Variant report

Variant	rs4688379
Chromosome Location	chr3:61207457-61207458
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 101 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:91)

rs_ID	r²[population]
rs10049007	0.83[ASN][1000 genomes]
rs10049287	0.83[ASN][1000 genomes]
rs10049452	0.83[ASN][1000 genomes]
rs10049454	0.83[ASN][1000 genomes]
rs11130821	0.93[EUR][1000 genomes]
rs11130822	0.95[EUR][1000 genomes]
rs11130826	0.98[EUR][1000 genomes]
rs11130827	0.81[EUR][1000 genomes]
rs11130828	0.87[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs11707984	0.83[ASN][1000 genomes]
rs11712122	0.83[ASN][1000 genomes]
rs11720254	0.95[EUR][1000 genomes]
rs12053817	0.84[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs12492551	0.98[EUR][1000 genomes]
rs12635622	0.83[ASN][1000 genomes]
rs13099397	0.91[ASN][1000 genomes]
rs13320646	0.83[ASN][1000 genomes]
rs1371095	0.83[ASN][1000 genomes]
rs1470035	0.93[EUR][1000 genomes]
rs1524019	0.92[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs1550343	0.83[ASN][1000 genomes]
rs1554599	0.96[EUR][1000 genomes]
rs1554601	0.83[ASN][1000 genomes]
rs17064630	0.95[EUR][1000 genomes]
rs1916800	0.95[EUR][1000 genomes]
rs1916801	0.95[EUR][1000 genomes]
rs1916802	0.83[AFR][1000 genomes];0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs1949772	0.96[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs1980308	0.96[EUR][1000 genomes]
rs1980309	0.96[EUR][1000 genomes]
rs1980310	0.96[EUR][1000 genomes]
rs1980311	0.95[EUR][1000 genomes]
rs2118811	0.83[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs2365389	0.97[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs34045993	0.92[ASN][1000 genomes]
rs34515056	0.83[EUR][1000 genomes]
rs35198002	0.95[EUR][1000 genomes]
rs4296587	1.00[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs4535219	0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs4605537	0.97[EUR][1000 genomes]
rs4688310	0.81[ASN][1000 genomes]
rs4688352	0.92[EUR][1000 genomes]
rs4688354	0.94[EUR][1000 genomes]
rs4688355	0.95[EUR][1000 genomes]
rs4688359	0.83[EUR][1000 genomes]
rs56076618	0.83[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs61275795	0.84[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs6445196	0.81[ASN][1000 genomes]
rs6445197	0.83[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs6445198	0.82[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs6445199	0.97[AMR][1000 genomes];0.95[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs6445200	0.96[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs6785875	0.94[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs6787292	0.95[EUR][1000 genomes]
rs6787313	0.92[EUR][1000 genomes]
rs6807748	0.83[ASN][1000 genomes]
rs6809031	0.96[AMR][1000 genomes];0.94[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs71296711	0.98[EUR][1000 genomes]
rs7432943	0.84[EUR][1000 genomes]
rs7631101	0.83[ASN][1000 genomes]
rs7631246	0.83[ASN][1000 genomes]
rs7636682	0.83[ASN][1000 genomes]
rs7641177	0.85[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs7647122	0.88[AMR][1000 genomes];0.91[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs815709	0.92[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs815710	0.90[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs815712	0.92[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs815715	0.83[EUR][1000 genomes]
rs815717	0.91[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs843812	0.91[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs863635	0.90[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs9811478	0.83[EUR][1000 genomes]
rs9814044	0.83[ASN][1000 genomes]
rs9831249	0.96[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs9832387	0.92[EUR][1000 genomes]
rs9832404	0.89[EUR][1000 genomes]
rs9839082	0.83[ASN][1000 genomes]
rs9843007	0.83[EUR][1000 genomes]
rs9844741	0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs9846073	0.95[EUR][1000 genomes]
rs9850114	0.98[EUR][1000 genomes]
rs9850125	0.83[ASN][1000 genomes]
rs9851485	0.83[ASN][1000 genomes]
rs9855716	0.98[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs9856859	0.87[EUR][1000 genomes]
rs9859004	0.94[AMR][1000 genomes];0.94[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs9860681	0.89[EUR][1000 genomes]
rs9871451	0.83[ASN][1000 genomes]
rs9871598	0.83[ASN][1000 genomes]
rs9875827	0.93[EUR][1000 genomes]
rs9882800	0.91[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:10 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv2759152	chr3:60781943-61220809	Enhancers Weak transcription Active TSS ZNF genes & repeats Flanking Active TSS Strong transcription Genic enhancers Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
2	nsv876866	chr3:61054494-61310328	Weak transcription Enhancers Active TSS Flanking Active TSS ZNF genes & repeats Strong transcription Bivalent Enhancer Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
3	nsv876867	chr3:61054494-61474575	Weak transcription Enhancers Flanking Active TSS Active TSS Bivalent Enhancer ZNF genes & repeats Strong transcription Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
4	nsv432423	chr3:61100255-61606060	Enhancers Active TSS Weak transcription Flanking Active TSS Flanking Bivalent TSS/Enh Strong transcription Bivalent Enhancer Genic enhancers Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	9 gene(s)	inside rSNPs	diseases
5	nsv1000378	chr3:61103229-61238089	Enhancers Active TSS Weak transcription Flanking Active TSS ZNF genes & repeats Strong transcription Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
6	esv2756994	chr3:61144427-61220809	Enhancers Flanking Active TSS Weak transcription ZNF genes & repeats Active TSS Strong transcription	Chromatin interactive region lncRNA	n/a	inside rSNPs	diseases
7	nsv876868	chr3:61145050-61282503	Enhancers Flanking Active TSS Weak transcription Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Strong transcription Bivalent Enhancer Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
8	nsv532626	chr3:61159646-61388418	Weak transcription Bivalent Enhancer Flanking Active TSS Enhancers Active TSS ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
9	nsv997718	chr3:61176349-61222975	ZNF genes & repeats Weak transcription Enhancers Flanking Active TSS Active TSS	Chromatin interactive region lncRNA	n/a	inside rSNPs	n/a
10	nsv1008399	chr3:61176965-61461349	Flanking Active TSS Enhancers Weak transcription ZNF genes & repeats Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:27 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:61201200-61221000	Weak transcription	Primary T cells from cord blood	blood
2	chr3:61202400-61207600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
3	chr3:61203200-61209200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
4	chr3:61203200-61215400	Weak transcription	Primary hematopoietic stem cells	blood
5	chr3:61203200-61222200	Weak transcription	Psoas Muscle	Psoas
6	chr3:61203400-61207600	Weak transcription	Gastric	stomach
7	chr3:61203400-61207600	Weak transcription	Ovary	ovary
8	chr3:61203400-61209200	Weak transcription	Stomach Smooth Muscle	stomach
9	chr3:61203400-61213400	Weak transcription	Fetal Lung	lung
10	chr3:61203400-61225600	Weak transcription	Lung	lung
11	chr3:61203400-61225600	Weak transcription	Pancreas	Pancrea
12	chr3:61204600-61207600	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
13	chr3:61204800-61207600	Weak transcription	Rectal Mucosa Donor 31	rectum
14	chr3:61206800-61208200	Enhancers	Brain Inferior Temporal Lobe	brain
15	chr3:61207000-61208200	Enhancers	Fetal Intestine Small	intestine
16	chr3:61207000-61211000	Enhancers	Fetal Brain Male	brain
17	chr3:61207200-61208200	Enhancers	Fetal Intestine Large	intestine
18	chr3:61207200-61208400	Enhancers	Liver	Liver
19	chr3:61207200-61208400	Enhancers	HepG2	liver
20	chr3:61207200-61219400	Weak transcription	GM12878-XiMat	blood
21	chr3:61207400-61207600	Enhancers	Duodenum Mucosa	Duodenum
22	chr3:61207400-61207600	Enhancers	Spleen	Spleen
23	chr3:61207400-61208000	Enhancers	Right Atrium	heart
24	chr3:61207400-61208000	Enhancers	Sigmoid Colon	Sigmoid Colon
25	chr3:61207400-61208200	Enhancers	Brain Cingulate Gyrus	brain
26	chr3:61207400-61208200	Enhancers	Left Ventricle	heart
27	chr3:61207400-61208600	Flanking Active TSS	Brain Substantia Nigra	brain

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