNF genes & repeats	n/a	n/a	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs1117213	SNTG1	cis	cerebellum	SCAN

Chromatin state (count:2 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr8:51276600-51289000	Weak transcription	Sigmoid Colon	Sigmoid Colon
2	chr8:51283800-51287600	Weak transcription	Rectal Mucosa Donor 31	rectum

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