Variant report

Variant	rs10199484
Chromosome Location	chr2:21513546-21513547
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 51 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:49)

rs_ID	r²[population]
rs10185261	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs10185535	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs10192339	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs10196906	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs10199765	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs12467767	0.84[EUR][1000 genomes]
rs21730	0.86[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs219505	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs219506	0.84[EUR][1000 genomes]
rs219507	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs219508	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs219509	0.84[EUR][1000 genomes]
rs219510	0.84[EUR][1000 genomes]
rs219531	0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs219532	0.81[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs219533	0.82[EUR][1000 genomes]
rs219534	0.81[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs219535	0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs219536	0.83[EUR][1000 genomes]
rs219537	0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs219538	0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs219539	0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs219540	0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs219541	0.83[EUR][1000 genomes]
rs219546	0.82[EUR][1000 genomes]
rs2217745	0.82[EUR][1000 genomes]
rs2337901	0.81[CEU][hapmap]
rs380969	0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs389795	0.86[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs390062	0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs391070	0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs399991	0.84[AFR][1000 genomes];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs401843	0.83[EUR][1000 genomes]
rs412558	0.86[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs418451	0.99[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs423277	0.86[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs425440	0.83[EUR][1000 genomes]
rs439907	0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4665702	0.84[TSI][hapmap]
rs55841071	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs56286635	0.83[EUR][1000 genomes]
rs59014890	0.90[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs59020225	0.96[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs59920883	0.82[EUR][1000 genomes]
rs61603728	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6708193	0.83[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs72789650	0.83[EUR][1000 genomes]
rs72789656	0.83[EUR][1000 genomes]
rs7369047	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[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	nsv1011486	chr2:21475803-22364002	Enhancers Weak transcription ZNF genes & repeats Flanking Active TSS Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases
2	nsv535602	chr2:21475803-22364002	Enhancers Weak transcription ZNF genes & repeats Active TSS Bivalent Enhancer Flanking Active TSS Strong transcription Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs10199484	GEN1	cis	cerebellum	SCAN
rs10199484	RHOB	cis	cerebellum	SCAN

Chromatin state (count:15 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:21510600-21513600	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
2	chr2:21510600-21514600	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
3	chr2:21510600-21514600	Enhancers	Cortex derived primary cultured neurospheres	brain
4	chr2:21511400-21527400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
5	chr2:21511800-21513600	Enhancers	Brain Substantia Nigra	brain
6	chr2:21512400-21513600	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
7	chr2:21512800-21513600	Enhancers	Rectal Smooth Muscle	rectum
8	chr2:21513000-21514600	Weak transcription	Brain Cingulate Gyrus	brain
9	chr2:21513000-21517400	Weak transcription	Brain Inferior Temporal Lobe	brain
10	chr2:21513000-21538200	Weak transcription	Aorta	Aorta
11	chr2:21513200-21514200	Weak transcription	Brain Hippocampus Middle	brain
12	chr2:21513200-21514400	Weak transcription	Brain Angular Gyrus	brain
13	chr2:21513200-21515400	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
14	chr2:21513400-21514600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
15	chr2:21513400-21517000	Weak transcription	Ovary	ovary

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