Variant report

Variant	rs433572
Chromosome Location	chr2:40404839-40404840
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 49 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:40)

rs_ID	r²[population]
rs105287	1.00[CHB][hapmap];0.85[CHD][hapmap];0.81[JPT][hapmap];0.89[ASN][1000 genomes]
rs106706	1.00[CHB][hapmap];0.86[CHD][hapmap];0.85[GIH][hapmap];0.90[JPT][hapmap];0.92[ASN][1000 genomes]
rs12993486	0.94[CHB][hapmap];0.90[CHD][hapmap];0.90[ASN][1000 genomes]
rs1428571	0.90[CHB][hapmap];0.82[CHD][hapmap]
rs1651354	0.90[ASN][1000 genomes]
rs17025367	1.00[CHB][hapmap];0.81[JPT][hapmap];0.89[ASN][1000 genomes]
rs17025372	1.00[CHB][hapmap];0.95[CHD][hapmap];0.85[JPT][hapmap];0.89[ASN][1000 genomes]
rs17025380	1.00[CHB][hapmap];0.85[JPT][hapmap];0.90[ASN][1000 genomes]
rs17025588	0.89[CHB][hapmap];0.85[CHD][hapmap]
rs2072529	1.00[CHB][hapmap];0.95[CHD][hapmap];0.85[JPT][hapmap];0.87[ASN][1000 genomes]
rs2072530	0.90[CHB][hapmap];0.90[CHD][hapmap];0.90[JPT][hapmap];0.82[ASN][1000 genomes]
rs2270327	0.88[ASN][1000 genomes]
rs2540904	0.89[CHB][hapmap];0.85[CHD][hapmap]
rs368577	0.82[CHD][hapmap]
rs371492	0.87[CHB][hapmap];0.85[JPT][hapmap]
rs372072	1.00[CHB][hapmap];0.95[CHD][hapmap];0.81[GIH][hapmap];0.90[JPT][hapmap];0.90[ASN][1000 genomes]
rs376303	0.89[CHB][hapmap]
rs376535	0.94[CHB][hapmap];0.90[CHD][hapmap];0.81[JPT][hapmap];0.86[ASN][1000 genomes]
rs379804	0.89[ASN][1000 genomes]
rs385341	1.00[CHB][hapmap];0.93[CHD][hapmap];0.85[JPT][hapmap];0.89[ASN][1000 genomes]
rs385665	0.94[CHB][hapmap];0.90[JPT][hapmap];0.90[ASN][1000 genomes]
rs388467	0.86[ASN][1000 genomes]
rs390145	0.95[CHB][hapmap]
rs392953	0.89[CHB][hapmap]
rs395987	0.89[CHB][hapmap];0.90[CHD][hapmap];0.81[JPT][hapmap];0.86[ASN][1000 genomes]
rs398898	0.89[ASN][1000 genomes]
rs402777	0.90[ASN][1000 genomes]
rs404005	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.95[GIH][hapmap];0.85[JPT][hapmap];0.89[LWK][hapmap];0.87[MEX][hapmap];0.81[YRI][hapmap];0.83[AMR][1000 genomes];0.83[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs404214	0.89[CHB][hapmap]
rs404226	0.89[CHB][hapmap]
rs405804	1.00[CHB][hapmap];0.90[JPT][hapmap];0.91[ASN][1000 genomes]
rs407148	0.89[CHB][hapmap];0.85[CHD][hapmap]
rs408263	0.89[CHB][hapmap];0.81[CHD][hapmap]
rs409522	1.00[CHB][hapmap];0.81[JPT][hapmap];0.89[ASN][1000 genomes]
rs410912	0.87[AMR][1000 genomes];0.88[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs446538	1.00[CHB][hapmap];0.85[CHD][hapmap];0.89[ASN][1000 genomes]
rs447136	0.89[CHB][hapmap];0.81[CHD][hapmap]
rs449383	0.88[CHD][hapmap];0.89[GIH][hapmap];0.86[MEX][hapmap];0.82[TSI][hapmap];0.85[AMR][1000 genomes];0.84[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs450450	0.89[CHB][hapmap]
rs72792740	0.80[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

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs433572	GALM	cis	cerebellum	SCAN
rs433572	FAM82A1	cis	cerebellum	SCAN

Chromatin state (count:25 , 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	chr2:40392000-40413200	Weak transcription	Fetal Brain Female	brain
3	chr2:40392600-40405200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
4	chr2:40393000-40420000	Weak transcription	Fetal Kidney	kidney
5	chr2:40393600-40416800	Weak transcription	Fetal Stomach	stomach
6	chr2:40394200-40406800	Weak transcription	Colon Smooth Muscle	Colon
7	chr2:40396400-40405400	Weak transcription	Duodenum Mucosa	Duodenum
8	chr2:40397000-40405000	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
9	chr2:40398400-40406200	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
10	chr2:40400600-40426800	Weak transcription	Osteobl	bone
11	chr2:40401000-40405400	Weak transcription	Muscle Satellite Cultured Cells	--
12	chr2:40402200-40407400	Enhancers	Fetal Heart	heart
13	chr2:40403200-40405200	Weak transcription	HSMMtube	muscle
14	chr2:40404400-40406600	Enhancers	Primary neutrophils fromperipheralblood	blood
15	chr2:40404600-40405000	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
16	chr2:40404600-40405000	Enhancers	NHDF-Ad	bronchial
17	chr2:40404600-40405200	Enhancers	Monocytes-CD14+_RO01746	blood
18	chr2:40404600-40405400	Genic enhancers	Primary monocytes fromperipheralblood	blood
19	chr2:40404600-40405800	Genic enhancers	HSMM	muscle
20	chr2:40404800-40405200	Strong transcription	Left Ventricle	heart
21	chr2:40404800-40405400	Strong transcription	Stomach Smooth Muscle	stomach
22	chr2:40404800-40405600	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
23	chr2:40404800-40405600	Genic enhancers	Right Ventricle	heart
24	chr2:40404800-40405600	Genic enhancers	Dnd41	blood
25	chr2:40404800-40407200	Enhancers	Fetal Thymus	thymus

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