Variant report

Variant	rs408662
Chromosome Location	chr2:40409668-40409669
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 80 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:71)

rs_ID	r²[population]
rs105288	0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs118899	0.89[AMR][1000 genomes];0.92[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs1641452	0.84[ASN][1000 genomes]
rs1641456	0.96[ASN][1000 genomes]
rs1641457	0.96[ASN][1000 genomes]
rs1641458	0.96[ASN][1000 genomes]
rs1651355	0.96[ASN][1000 genomes]
rs28628343	0.91[ASN][1000 genomes]
rs35487690	0.88[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs368642	0.93[AFR][1000 genomes];0.84[AMR][1000 genomes];0.83[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs369140	0.96[ASN][1000 genomes]
rs372052	0.96[ASN][1000 genomes]
rs373602	0.96[ASN][1000 genomes]
rs373606	0.81[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs374159	0.84[ASN][1000 genomes]
rs374711	0.91[AFR][1000 genomes];0.88[AMR][1000 genomes];0.83[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs375180	0.97[ASN][1000 genomes]
rs376170	0.96[ASN][1000 genomes]
rs376491	0.91[ASN][1000 genomes]
rs379410	0.94[AFR][1000 genomes];0.92[AMR][1000 genomes];0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs380975	0.96[ASN][1000 genomes]
rs384511	0.93[AFR][1000 genomes];0.84[AMR][1000 genomes];0.83[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs384791	0.96[ASN][1000 genomes]
rs384994	0.84[ASN][1000 genomes]
rs385561	0.96[ASN][1000 genomes]
rs389109	0.96[ASN][1000 genomes]
rs391631	0.93[ASN][1000 genomes]
rs393711	0.96[ASN][1000 genomes]
rs399061	0.80[ASN][1000 genomes]
rs402307	0.84[ASN][1000 genomes]
rs406736	0.84[ASN][1000 genomes]
rs406880	0.88[AMR][1000 genomes];0.80[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs407267	0.84[ASN][1000 genomes]
rs407889	0.88[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs408009	0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs410031	0.92[ASN][1000 genomes]
rs410480	0.95[ASN][1000 genomes]
rs413711	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs414766	0.92[ASN][1000 genomes]
rs417464	0.81[ASN][1000 genomes]
rs417591	0.95[ASN][1000 genomes]
rs417873	0.91[AFR][1000 genomes];0.85[AMR][1000 genomes];0.83[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs418380	0.96[ASN][1000 genomes]
rs418780	0.88[AMR][1000 genomes];0.91[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs421870	0.96[AMR][1000 genomes];0.92[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs422411	0.89[AFR][1000 genomes];0.85[AMR][1000 genomes];0.93[ASN][1000 genomes]
rs423075	0.93[AFR][1000 genomes];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs426295	0.96[ASN][1000 genomes]
rs427632	0.84[ASN][1000 genomes]
rs429227	0.84[ASN][1000 genomes]
rs430314	0.91[AFR][1000 genomes];0.88[AMR][1000 genomes];0.83[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs430394	0.81[ASN][1000 genomes]
rs430473	0.93[ASN][1000 genomes]
rs432142	0.80[ASN][1000 genomes]
rs432981	0.84[ASN][1000 genomes]
rs434326	0.96[ASN][1000 genomes]
rs439960	0.93[AFR][1000 genomes];0.84[AMR][1000 genomes];0.83[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs441196	0.89[AMR][1000 genomes];0.95[ASN][1000 genomes]
rs441413	0.95[AMR][1000 genomes];0.89[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs441593	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs441802	0.93[ASN][1000 genomes]
rs442476	0.84[ASN][1000 genomes]
rs444504	0.80[ASN][1000 genomes]
rs450116	0.95[ASN][1000 genomes]
rs451074	0.95[AMR][1000 genomes];0.91[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs452138	0.84[ASN][1000 genomes]
rs479909	0.81[ASN][1000 genomes]
rs581477	0.92[AMR][1000 genomes];0.87[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs581568	0.92[AMR][1000 genomes];0.87[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs679339	0.90[AFR][1000 genomes];0.84[AMR][1000 genomes];0.81[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs688673	0.97[AMR][1000 genomes];0.87[EUR][1000 genomes];0.96[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:9 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv529606	chr2:40206280-40896881	Flanking Active TSS Enhancers Active TSS Weak transcription Genic enhancers ZNF genes & repeats Strong transcription Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
2	nsv873902	chr2:40231282-40466268	Weak transcription Strong transcription Enhancers Flanking Active TSS Genic enhancers Active TSS ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
3	nsv1004092	chr2:40264608-40451701	Weak transcription Enhancers Genic enhancers Strong transcription Flanking Active TSS ZNF genes & repeats Bivalent Enhancer Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
4	nsv1000572	chr2:40271958-40458911	Weak transcription Enhancers Genic enhancers Strong transcription Flanking Active TSS Active TSS ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
5	nsv535654	chr2:40271958-40458911	Enhancers Weak transcription Genic enhancers Strong transcription Flanking Active TSS ZNF genes & repeats Active TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
6	nsv581502	chr2:40273903-40459645	Weak transcription Enhancers Strong transcription Flanking Active TSS Genic enhancers Active TSS ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
7	nsv873904	chr2:40292289-40466268	Enhancers Strong transcription Weak transcription Flanking Active TSS Genic enhancers Active TSS ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
8	nsv873910	chr2:40391907-40466268	Weak transcription Enhancers Flanking Active TSS Strong transcription Genic enhancers ZNF genes & repeats Active TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
9	esv1851152	chr2:40393223-40512023	Weak transcription Active TSS Enhancers Strong transcription Flanking Active TSS ZNF genes & repeats Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:16 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:40392000-40413200	Weak transcription	Fetal Brain Female	brain
2	chr2:40393000-40420000	Weak transcription	Fetal Kidney	kidney
3	chr2:40393600-40416800	Weak transcription	Fetal Stomach	stomach
4	chr2:40400600-40426800	Weak transcription	Osteobl	bone
5	chr2:40405400-40430000	Weak transcription	Stomach Smooth Muscle	stomach
6	chr2:40405600-40410600	Weak transcription	Left Ventricle	heart
7	chr2:40405600-40421800	Weak transcription	Right Ventricle	heart
8	chr2:40406400-40416600	Weak transcription	Fetal Muscle Leg	muscle
9	chr2:40406600-40409800	Weak transcription	Thymus	Thymus
10	chr2:40406600-40416800	Weak transcription	Monocytes-CD14+_RO01746	blood
11	chr2:40407200-40410600	Weak transcription	HSMMtube	muscle
12	chr2:40407200-40419800	Weak transcription	HSMM	muscle
13	chr2:40407600-40410000	Weak transcription	Dnd41	blood
14	chr2:40408800-40412200	Enhancers	Fetal Heart	heart
15	chr2:40409200-40414600	Weak transcription	Pancreatic Islets	Pancreatic Islet
16	chr2:40409600-40410000	Weak transcription	Fetal Thymus	thymus

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