Variant report

Variant	rs12993486
Chromosome Location	chr2:40396296-40396297
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr2:40395306..40398028-chr2:40400733..40404513,3	K562	blood:
2	chr2:40395306..40398028-chr2:40400733..40404513,4	K562	blood:

Extended variants
information (count: 64 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:55)

rs_ID	r²[population]
rs105287	0.94[CHB][hapmap];0.86[CHD][hapmap];0.88[GIH][hapmap];0.85[JPT][hapmap];0.89[MEX][hapmap];0.83[AMR][1000 genomes];0.98[ASN][1000 genomes]
rs106706	0.94[CHB][hapmap];0.86[CHD][hapmap];0.86[GIH][hapmap];0.84[JPT][hapmap];0.96[ASN][1000 genomes]
rs13017329	1.00[CEU][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs1428571	0.85[CHB][hapmap];0.83[CHD][hapmap];0.82[LWK][hapmap];0.83[ASN][1000 genomes]
rs1641454	0.80[ASN][1000 genomes]
rs1651354	0.82[AMR][1000 genomes];0.96[ASN][1000 genomes]
rs17025367	0.94[CHB][hapmap];0.85[JPT][hapmap];0.82[YRI][hapmap];0.95[AMR][1000 genomes];0.99[ASN][1000 genomes]
rs17025372	0.91[ASW][hapmap];0.94[CHB][hapmap];0.95[CHD][hapmap];0.95[GIH][hapmap];0.90[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];0.85[TSI][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[ASN][1000 genomes]
rs17025380	0.94[CHB][hapmap];0.90[JPT][hapmap];0.83[YRI][hapmap];0.91[AMR][1000 genomes];0.85[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17025588	0.83[CHB][hapmap]
rs2072529	1.00[ASW][hapmap];1.00[CEU][hapmap];0.94[CHB][hapmap];0.95[CHD][hapmap];1.00[GIH][hapmap];0.90[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.96[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2072530	0.85[CHB][hapmap];0.90[CHD][hapmap];0.86[GIH][hapmap];0.84[JPT][hapmap];0.89[MEX][hapmap];0.82[YRI][hapmap];0.93[AMR][1000 genomes];0.92[ASN][1000 genomes]
rs2270327	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2540904	0.83[CHB][hapmap];0.81[JPT][hapmap];0.82[ASN][1000 genomes]
rs367596	0.82[ASN][1000 genomes]
rs368577	0.82[CHD][hapmap];0.85[ASN][1000 genomes]
rs368613	0.86[ASN][1000 genomes]
rs371492	0.81[CHB][hapmap];0.80[JPT][hapmap];0.82[ASN][1000 genomes]
rs372072	0.94[CHB][hapmap];0.95[CHD][hapmap];0.95[GIH][hapmap];0.84[JPT][hapmap];0.89[MEX][hapmap];0.85[AMR][1000 genomes];0.96[ASN][1000 genomes]
rs373273	0.83[ASN][1000 genomes]
rs376303	0.83[CHB][hapmap];0.81[ASN][1000 genomes]
rs376535	0.89[CHB][hapmap];0.91[CHD][hapmap];0.83[GIH][hapmap];0.94[MEX][hapmap];0.91[AMR][1000 genomes];0.93[ASN][1000 genomes]
rs379804	0.95[ASN][1000 genomes]
rs381610	0.84[ASN][1000 genomes]
rs385341	0.94[CHB][hapmap];0.93[CHD][hapmap];0.93[GIH][hapmap];0.90[JPT][hapmap];0.89[MEX][hapmap];0.82[AMR][1000 genomes];0.98[ASN][1000 genomes]
rs385665	0.89[CHB][hapmap];0.84[JPT][hapmap];0.82[AMR][1000 genomes];0.95[ASN][1000 genomes]
rs388467	0.93[ASN][1000 genomes]
rs390145	0.89[CHB][hapmap]
rs392953	0.83[CHB][hapmap];0.83[ASN][1000 genomes]
rs395755	0.83[ASN][1000 genomes]
rs395987	0.83[CHB][hapmap];0.91[CHD][hapmap];0.86[GIH][hapmap];0.84[MEX][hapmap];0.92[ASN][1000 genomes]
rs398006	0.86[ASN][1000 genomes]
rs398898	0.82[AMR][1000 genomes];0.95[ASN][1000 genomes]
rs402777	0.96[ASN][1000 genomes]
rs404005	0.94[CHB][hapmap];0.90[CHD][hapmap];0.90[JPT][hapmap];0.99[ASN][1000 genomes]
rs404214	0.83[CHB][hapmap];0.81[ASN][1000 genomes]
rs404226	0.83[CHB][hapmap];0.82[ASN][1000 genomes]
rs405804	0.94[CHB][hapmap];0.84[JPT][hapmap];0.82[AMR][1000 genomes];0.95[ASN][1000 genomes]
rs407148	0.83[CHB][hapmap];0.82[ASN][1000 genomes]
rs408263	0.83[CHB][hapmap];0.81[CHD][hapmap];0.83[ASN][1000 genomes]
rs409522	0.94[CHB][hapmap];0.85[JPT][hapmap];0.82[AMR][1000 genomes];0.98[ASN][1000 genomes]
rs410912	0.94[ASN][1000 genomes]
rs419125	0.82[ASN][1000 genomes]
rs433572	0.94[CHB][hapmap];0.90[CHD][hapmap];0.90[ASN][1000 genomes]
rs446538	0.94[CHB][hapmap];0.86[CHD][hapmap];0.91[GIH][hapmap];0.93[ASN][1000 genomes]
rs447136	0.83[CHB][hapmap];0.81[CHD][hapmap];0.83[ASN][1000 genomes]
rs449383	0.86[ASN][1000 genomes]
rs450450	0.83[CHB][hapmap];0.85[ASN][1000 genomes]
rs473400	0.85[ASN][1000 genomes]
rs481800	0.82[ASN][1000 genomes]
rs530048	0.83[ASN][1000 genomes]
rs62148799	0.82[ASN][1000 genomes]
rs6706969	0.82[ASN][1000 genomes]
rs671010	0.85[ASN][1000 genomes]
rs72792740	0.87[AFR][1000 genomes];0.95[AMR][1000 genomes];0.90[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:9 , 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	nsv1004092	chr2:40264608-40451701	Weak transcription Enhancers Genic enhancers Strong transcription Flanking Active TSS ZNF genes & repeats Bivalent Enhancer Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
4	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
5	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
6	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
7	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
8	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
9	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

No data

Chromatin state (count:40 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:40357800-40406400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
2	chr2:40366600-40403000	Weak transcription	Brain Germinal Matrix	brain
3	chr2:40375600-40401800	Weak transcription	HSMMtube	muscle
4	chr2:40378000-40399000	Weak transcription	Brain Inferior Temporal Lobe	brain
5	chr2:40381600-40398800	Weak transcription	Brain Angular Gyrus	brain
6	chr2:40388400-40396400	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
7	chr2:40391600-40397600	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
8	chr2:40392000-40413200	Weak transcription	Fetal Brain Female	brain
9	chr2:40392600-40405200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
10	chr2:40392800-40397400	Weak transcription	Dnd41	blood
11	chr2:40393000-40398000	Weak transcription	Fetal Brain Male	brain
12	chr2:40393000-40420000	Weak transcription	Fetal Kidney	kidney
13	chr2:40393200-40401200	Weak transcription	Duodenum Smooth Muscle	Duodenum
14	chr2:40393400-40400000	Weak transcription	NHDF-Ad	bronchial
15	chr2:40393600-40396400	Weak transcription	Left Ventricle	heart
16	chr2:40393600-40396600	Weak transcription	Gastric	stomach
17	chr2:40393600-40396800	Weak transcription	Right Atrium	heart
18	chr2:40393600-40397200	Weak transcription	Stomach Smooth Muscle	stomach
19	chr2:40393600-40416800	Weak transcription	Fetal Stomach	stomach
20	chr2:40393800-40399000	Weak transcription	Rectal Smooth Muscle	rectum
21	chr2:40394200-40396400	Weak transcription	Monocytes-CD14+_RO01746	blood
22	chr2:40394200-40406800	Weak transcription	Colon Smooth Muscle	Colon
23	chr2:40394600-40396800	Enhancers	Rectal Mucosa Donor 31	rectum
24	chr2:40395200-40396400	Enhancers	Duodenum Mucosa	Duodenum
25	chr2:40395200-40396600	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
26	chr2:40395200-40396800	Enhancers	Fetal Intestine Small	intestine
27	chr2:40395200-40397000	Enhancers	Fetal Intestine Large	intestine
28	chr2:40395200-40397400	Enhancers	Fetal Heart	heart
29	chr2:40395400-40400400	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
30	chr2:40395600-40396400	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
31	chr2:40395600-40396600	Weak transcription	Primary monocytes fromperipheralblood	blood
32	chr2:40395600-40396800	Enhancers	Muscle Satellite Cultured Cells	--
33	chr2:40396000-40396800	Enhancers	HSMM	muscle
34	chr2:40396200-40396400	Weak transcription	Pancreatic Islets	Pancreatic Islet
35	chr2:40396200-40396400	Enhancers	Sigmoid Colon	Sigmoid Colon
36	chr2:40396200-40396400	Enhancers	Osteobl	bone
37	chr2:40396200-40397000	Enhancers	Fetal Muscle Leg	muscle
38	chr2:40396200-40397000	Enhancers	Placenta	Placenta
39	chr2:40396200-40397200	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
40	chr2:40396200-40397600	Genic enhancers	Right Ventricle	heart

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