Variant report

Variant	rs17503184
Chromosome Location	chr2:40400332-40400333
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 32 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:23)

rs_ID	r²[population]
rs1005213	0.93[CHB][hapmap];0.82[JPT][hapmap];0.87[ASN][1000 genomes]
rs1019781	0.98[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs10490208	0.83[MEX][hapmap]
rs11691259	1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[ASN][1000 genomes]
rs118900	1.00[CHB][hapmap];0.81[GIH][hapmap];0.88[JPT][hapmap];0.93[ASN][1000 genomes]
rs12104840	0.87[CEU][hapmap];0.85[CHB][hapmap];0.94[JPT][hapmap];0.91[MEX][hapmap];0.85[TSI][hapmap];0.92[AMR][1000 genomes];0.83[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs13390338	0.95[CEU][hapmap];1.00[CHB][hapmap];0.94[JPT][hapmap];0.87[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs13394655	1.00[CHB][hapmap];0.88[JPT][hapmap];0.88[AMR][1000 genomes];0.86[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs17504446	0.82[CEU][hapmap];0.89[GIH][hapmap];0.80[MKK][hapmap]
rs17504670	0.81[GIH][hapmap];0.83[MEX][hapmap]
rs2192919	0.93[CHB][hapmap];0.83[GIH][hapmap];0.81[TSI][hapmap]
rs35963830	0.86[AMR][1000 genomes]
rs3828295	1.00[CHB][hapmap];0.83[GIH][hapmap];0.94[JPT][hapmap]
rs4624433	0.83[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs4952401	0.85[GIH][hapmap];0.83[MEX][hapmap]
rs4952532	1.00[CEU][hapmap];1.00[CHB][hapmap];0.88[JPT][hapmap];0.85[YRI][hapmap];0.96[AMR][1000 genomes];0.93[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs4952591	0.82[CEU][hapmap];0.85[GIH][hapmap];0.83[MEX][hapmap];0.85[TSI][hapmap];0.85[AMR][1000 genomes]
rs62148765	0.90[AMR][1000 genomes];0.82[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs6734847	1.00[CHB][hapmap];0.94[JPT][hapmap];0.96[ASN][1000 genomes]
rs7558668	1.00[CHB][hapmap];0.88[JPT][hapmap];0.85[YRI][hapmap];0.85[AFR][1000 genomes];0.97[AMR][1000 genomes];0.86[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7558770	1.00[ASW][hapmap];0.95[CEU][hapmap];1.00[CHB][hapmap];0.81[CHD][hapmap];0.93[GIH][hapmap];0.88[JPT][hapmap];0.83[LWK][hapmap];1.00[MEX][hapmap];0.84[MKK][hapmap];0.97[TSI][hapmap];0.85[YRI][hapmap];0.89[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7558787	1.00[ASW][hapmap];0.95[CEU][hapmap];1.00[CHB][hapmap];0.93[GIH][hapmap];0.88[JPT][hapmap];0.82[LWK][hapmap];1.00[MEX][hapmap];0.84[MKK][hapmap];0.97[TSI][hapmap];0.85[YRI][hapmap];0.89[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs918050	0.82[CEU][hapmap];0.80[TSI][hapmap]

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:1)

SNP	Gene	Cis/trans	Tissue	Source
rs17503184	GALM	cis	cerebellum	SCAN

Chromatin state (count:29 , 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	chr2:40392000-40413200	Weak transcription	Fetal Brain Female	brain
5	chr2:40392600-40405200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
6	chr2:40393000-40420000	Weak transcription	Fetal Kidney	kidney
7	chr2:40393200-40401200	Weak transcription	Duodenum Smooth Muscle	Duodenum
8	chr2:40393600-40416800	Weak transcription	Fetal Stomach	stomach
9	chr2:40394200-40406800	Weak transcription	Colon Smooth Muscle	Colon
10	chr2:40395400-40400400	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
11	chr2:40396400-40405400	Weak transcription	Duodenum Mucosa	Duodenum
12	chr2:40396600-40401800	Strong transcription	Primary monocytes fromperipheralblood	blood
13	chr2:40396800-40400400	Weak transcription	Muscle Satellite Cultured Cells	--
14	chr2:40397000-40405000	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
15	chr2:40397600-40401600	Weak transcription	Pancreatic Islets	Pancreatic Islet
16	chr2:40397600-40404800	Weak transcription	Right Ventricle	heart
17	chr2:40397800-40404800	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
18	chr2:40398200-40404800	Weak transcription	Stomach Smooth Muscle	stomach
19	chr2:40398400-40406200	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
20	chr2:40399200-40404800	Weak transcription	Left Ventricle	heart
21	chr2:40399400-40404800	Weak transcription	Dnd41	blood
22	chr2:40399600-40400600	Weak transcription	HSMM	muscle
23	chr2:40399600-40402200	Weak transcription	Fetal Heart	heart
24	chr2:40400000-40400800	Enhancers	NHDF-Ad	bronchial
25	chr2:40400000-40404600	Weak transcription	Monocytes-CD14+_RO01746	blood
26	chr2:40400200-40400600	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
27	chr2:40400200-40400600	Enhancers	Osteobl	bone
28	chr2:40400200-40400800	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
29	chr2:40400200-40401000	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin

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