Variant report

Variant	rs401302
Chromosome Location	chr5:79355471-79355472
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 46 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:44)

rs_ID	r²[population]
rs194375	0.92[AMR][1000 genomes];0.87[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2434270	0.82[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs2434272	0.82[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs2434273	0.83[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs2434274	0.80[EUR][1000 genomes]
rs2434275	0.80[EUR][1000 genomes]
rs2434309	0.85[EUR][1000 genomes]
rs2434310	0.85[EUR][1000 genomes]
rs2434311	0.86[CHB][hapmap];0.91[AMR][1000 genomes];0.87[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs2434314	0.81[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs2434315	0.81[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs2434318	0.82[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs2434319	0.83[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs2438604	0.81[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs2438605	0.81[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs2438607	0.82[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs2438609	0.82[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs2438610	0.81[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs2438611	0.83[AMR][1000 genomes];0.86[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs2438612	0.82[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs2438613	0.83[AMR][1000 genomes];0.86[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs2438614	0.82[AMR][1000 genomes];0.86[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs2438617	0.85[EUR][1000 genomes]
rs2438618	0.85[EUR][1000 genomes]
rs2438650	0.80[CHB][hapmap];0.91[AMR][1000 genomes];0.87[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs2438651	0.81[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs2451933	0.81[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs2451940	0.80[CHB][hapmap];0.82[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs256440	0.80[CHB][hapmap];0.94[CHD][hapmap];1.00[GIH][hapmap];0.91[LWK][hapmap];0.90[MEX][hapmap];0.84[TSI][hapmap];0.92[AMR][1000 genomes];0.87[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs256441	0.91[AMR][1000 genomes];0.87[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs256444	0.80[CHB][hapmap];0.94[CHD][hapmap];1.00[GIH][hapmap];0.89[LWK][hapmap];0.90[MEX][hapmap];0.84[TSI][hapmap];0.92[AMR][1000 genomes];0.87[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs256446	0.92[AMR][1000 genomes];0.87[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs256447	0.80[CHB][hapmap];0.94[CHD][hapmap];0.97[GIH][hapmap];0.89[LWK][hapmap];0.90[MEX][hapmap];0.84[TSI][hapmap];0.92[AMR][1000 genomes];0.87[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs256448	0.92[AMR][1000 genomes];0.87[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs256450	0.83[EUR][1000 genomes]
rs256451	0.83[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs366471	0.82[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs366553	0.91[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs385771	0.82[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs391521	0.94[AMR][1000 genomes];0.87[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs398774	0.91[AMR][1000 genomes];0.87[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs423906	0.80[CHB][hapmap];0.97[CHD][hapmap];1.00[GIH][hapmap];0.89[LWK][hapmap];0.95[MEX][hapmap];0.94[TSI][hapmap];0.96[AMR][1000 genomes];0.88[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs434409	0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6874832	0.81[AMR][1000 genomes];0.82[EUR][1000 genomes];0.81[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	nsv432748	chr5:79300434-79577760	Enhancers Genic enhancers Weak transcription Bivalent Enhancer Flanking Active TSS Strong transcription ZNF genes & repeats Bivalent/Poised TSS Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	22 gene(s)	inside rSNPs	diseases
2	nsv882223	chr5:79330559-79357117	Active TSS Flanking Bivalent TSS/Enh Weak transcription Bivalent Enhancer Enhancers Flanking Active TSS Bivalent/Poised TSS Strong transcription Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs401302	BHMT2	cis	cerebellum	SCAN

Chromatin state (count:31 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:79338200-79363600	Weak transcription	Brain Inferior Temporal Lobe	brain
2	chr5:79338200-79367600	Weak transcription	Duodenum Smooth Muscle	Duodenum
3	chr5:79340000-79363400	Weak transcription	Left Ventricle	heart
4	chr5:79345200-79364200	Weak transcription	Right Ventricle	heart
5	chr5:79347800-79355600	Weak transcription	Brain Hippocampus Middle	brain
6	chr5:79348200-79366400	Weak transcription	Brain Substantia Nigra	brain
7	chr5:79350600-79363200	Weak transcription	Psoas Muscle	Psoas
8	chr5:79351600-79379200	Weak transcription	Pancreas	Pancrea
9	chr5:79351800-79361800	Weak transcription	Primary T cells from cord blood	blood
10	chr5:79352000-79355600	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
11	chr5:79352000-79361200	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
12	chr5:79352000-79365200	Weak transcription	H9 Cell Line	embryonic stem cell
13	chr5:79352000-79365600	Weak transcription	ES-I3 Cell Line	embryonic stem cell
14	chr5:79352000-79365800	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
15	chr5:79352200-79356600	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
16	chr5:79352200-79359600	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
17	chr5:79352400-79378200	Weak transcription	Breast Myoepithelial Primary Cells	Breast
18	chr5:79352600-79356800	Weak transcription	Fetal Heart	heart
19	chr5:79352800-79363400	Weak transcription	Fetal Muscle Trunk	muscle
20	chr5:79353200-79365600	Weak transcription	Skeletal Muscle Male	skeletal muscle
21	chr5:79353600-79363400	Weak transcription	Brain Cingulate Gyrus	brain
22	chr5:79353600-79365600	Weak transcription	Fetal Intestine Small	intestine
23	chr5:79354000-79355600	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
24	chr5:79354200-79359800	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
25	chr5:79354600-79356800	Strong transcription	Ganglion Eminence derived primary cultured neurospheres	brain
26	chr5:79354600-79378400	Weak transcription	Skeletal Muscle Female	skeletal muscle
27	chr5:79354800-79356600	Weak transcription	NHDF-Ad	bronchial
28	chr5:79355200-79355800	ZNF genes & repeats	H9 Derived Neuron Cultured Cells	ES cell derived
29	chr5:79355200-79356000	Strong transcription	Brain Anterior Caudate	brain
30	chr5:79355200-79356200	Weak transcription	Fetal Muscle Leg	muscle
31	chr5:79355400-79357400	Enhancers	Osteobl	bone

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