Variant report

Variant	rs2302797
Chromosome Location	chr2:53956883-53956884
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 65 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:61)

rs_ID	r²[population]
rs10490468	0.92[CHB][hapmap];0.96[CHD][hapmap];0.90[JPT][hapmap];0.88[MKK][hapmap];0.93[ASN][1000 genomes]
rs11897282	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.96[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.95[MKK][hapmap];1.00[TSI][hapmap];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11901698	1.00[CEU][hapmap];1.00[CHB][hapmap];0.80[JPT][hapmap];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs1232	0.84[CHB][hapmap]
rs13408029	0.91[CHB][hapmap];0.90[JPT][hapmap];0.83[AMR][1000 genomes];0.96[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs17039525	0.81[AMR][1000 genomes]
rs17045176	1.00[CHB][hapmap];1.00[JPT][hapmap];0.97[ASN][1000 genomes]
rs17045203	1.00[CHB][hapmap];0.92[CHD][hapmap];0.80[JPT][hapmap];0.85[ASN][1000 genomes]
rs17520505	0.92[CHB][hapmap];0.90[JPT][hapmap];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs17521008	1.00[ASW][hapmap];0.89[CHD][hapmap];1.00[GIH][hapmap];1.00[MKK][hapmap];0.88[TSI][hapmap];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2008082	0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2287340	1.00[CHB][hapmap];0.89[CHD][hapmap];0.84[ASN][1000 genomes]
rs2542572	0.94[CEU][hapmap];1.00[CHB][hapmap];0.90[JPT][hapmap];0.97[AMR][1000 genomes];0.92[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2542573	0.85[ASN][1000 genomes]
rs2542578	0.88[AMR][1000 genomes];0.89[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs2542580	0.85[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs2542581	1.00[ASW][hapmap];1.00[CEU][hapmap];0.84[CHD][hapmap];0.96[GIH][hapmap];0.93[MEX][hapmap];0.97[MKK][hapmap];1.00[TSI][hapmap];0.98[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs2542582	0.92[CHB][hapmap];0.83[LWK][hapmap];0.82[MKK][hapmap];1.00[YRI][hapmap]
rs2542583	0.82[ASN][1000 genomes]
rs2542589	0.92[CHB][hapmap];0.87[ASN][1000 genomes]
rs2542590	0.87[ASN][1000 genomes]
rs2542591	0.92[CHB][hapmap];0.80[JPT][hapmap];0.87[ASN][1000 genomes]
rs2542592	0.84[CHB][hapmap];0.80[JPT][hapmap];0.84[ASN][1000 genomes]
rs2543629	0.90[ASW][hapmap];1.00[CEU][hapmap];0.92[CHB][hapmap];0.93[GIH][hapmap];0.88[MEX][hapmap];0.87[TSI][hapmap];0.81[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2692512	0.83[ASN][1000 genomes]
rs2692513	0.83[ASN][1000 genomes]
rs2692519	0.92[CHB][hapmap];1.00[CHD][hapmap];0.80[JPT][hapmap];0.86[MKK][hapmap];0.88[ASN][1000 genomes]
rs2692521	0.84[ASN][1000 genomes]
rs2692522	0.85[ASN][1000 genomes]
rs2692523	0.88[AMR][1000 genomes];0.89[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs2692533	0.92[CHB][hapmap];0.89[CHD][hapmap];0.80[JPT][hapmap];0.86[MKK][hapmap];0.81[ASN][1000 genomes]
rs2909262	0.84[ASN][1000 genomes]
rs2949813	0.92[CHB][hapmap];0.90[JPT][hapmap];0.88[ASN][1000 genomes]
rs35772199	0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs3770394	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs3770395	1.00[ASN][1000 genomes]
rs3770397	0.97[ASN][1000 genomes]
rs3770399	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3770411	0.89[ASW][hapmap];0.84[CEU][hapmap];0.92[CHB][hapmap];0.92[CHD][hapmap];0.87[TSI][hapmap];0.86[ASN][1000 genomes]
rs3922262	0.81[ASN][1000 genomes]
rs4116709	0.92[CHB][hapmap];0.90[JPT][hapmap];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs55897904	0.90[ASN][1000 genomes]
rs56214822	0.88[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs58326257	0.90[ASN][1000 genomes]
rs62137565	0.91[AFR][1000 genomes];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs62137573	0.99[ASN][1000 genomes]
rs62137602	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs62137605	0.88[ASN][1000 genomes]
rs62137606	0.97[ASN][1000 genomes]
rs62137610	0.88[ASN][1000 genomes]
rs62137611	0.88[ASN][1000 genomes]
rs62137612	0.85[ASN][1000 genomes]
rs6730006	1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs719127	1.00[CEU][hapmap];1.00[CHB][hapmap];0.90[JPT][hapmap];0.90[AMR][1000 genomes];0.99[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs72901256	0.99[ASN][1000 genomes]
rs7558968	0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs7583622	0.90[CEU][hapmap];0.97[LWK][hapmap];0.81[TSI][hapmap]
rs7600817	1.00[ASN][1000 genomes]
rs805316	0.84[CHB][hapmap]
rs805435	0.81[AMR][1000 genomes];0.82[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs805437	0.84[CHB][hapmap]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1003263	chr2:53863287-54055359	Strong transcription Enhancers Active TSS Flanking Active TSS Weak transcription ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	20 gene(s)	inside rSNPs	diseases
2	nsv535720	chr2:53863287-54055359	Enhancers Weak transcription Strong transcription Active TSS Flanking Active TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	20 gene(s)	inside rSNPs	diseases
3	nsv834058	chr2:53900674-54072011	Strong transcription Flanking Active TSS Weak transcription Enhancers ZNF genes & repeats Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	20 gene(s)	inside rSNPs	diseases
4	esv1844655	chr2:53929855-53972693	Strong transcription ZNF genes & repeats Weak transcription Genic enhancers Flanking Active TSS Enhancers Active TSS Transcr. at gene 5' and 3'	Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs2302797	RAE1	trans	cerebellum	SCAN
rs2302797	PSME4	cis	cerebellum	SCAN

Chromatin state (count:112 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:53898000-53957400	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
2	chr2:53908600-53982200	Weak transcription	Small Intestine	intestine
3	chr2:53910000-53994000	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
4	chr2:53910200-53990600	Weak transcription	Primary T killer memory cells from peripheral blood	blood
5	chr2:53918400-53994000	Weak transcription	Fetal Heart	heart
6	chr2:53925400-53979400	Weak transcription	Psoas Muscle	Psoas
7	chr2:53927600-53960200	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
8	chr2:53936600-53968400	Weak transcription	Pancreas	Pancrea
9	chr2:53936600-53978600	Weak transcription	Hela-S3	cervix
10	chr2:53936800-53985400	Weak transcription	Stomach Smooth Muscle	stomach
11	chr2:53937000-53983800	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
12	chr2:53937000-53994400	Weak transcription	Placenta Amnion	Placenta Amnion
13	chr2:53937200-53961400	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
14	chr2:53937200-53964400	Weak transcription	Aorta	Aorta
15	chr2:53937200-53966800	Weak transcription	Gastric	stomach
16	chr2:53937200-53978600	Weak transcription	NH-A	brain
17	chr2:53937200-53983600	Weak transcription	Right Ventricle	heart
18	chr2:53937200-53994200	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
19	chr2:53937400-53964000	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
20	chr2:53937400-53979600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
21	chr2:53937400-53990200	Weak transcription	Primary T helper naive cells from peripheral blood	blood
22	chr2:53937400-53994400	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
23	chr2:53937600-53961600	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
24	chr2:53937800-53957000	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
25	chr2:53938000-53961400	Weak transcription	NHEK	skin
26	chr2:53938000-53974800	Weak transcription	H1 Cell Line	embryonic stem cell
27	chr2:53938000-53974800	Weak transcription	Placenta	Placenta
28	chr2:53938200-53967000	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
29	chr2:53938200-53975200	Weak transcription	Duodenum Mucosa	Duodenum
30	chr2:53938400-53963600	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
31	chr2:53938400-53969400	Weak transcription	Rectal Smooth Muscle	rectum
32	chr2:53938400-53969600	Weak transcription	Esophagus	oesophagus
33	chr2:53938400-53975000	Weak transcription	Fetal Kidney	kidney
34	chr2:53938400-53982800	Weak transcription	HUES48 Cell Line	embryonic stem cell
35	chr2:53938400-53983400	Weak transcription	HSMMtube	muscle
36	chr2:53938400-53992400	Weak transcription	K562	blood
37	chr2:53938600-53961000	Weak transcription	HUES6 Cell Line	embryonic stem cell
38	chr2:53938600-53972000	Weak transcription	HSMM	muscle
39	chr2:53940600-53957400	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
40	chr2:53941800-53957400	Weak transcription	Liver	Liver
41	chr2:53941800-53974400	Weak transcription	iPS-20b Cell Line	embryonic stem cell
42	chr2:53941800-53976400	Weak transcription	Colon Smooth Muscle	Colon
43	chr2:53943800-53960600	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
44	chr2:53943800-53974800	Weak transcription	Rectal Mucosa Donor 29	rectum
45	chr2:53943800-53983600	Weak transcription	Ovary	ovary
46	chr2:53943800-53983600	Weak transcription	Thymus	Thymus
47	chr2:53943800-53983800	Weak transcription	Left Ventricle	heart
48	chr2:53944000-53960200	Weak transcription	Rectal Mucosa Donor 31	rectum
49	chr2:53944000-53974600	Weak transcription	Duodenum Smooth Muscle	Duodenum
50	chr2:53945400-53957800	Weak transcription	HUVEC	blood vessel

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