Variant report

Variant	rs3821080
Chromosome Location	chr2:53967246-53967247
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 71 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:67)

rs_ID	r²[population]
rs10181752	0.87[ASN][1000 genomes]
rs10181876	0.98[AMR][1000 genomes];0.94[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs10185375	0.91[CHB][hapmap];0.93[ASN][1000 genomes]
rs10187718	0.93[CEU][hapmap];0.89[YRI][hapmap];0.85[AFR][1000 genomes];0.90[AMR][1000 genomes];0.93[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10190578	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.86[MEX][hapmap];1.00[TSI][hapmap];0.94[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs10191950	0.85[AMR][1000 genomes];0.94[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs10193711	0.81[AMR][1000 genomes];0.91[ASN][1000 genomes]
rs10197062	0.82[AFR][1000 genomes];0.83[AMR][1000 genomes];0.88[ASN][1000 genomes]
rs10200897	0.91[AFR][1000 genomes];0.90[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs10210726	0.88[CHB][hapmap];0.89[ASN][1000 genomes]
rs10211188	0.92[AFR][1000 genomes];0.90[AMR][1000 genomes];0.92[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10211650	0.90[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs10490470	1.00[CHB][hapmap];1.00[JPT][hapmap];0.85[YRI][hapmap];0.84[AFR][1000 genomes];0.83[AMR][1000 genomes];0.93[ASN][1000 genomes]
rs11684574	0.90[ASN][1000 genomes]
rs12612589	0.91[CHB][hapmap];0.88[ASN][1000 genomes]
rs12613353	0.83[ASW][hapmap];0.87[LWK][hapmap];0.82[MEX][hapmap];0.80[AFR][1000 genomes];0.80[AMR][1000 genomes]
rs12613682	0.91[CHB][hapmap];0.91[ASN][1000 genomes]
rs12616124	0.91[ASN][1000 genomes]
rs12616774	0.93[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[YRI][hapmap];0.92[AFR][1000 genomes];0.90[AMR][1000 genomes];0.87[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12617360	0.88[ASN][1000 genomes]
rs12617668	0.87[ASN][1000 genomes]
rs12620190	0.86[ASN][1000 genomes]
rs12620208	0.86[ASN][1000 genomes]
rs12620325	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12621547	0.88[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs12621557	0.92[ASN][1000 genomes]
rs12621635	0.91[CHB][hapmap];0.90[CHD][hapmap];0.95[GIH][hapmap];0.92[ASN][1000 genomes]
rs13383167	0.85[AMR][1000 genomes];0.92[ASN][1000 genomes]
rs13393197	0.88[ASN][1000 genomes]
rs13414183	0.82[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.90[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.98[LWK][hapmap];0.93[MEX][hapmap];0.91[MKK][hapmap];1.00[TSI][hapmap];0.95[YRI][hapmap];0.93[AFR][1000 genomes];0.90[AMR][1000 genomes];0.94[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs13414472	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[YRI][hapmap];0.92[AFR][1000 genomes];0.90[AMR][1000 genomes];0.94[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs13415842	0.87[ASN][1000 genomes]
rs13421512	0.88[ASN][1000 genomes]
rs13423576	0.91[AFR][1000 genomes];0.89[AMR][1000 genomes];0.94[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs17045114	0.88[JPT][hapmap];0.88[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs17045116	0.84[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs17045125	0.82[CHB][hapmap];0.87[ASN][1000 genomes]
rs17045215	0.91[CHB][hapmap];0.86[ASN][1000 genomes]
rs2009149	0.89[ASN][1000 genomes]
rs2068017	0.86[CEU][hapmap];0.92[TSI][hapmap]
rs2272249	0.87[CHD][hapmap]
rs2287344	0.91[CHB][hapmap];0.94[CHD][hapmap];0.86[ASN][1000 genomes]
rs2287345	0.91[CHB][hapmap];0.86[ASN][1000 genomes]
rs2287348	0.87[CEU][hapmap];0.82[MEX][hapmap]
rs2287512	0.87[CHD][hapmap];0.91[GIH][hapmap];0.96[TSI][hapmap];0.86[EUR][1000 genomes]
rs2357491	0.91[CHD][hapmap];0.81[GIH][hapmap]
rs28439002	0.91[ASN][1000 genomes]
rs3731973	0.93[CEU][hapmap];0.88[TSI][hapmap]
rs3755120	0.82[CHB][hapmap];0.97[CHD][hapmap];0.87[ASN][1000 genomes]
rs3770398	0.93[AFR][1000 genomes];0.90[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs3770400	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[YRI][hapmap];0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs3770401	0.91[CHB][hapmap];0.87[CHD][hapmap];0.95[GIH][hapmap];0.89[ASN][1000 genomes]
rs3770412	0.85[EUR][1000 genomes]
rs3850345	0.87[ASN][1000 genomes]
rs3861570	0.87[AMR][1000 genomes];0.83[ASN][1000 genomes]
rs55839073	0.88[ASN][1000 genomes]
rs6705484	0.92[CHB][hapmap];0.90[CHD][hapmap];0.89[JPT][hapmap];0.88[ASN][1000 genomes]
rs6712204	1.00[CHB][hapmap];0.94[CHD][hapmap];0.80[GIH][hapmap];1.00[JPT][hapmap];0.82[LWK][hapmap];0.93[MEX][hapmap];0.88[TSI][hapmap];0.83[AMR][1000 genomes];0.91[ASN][1000 genomes]
rs6714424	0.82[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.90[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.98[LWK][hapmap];0.93[MEX][hapmap];0.80[MKK][hapmap];1.00[TSI][hapmap];0.90[YRI][hapmap];0.92[AFR][1000 genomes];0.90[AMR][1000 genomes];0.94[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6717642	0.92[AFR][1000 genomes];0.90[AMR][1000 genomes];0.94[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs72793658	0.90[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs7568771	0.88[ASN][1000 genomes]
rs7582542	0.85[AMR][1000 genomes];0.94[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7586686	1.00[CHB][hapmap];0.87[CHD][hapmap];0.80[GIH][hapmap];1.00[JPT][hapmap];0.82[LWK][hapmap];0.93[MEX][hapmap];0.88[TSI][hapmap];0.81[YRI][hapmap];0.85[AMR][1000 genomes];0.88[ASN][1000 genomes]
rs7595713	0.91[CHB][hapmap];0.88[ASN][1000 genomes]
rs7595816	0.92[CHB][hapmap];1.00[CHD][hapmap];0.89[JPT][hapmap];0.90[ASN][1000 genomes]
rs7609067	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.85[AMR][1000 genomes];0.94[EUR][1000 genomes];0.94[ASN][1000 genomes]

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

No data

Chromatin state (count:115 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:53908600-53982200	Weak transcription	Small Intestine	intestine
2	chr2:53910000-53994000	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
3	chr2:53910200-53990600	Weak transcription	Primary T killer memory cells from peripheral blood	blood
4	chr2:53918400-53994000	Weak transcription	Fetal Heart	heart
5	chr2:53925400-53979400	Weak transcription	Psoas Muscle	Psoas
6	chr2:53936600-53968400	Weak transcription	Pancreas	Pancrea
7	chr2:53936600-53978600	Weak transcription	Hela-S3	cervix
8	chr2:53936800-53985400	Weak transcription	Stomach Smooth Muscle	stomach
9	chr2:53937000-53983800	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
10	chr2:53937000-53994400	Weak transcription	Placenta Amnion	Placenta Amnion
11	chr2:53937200-53978600	Weak transcription	NH-A	brain
12	chr2:53937200-53983600	Weak transcription	Right Ventricle	heart
13	chr2:53937200-53994200	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
14	chr2:53937400-53979600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
15	chr2:53937400-53990200	Weak transcription	Primary T helper naive cells from peripheral blood	blood
16	chr2:53937400-53994400	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
17	chr2:53938000-53974800	Weak transcription	H1 Cell Line	embryonic stem cell
18	chr2:53938000-53974800	Weak transcription	Placenta	Placenta
19	chr2:53938200-53975200	Weak transcription	Duodenum Mucosa	Duodenum
20	chr2:53938400-53969400	Weak transcription	Rectal Smooth Muscle	rectum
21	chr2:53938400-53969600	Weak transcription	Esophagus	oesophagus
22	chr2:53938400-53975000	Weak transcription	Fetal Kidney	kidney
23	chr2:53938400-53982800	Weak transcription	HUES48 Cell Line	embryonic stem cell
24	chr2:53938400-53983400	Weak transcription	HSMMtube	muscle
25	chr2:53938400-53992400	Weak transcription	K562	blood
26	chr2:53938600-53972000	Weak transcription	HSMM	muscle
27	chr2:53941800-53974400	Weak transcription	iPS-20b Cell Line	embryonic stem cell
28	chr2:53941800-53976400	Weak transcription	Colon Smooth Muscle	Colon
29	chr2:53943800-53974800	Weak transcription	Rectal Mucosa Donor 29	rectum
30	chr2:53943800-53983600	Weak transcription	Ovary	ovary
31	chr2:53943800-53983600	Weak transcription	Thymus	Thymus
32	chr2:53943800-53983800	Weak transcription	Left Ventricle	heart
33	chr2:53944000-53974600	Weak transcription	Duodenum Smooth Muscle	Duodenum
34	chr2:53945800-53968400	Weak transcription	Brain Anterior Caudate	brain
35	chr2:53949800-53974200	Weak transcription	HUES64 Cell Line	embryonic stem cell
36	chr2:53952200-53978600	Weak transcription	Osteobl	bone
37	chr2:53952400-53983600	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
38	chr2:53952600-53974800	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
39	chr2:53954400-53972000	Weak transcription	NHDF-Ad	bronchial
40	chr2:53954800-53969600	Weak transcription	Muscle Satellite Cultured Cells	--
41	chr2:53954800-53982000	Weak transcription	Sigmoid Colon	Sigmoid Colon
42	chr2:53954800-53983800	Weak transcription	Lung	lung
43	chr2:53955800-53974600	Weak transcription	iPS-18 Cell Line	embryonic stem cell
44	chr2:53956000-53979600	Weak transcription	ES-I3 Cell Line	embryonic stem cell
45	chr2:53956000-53983400	Weak transcription	Fetal Brain Male	brain
46	chr2:53956200-53983000	Weak transcription	Fetal Muscle Leg	muscle
47	chr2:53956800-53967800	Weak transcription	Brain Substantia Nigra	brain
48	chr2:53956800-53968400	Weak transcription	Brain Cingulate Gyrus	brain
49	chr2:53956800-53974600	Weak transcription	Skeletal Muscle Female	skeletal muscle
50	chr2:53957000-53983800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived

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