Variant report

Variant	rs4683166
Chromosome Location	chr3:46089341-46089342
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 133 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:128)

rs_ID	r²[population]
rs12108042	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs13060287	0.88[EUR][1000 genomes]
rs13063527	0.82[EUR][1000 genomes]
rs13066062	0.81[EUR][1000 genomes]
rs13068410	0.89[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13068570	0.82[EUR][1000 genomes]
rs13069079	0.81[CEU][hapmap];0.81[GIH][hapmap]
rs13069742	0.82[EUR][1000 genomes]
rs13071283	0.80[CEU][hapmap]
rs13072267	0.82[EUR][1000 genomes]
rs13074382	0.81[CEU][hapmap];0.82[CHB][hapmap];0.88[GIH][hapmap];0.89[LWK][hapmap];0.93[YRI][hapmap];0.88[EUR][1000 genomes]
rs13075528	0.82[EUR][1000 genomes]
rs13075758	0.81[CEU][hapmap];0.82[EUR][1000 genomes]
rs13078739	0.81[CEU][hapmap];0.83[GIH][hapmap]
rs13079869	0.81[CEU][hapmap];0.83[GIH][hapmap];0.81[EUR][1000 genomes]
rs13081151	0.87[EUR][1000 genomes]
rs13081213	0.82[CHB][hapmap];0.88[GIH][hapmap];0.93[YRI][hapmap];0.88[EUR][1000 genomes]
rs13082697	0.88[EUR][1000 genomes]
rs13089554	0.82[EUR][1000 genomes]
rs13089855	0.90[EUR][1000 genomes]
rs13090194	0.81[CEU][hapmap];0.82[CHB][hapmap];0.88[GIH][hapmap];0.89[LWK][hapmap];0.93[YRI][hapmap];0.88[EUR][1000 genomes]
rs13091868	0.82[EUR][1000 genomes]
rs13093179	0.82[EUR][1000 genomes]
rs13094262	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13095602	0.82[EUR][1000 genomes]
rs13095717	0.82[EUR][1000 genomes]
rs13096741	0.83[EUR][1000 genomes]
rs13097556	0.88[EUR][1000 genomes]
rs13433997	0.86[EUR][1000 genomes]
rs1491950	0.82[EUR][1000 genomes]
rs1491951	0.82[EUR][1000 genomes]
rs17214952	0.81[CEU][hapmap];0.83[GIH][hapmap]
rs17215008	0.81[CEU][hapmap];0.81[EUR][1000 genomes]
rs17215981	0.82[EUR][1000 genomes]
rs17280623	0.81[CEU][hapmap]
rs17330872	0.81[CEU][hapmap];0.86[GIH][hapmap];0.83[EUR][1000 genomes]
rs2088690	0.88[EUR][1000 genomes]
rs2088692	0.88[EUR][1000 genomes]
rs2088693	0.87[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2102055	0.82[CHB][hapmap];0.93[YRI][hapmap];0.88[EUR][1000 genomes]
rs2102056	0.83[EUR][1000 genomes]
rs2230322	0.81[CEU][hapmap];0.82[CHB][hapmap];0.88[GIH][hapmap];0.89[LWK][hapmap];0.93[YRI][hapmap];0.88[EUR][1000 genomes]
rs2276856	0.82[YRI][hapmap]
rs33910087	0.81[EUR][1000 genomes]
rs34047915	0.82[EUR][1000 genomes]
rs34093271	0.82[EUR][1000 genomes]
rs34127208	0.82[EUR][1000 genomes]
rs34168660	0.88[EUR][1000 genomes]
rs34283240	0.88[EUR][1000 genomes]
rs34339943	0.87[EUR][1000 genomes]
rs34340587	0.84[EUR][1000 genomes]
rs34438204	0.87[EUR][1000 genomes]
rs34442130	0.82[EUR][1000 genomes]
rs34452002	0.82[EUR][1000 genomes]
rs34460587	0.82[EUR][1000 genomes]
rs34492478	0.82[EUR][1000 genomes]
rs34493660	0.90[EUR][1000 genomes]
rs34562820	0.87[EUR][1000 genomes]
rs34584867	0.88[EUR][1000 genomes]
rs34619093	0.87[EUR][1000 genomes]
rs34679077	0.87[EUR][1000 genomes]
rs34718164	0.83[EUR][1000 genomes]
rs34754340	0.88[EUR][1000 genomes]
rs34766614	0.82[EUR][1000 genomes]
rs34774687	0.88[EUR][1000 genomes]
rs34805664	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34836513	0.88[EUR][1000 genomes]
rs34863575	0.87[EUR][1000 genomes]
rs34867672	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34924300	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35028116	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35110864	0.82[EUR][1000 genomes]
rs35159820	0.88[EUR][1000 genomes]
rs35161099	0.87[EUR][1000 genomes]
rs35334665	0.87[EUR][1000 genomes]
rs35454877	0.88[EUR][1000 genomes]
rs35539222	0.82[EUR][1000 genomes]
rs35669129	0.81[CEU][hapmap];0.82[CHB][hapmap];0.88[GIH][hapmap];0.89[LWK][hapmap];0.93[YRI][hapmap];0.88[EUR][1000 genomes]
rs35751180	0.87[EUR][1000 genomes]
rs35772789	0.87[EUR][1000 genomes]
rs35814488	0.88[EUR][1000 genomes]
rs35883205	0.89[EUR][1000 genomes]
rs35921206	0.88[EUR][1000 genomes]
rs35930050	0.88[EUR][1000 genomes]
rs36023124	0.88[EUR][1000 genomes]
rs36040135	0.88[EUR][1000 genomes]
rs36057789	0.82[EUR][1000 genomes]
rs36122610	0.82[EUR][1000 genomes]
rs3851346	0.81[CEU][hapmap];0.82[CHB][hapmap];0.88[GIH][hapmap];0.89[EUR][1000 genomes]
rs41289622	0.81[EUR][1000 genomes]
rs4362758	0.88[EUR][1000 genomes]
rs4373103	0.82[EUR][1000 genomes]
rs4388012	0.81[CEU][hapmap]
rs55875328	0.90[EUR][1000 genomes]
rs60019065	0.88[EUR][1000 genomes]
rs61556067	0.90[EUR][1000 genomes]
rs61650989	0.90[EUR][1000 genomes]
rs67200151	0.90[EUR][1000 genomes]
rs6780028	0.88[EUR][1000 genomes]
rs6785091	0.81[CEU][hapmap]
rs6790866	0.88[EUR][1000 genomes]
rs6791016	0.88[EUR][1000 genomes]
rs67937868	0.88[EUR][1000 genomes]
rs68087193	0.85[EUR][1000 genomes]
rs71325098	0.81[EUR][1000 genomes]
rs71325100	0.81[EUR][1000 genomes]
rs71327003	0.88[EUR][1000 genomes]
rs71327006	0.87[EUR][1000 genomes]
rs71327007	0.87[EUR][1000 genomes]
rs71327009	0.87[EUR][1000 genomes]
rs71327010	0.87[EUR][1000 genomes]
rs71327014	0.82[EUR][1000 genomes]
rs71327015	0.82[EUR][1000 genomes]
rs71327017	0.82[EUR][1000 genomes]
rs71327021	0.82[EUR][1000 genomes]
rs71327023	0.82[EUR][1000 genomes]
rs71327024	0.82[EUR][1000 genomes]
rs71327025	0.82[EUR][1000 genomes]
rs71615438	0.88[EUR][1000 genomes]
rs751667	0.81[MKK][hapmap]
rs7642229	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7642320	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7652478	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs876668	0.88[EUR][1000 genomes]
rs9824651	0.82[EUR][1000 genomes]
rs9825081	0.82[EUR][1000 genomes]
rs9845382	0.82[EUR][1000 genomes]
rs9877748	0.82[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:5 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv876734	chr3:45725031-46468467	Weak transcription Enhancers Active TSS Flanking Active TSS Genic enhancers Bivalent/Poised TSS Strong transcription Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	42 gene(s)	inside rSNPs	diseases
2	nsv498008	chr3:45733423-46319401	Strong transcription Active TSS Genic enhancers Enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Weak transcription Flanking Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	29 gene(s)	inside rSNPs	diseases
3	esv2756987	chr3:46016464-46120400	Enhancers Flanking Active TSS Weak transcription Flanking Bivalent TSS/Enh Active TSS Strong transcription Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases
4	esv2759145	chr3:46016464-46120400	Flanking Active TSS Strong transcription Enhancers Weak transcription Active TSS Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases
5	esv1805205	chr3:46032847-46111081	Flanking Active TSS Active TSS Enhancers Weak transcription Genic enhancers ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS Strong transcription	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
rs4683166	TDGF1	cis	parietal	SCAN
rs4683166	CDC25A	cis	cerebellum	SCAN

Chromatin state (count:9 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:46086600-46090000	Enhancers	Dnd41	blood
2	chr3:46086800-46089400	Enhancers	Primary T helper 17 cells PMA-I stimulated	--
3	chr3:46087400-46089400	Enhancers	Primary T helper naive cells fromperipheralblood	blood
4	chr3:46087600-46090200	Enhancers	Primary T cells fromperipheralblood	blood
5	chr3:46087600-46095800	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
6	chr3:46088000-46090400	Weak transcription	Placenta	Placenta
7	chr3:46088600-46090400	Weak transcription	NHEK	skin
8	chr3:46088800-46090000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
9	chr3:46089200-46089600	Enhancers	Brain Germinal Matrix	brain

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