Variant report

Variant	rs2072531
Chromosome Location	chr2:40388357-40388358
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 21 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:14)

rs_ID	r²[population]
rs10172414	0.88[CEU][hapmap];0.93[CHB][hapmap];1.00[JPT][hapmap];0.92[AMR][1000 genomes];0.92[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs10175725	0.92[CEU][hapmap];0.93[CHB][hapmap];1.00[JPT][hapmap];0.96[AMR][1000 genomes];0.93[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12466767	0.91[TSI][hapmap]
rs12470980	0.84[TSI][hapmap]
rs1428566	0.92[CEU][hapmap];0.93[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.99[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1428567	0.92[CEU][hapmap];0.93[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];0.99[AMR][1000 genomes];0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1428568	0.92[CEU][hapmap];0.93[CHB][hapmap];1.00[JPT][hapmap];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs17501526	0.91[TSI][hapmap];0.81[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs2072532	0.87[TSI][hapmap]
rs2373792	0.91[TSI][hapmap]
rs2888657	0.91[TSI][hapmap]
rs4952498	1.00[CHB][hapmap];0.92[JPT][hapmap];0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs5551	0.87[TSI][hapmap]
rs929642	0.87[TSI][hapmap]

Variant overlapped rSNPs/rCNVs (count:7 , 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

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs2072531	GALM	cis	cerebellum	SCAN

Chromatin state (count:58 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:40357800-40406400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
2	chr2:40358000-40392200	Weak transcription	Duodenum Smooth Muscle	Duodenum
3	chr2:40358200-40392200	Weak transcription	NHLF	lung
4	chr2:40358800-40389200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
5	chr2:40365200-40396200	Weak transcription	Sigmoid Colon	Sigmoid Colon
6	chr2:40366600-40403000	Weak transcription	Brain Germinal Matrix	brain
7	chr2:40366800-40391800	Weak transcription	Fetal Muscle Trunk	muscle
8	chr2:40369600-40391600	Weak transcription	Rectal Smooth Muscle	rectum
9	chr2:40371800-40391800	Weak transcription	NHDF-Ad	bronchial
10	chr2:40375600-40401800	Weak transcription	HSMMtube	muscle
11	chr2:40376800-40394200	Strong transcription	Monocytes-CD14+_RO01746	blood
12	chr2:40378000-40391200	Weak transcription	Brain Anterior Caudate	brain
13	chr2:40378000-40391200	Weak transcription	Fetal Thymus	thymus
14	chr2:40378000-40399000	Weak transcription	Brain Inferior Temporal Lobe	brain
15	chr2:40378200-40392000	Weak transcription	Gastric	stomach
16	chr2:40379200-40393400	Strong transcription	Primary monocytes fromperipheralblood	blood
17	chr2:40381200-40391800	Weak transcription	Adipose Nuclei	Adipose
18	chr2:40381400-40390200	Weak transcription	Fetal Intestine Small	intestine
19	chr2:40381600-40398800	Weak transcription	Brain Angular Gyrus	brain
20	chr2:40381800-40395200	Weak transcription	Spleen	Spleen
21	chr2:40382400-40392800	Strong transcription	Dnd41	blood
22	chr2:40382600-40391800	Strong transcription	Left Ventricle	heart
23	chr2:40382800-40391400	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
24	chr2:40383000-40392400	Strong transcription	Foreskin Fibroblast Primary Cells skin01	Skin
25	chr2:40383400-40392200	Weak transcription	Aorta	Aorta
26	chr2:40383400-40392600	Strong transcription	HSMM	muscle
27	chr2:40384200-40392200	Weak transcription	Fetal Kidney	kidney
28	chr2:40384600-40391800	Weak transcription	Right Ventricle	heart
29	chr2:40385000-40389800	Weak transcription	Fetal Muscle Leg	muscle
30	chr2:40385000-40391200	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
31	chr2:40386000-40388600	Strong transcription	Fetal Heart	heart
32	chr2:40386000-40391600	Strong transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
33	chr2:40386000-40395200	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
34	chr2:40386000-40395200	Weak transcription	Rectal Mucosa Donor 29	rectum
35	chr2:40386200-40390600	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
36	chr2:40386400-40392200	Weak transcription	Fetal Brain Male	brain
37	chr2:40386400-40392200	Weak transcription	Rectal Mucosa Donor 31	rectum
38	chr2:40386400-40395200	Weak transcription	Fetal Intestine Large	intestine
39	chr2:40387000-40389800	Weak transcription	Liver	Liver
40	chr2:40387000-40391400	Strong transcription	Colon Smooth Muscle	Colon
41	chr2:40387200-40388800	Weak transcription	HMEC	breast
42	chr2:40387200-40389000	Enhancers	Fetal Lung	lung
43	chr2:40387200-40392800	Strong transcription	Muscle Satellite Cultured Cells	--
44	chr2:40387400-40388400	Strong transcription	Foreskin Fibroblast Primary Cells skin02	Skin
45	chr2:40387400-40388600	Enhancers	Brain Cingulate Gyrus	brain
46	chr2:40387400-40389000	Enhancers	Fetal Stomach	stomach
47	chr2:40387400-40389000	Enhancers	Ovary	ovary
48	chr2:40387400-40389600	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
49	chr2:40387800-40388400	Weak transcription	Stomach Smooth Muscle	stomach
50	chr2:40387800-40388800	Enhancers	Brain Hippocampus Middle	brain

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