Variant report

Variant	rs404214
Chromosome Location	chr2:40454348-40454349
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 76 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:64)

rs_ID	r²[population]
rs1012311	0.91[GIH][hapmap]
rs10490209	0.92[CEU][hapmap];0.91[GIH][hapmap]
rs105287	0.89[CHB][hapmap];0.81[JPT][hapmap]
rs106706	0.89[CHB][hapmap];0.83[CHD][hapmap];0.81[JPT][hapmap]
rs107008	0.89[AMR][1000 genomes];0.95[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs12993486	0.83[CHB][hapmap];0.81[ASN][1000 genomes]
rs1428571	0.86[CHD][hapmap]
rs1617492	0.82[ASN][1000 genomes]
rs1641453	0.85[AMR][1000 genomes];0.87[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs1641454	0.96[ASN][1000 genomes]
rs17025367	0.89[CHB][hapmap];0.81[JPT][hapmap]
rs17025372	0.89[CHB][hapmap];0.83[CHD][hapmap];0.86[JPT][hapmap]
rs17025380	0.89[CHB][hapmap];0.86[JPT][hapmap];0.81[ASN][1000 genomes]
rs17025588	1.00[CHB][hapmap];0.93[CHD][hapmap];0.91[GIH][hapmap];0.95[JPT][hapmap]
rs2072529	0.89[CHB][hapmap];0.83[CHD][hapmap];0.86[JPT][hapmap]
rs2072530	0.88[CHD][hapmap];0.81[JPT][hapmap]
rs2540904	1.00[CHB][hapmap];0.88[CHD][hapmap];0.89[GIH][hapmap];1.00[JPT][hapmap];0.97[ASN][1000 genomes]
rs367596	0.97[ASN][1000 genomes]
rs368577	0.85[CHB][hapmap];0.88[CHD][hapmap];0.90[JPT][hapmap]
rs369251	0.92[CEU][hapmap];0.82[CHB][hapmap]
rs371492	1.00[CHB][hapmap];1.00[JPT][hapmap];0.97[ASN][1000 genomes]
rs372072	0.89[CHB][hapmap];0.84[CHD][hapmap];0.81[JPT][hapmap]
rs373273	0.84[AMR][1000 genomes];0.92[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs376303	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[AMR][1000 genomes];0.94[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs376535	0.94[CHB][hapmap];0.88[CHD][hapmap];0.84[GIH][hapmap]
rs379804	0.81[ASN][1000 genomes]
rs380590	0.80[CHB][hapmap];0.88[CHD][hapmap];0.93[GIH][hapmap];0.82[JPT][hapmap]
rs381610	0.85[CHB][hapmap];0.86[CHD][hapmap];0.84[GIH][hapmap];0.90[JPT][hapmap]
rs384673	0.86[ASN][1000 genomes]
rs385341	0.89[CHB][hapmap];0.85[CHD][hapmap];0.86[JPT][hapmap]
rs385665	0.83[CHB][hapmap];0.81[JPT][hapmap]
rs386984	0.88[AMR][1000 genomes];0.95[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs390145	0.95[CHB][hapmap];0.95[JPT][hapmap];0.93[ASN][1000 genomes]
rs392317	0.81[CHB][hapmap];0.82[JPT][hapmap]
rs392953	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.93[YRI][hapmap];0.96[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs395755	0.84[AMR][1000 genomes];0.92[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs395987	1.00[CHB][hapmap];0.88[CHD][hapmap];0.82[GIH][hapmap]
rs398898	0.81[ASN][1000 genomes]
rs404005	0.89[CHB][hapmap];0.86[JPT][hapmap]
rs404226	1.00[CHB][hapmap];0.95[JPT][hapmap];0.97[ASN][1000 genomes]
rs405804	0.89[CHB][hapmap];0.81[JPT][hapmap]
rs407148	1.00[CHB][hapmap];0.88[CHD][hapmap];0.84[GIH][hapmap];1.00[JPT][hapmap];0.97[ASN][1000 genomes]
rs408263	1.00[CHB][hapmap];0.98[CHD][hapmap];0.89[GIH][hapmap];1.00[JPT][hapmap];0.96[ASN][1000 genomes]
rs409522	0.89[CHB][hapmap];0.81[JPT][hapmap]
rs410912	0.81[ASN][1000 genomes]
rs41483748	0.80[GIH][hapmap]
rs419125	0.87[AMR][1000 genomes];0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs426140	0.81[ASN][1000 genomes]
rs433572	0.89[CHB][hapmap]
rs435404	0.92[CEU][hapmap];0.85[CHB][hapmap];0.95[JPT][hapmap];0.80[YRI][hapmap];0.89[AMR][1000 genomes];0.95[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs436245	0.82[ASW][hapmap];0.85[CHB][hapmap];0.91[JPT][hapmap];0.84[TSI][hapmap];0.81[AMR][1000 genomes];0.84[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs446538	0.89[CHB][hapmap];0.82[MEX][hapmap]
rs447136	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.98[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.90[LWK][hapmap];0.88[MEX][hapmap];0.97[MKK][hapmap];1.00[TSI][hapmap];0.89[YRI][hapmap];0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs449383	0.85[CHB][hapmap];0.81[CHD][hapmap];0.90[JPT][hapmap]
rs450450	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.84[AMR][1000 genomes];0.92[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs473400	0.84[AMR][1000 genomes];0.92[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs481800	0.83[AMR][1000 genomes];0.96[ASN][1000 genomes]
rs530048	0.87[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs60592471	0.83[ASN][1000 genomes]
rs62148799	0.89[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs66950674	0.85[AMR][1000 genomes];0.84[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs6706969	0.97[ASN][1000 genomes]
rs671010	0.84[AMR][1000 genomes];0.94[ASN][1000 genomes]
rs6757136	0.83[AMR][1000 genomes];0.82[EUR][1000 genomes];0.88[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:12 , 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	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
4	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
5	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
6	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
7	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
8	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
9	nsv873911	chr2:40423454-41161464	ZNF genes & repeats Enhancers Weak transcription Active TSS Strong transcription Flanking Active TSS Flanking Bivalent TSS/Enh Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
10	nsv1008190	chr2:40429442-40506772	Enhancers Weak transcription ZNF genes & repeats Flanking Active TSS Active TSS Genic enhancers Strong transcription Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
11	esv34071	chr2:40435231-40578229	Weak transcription Active TSS Enhancers Flanking Active TSS Strong transcription ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
12	nsv524586	chr2:40447587-40497501	Weak transcription Enhancers Flanking Active TSS Genic enhancers ZNF genes & repeats Active TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs404214	FAM82A1	cis	cerebellum	SCAN

Chromatin state (count:34 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:40446400-40454400	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
2	chr2:40446400-40455400	Weak transcription	Psoas Muscle	Psoas
3	chr2:40447800-40454400	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
4	chr2:40447800-40457600	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
5	chr2:40448000-40487400	Weak transcription	Monocytes-CD14+_RO01746	blood
6	chr2:40448200-40455400	Weak transcription	HSMM	muscle
7	chr2:40451400-40455600	Weak transcription	Aorta	Aorta
8	chr2:40451400-40490000	Weak transcription	Dnd41	blood
9	chr2:40452000-40454600	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
10	chr2:40452400-40454400	Enhancers	Fetal Heart	heart
11	chr2:40452400-40454800	Enhancers	Foreskin Fibroblast Primary Cells skin02	Skin
12	chr2:40452600-40454600	Enhancers	Colon Smooth Muscle	Colon
13	chr2:40452600-40455600	Enhancers	Cortex derived primary cultured neurospheres	brain
14	chr2:40453400-40454400	Weak transcription	HUES6 Cell Line	embryonic stem cell
15	chr2:40453600-40454400	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
16	chr2:40453600-40454400	Weak transcription	iPS-18 Cell Line	embryonic stem cell
17	chr2:40453600-40454800	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
18	chr2:40453600-40455400	Weak transcription	Left Ventricle	heart
19	chr2:40453600-40455400	Weak transcription	HSMMtube	muscle
20	chr2:40453600-40455600	Enhancers	Muscle Satellite Cultured Cells	--
21	chr2:40453600-40455800	Weak transcription	HUES48 Cell Line	embryonic stem cell
22	chr2:40453600-40457200	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
23	chr2:40453600-40457200	Weak transcription	Duodenum Smooth Muscle	Duodenum
24	chr2:40453600-40459400	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
25	chr2:40453800-40455600	Weak transcription	Fetal Muscle Leg	muscle
26	chr2:40453800-40455600	Weak transcription	Skeletal Muscle Female	skeletal muscle
27	chr2:40453800-40471000	Weak transcription	Right Ventricle	heart
28	chr2:40453800-40471400	Weak transcription	Right Atrium	heart
29	chr2:40454000-40455000	Weak transcription	Brain Germinal Matrix	brain
30	chr2:40454000-40455600	Weak transcription	Fetal Brain Male	brain
31	chr2:40454200-40454400	Enhancers	Rectal Smooth Muscle	rectum
32	chr2:40454200-40454400	Enhancers	Osteobl	bone
33	chr2:40454200-40455400	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
34	chr2:40454200-40458000	Weak transcription	Stomach Smooth Muscle	stomach

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