Variant report

Variant	rs17540509
Chromosome Location	chr12:56943840-56943841
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 32 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:29)

rs_ID	r²[population]
rs11171894	0.84[CEU][hapmap];0.89[CHB][hapmap];0.94[CHD][hapmap];0.95[GIH][hapmap];0.84[JPT][hapmap];0.86[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2638297	0.85[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2638316	0.86[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs2657888	0.91[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.83[MEX][hapmap];0.92[TSI][hapmap];0.92[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2657890	0.90[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2657897	0.86[EUR][1000 genomes]
rs2657898	0.86[EUR][1000 genomes]
rs2657899	0.87[EUR][1000 genomes]
rs2657900	0.86[EUR][1000 genomes]
rs2657901	0.95[CEU][hapmap];1.00[CHB][hapmap];0.94[JPT][hapmap];0.92[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2657902	0.91[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];0.83[MEX][hapmap];0.92[TSI][hapmap];0.92[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2657903	0.91[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.83[MEX][hapmap];0.92[TSI][hapmap];0.92[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2657905	0.92[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2694907	0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2694909	0.91[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.83[MEX][hapmap];0.92[TSI][hapmap];0.91[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2694910	0.81[EUR][1000 genomes]
rs2694912	0.88[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2694913	0.86[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs28697089	0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2939308	0.85[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2939309	0.86[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs2939312	0.91[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs36073309	0.92[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs67036743	0.90[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7300877	0.80[AMR][1000 genomes];0.92[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7301093	0.80[AMR][1000 genomes];0.92[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7309685	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7310284	1.00[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.83[MKK][hapmap];1.00[TSI][hapmap];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs73118833	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1043622	chr12:56571476-56974448	Enhancers Weak transcription Active TSS Strong transcription Flanking Active TSS Transcr. at gene 5' and 3' Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	95 gene(s)	inside rSNPs	diseases
2	nsv541500	chr12:56571476-56974448	Weak transcription Strong transcription Bivalent/Poised TSS Active TSS Enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	95 gene(s)	inside rSNPs	diseases
3	nsv899106	chr12:56905558-57004668	Strong transcription Enhancers Weak transcription Flanking Active TSS Active TSS Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	18 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs17540509	AMHR2	cis	cerebellum	SCAN
rs17540509	CALCOCO1	cis	parietal	SCAN
rs17540509	ITGB7	cis	cerebellum	SCAN

Chromatin state (count:55 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:56917000-56958000	Weak transcription	Ovary	ovary
2	chr12:56917200-56956200	Weak transcription	Primary T cells from cord blood	blood
3	chr12:56917200-56959200	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
4	chr12:56921400-56956200	Weak transcription	Rectal Mucosa Donor 31	rectum
5	chr12:56922400-56956200	Weak transcription	HSMM	muscle
6	chr12:56922400-56959200	Weak transcription	Fetal Kidney	kidney
7	chr12:56923200-56949200	Weak transcription	Fetal Muscle Trunk	muscle
8	chr12:56923800-56959400	Weak transcription	Aorta	Aorta
9	chr12:56924800-56959200	Weak transcription	ES-I3 Cell Line	embryonic stem cell
10	chr12:56925000-56959200	Weak transcription	HSMMtube	muscle
11	chr12:56927600-56946800	Weak transcription	Left Ventricle	heart
12	chr12:56928400-56952400	Weak transcription	Fetal Intestine Large	intestine
13	chr12:56929800-56955600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
14	chr12:56931000-56949600	Weak transcription	Placenta	Placenta
15	chr12:56931400-56956800	Weak transcription	Duodenum Smooth Muscle	Duodenum
16	chr12:56931400-56959400	Weak transcription	Placenta Amnion	Placenta Amnion
17	chr12:56931600-56946000	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
18	chr12:56931600-56952400	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
19	chr12:56931600-56954800	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
20	chr12:56931600-56955800	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
21	chr12:56931600-56956200	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
22	chr12:56931600-56965000	Weak transcription	Hela-S3	cervix
23	chr12:56931800-56949200	Weak transcription	Stomach Smooth Muscle	stomach
24	chr12:56931800-56956400	Weak transcription	NHLF	lung
25	chr12:56932200-56959200	Weak transcription	Sigmoid Colon	Sigmoid Colon
26	chr12:56933200-56959000	Weak transcription	Monocytes-CD14+_RO01746	blood
27	chr12:56933200-56959200	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
28	chr12:56933400-56959200	Weak transcription	Rectal Mucosa Donor 29	rectum
29	chr12:56933600-56956000	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
30	chr12:56933600-56956200	Weak transcription	NH-A	brain
31	chr12:56933800-56948600	Weak transcription	NHEK	skin
32	chr12:56934600-56952600	Weak transcription	Fetal Muscle Leg	muscle
33	chr12:56934600-56955800	Weak transcription	Osteobl	bone
34	chr12:56934800-56946200	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
35	chr12:56934800-56948000	Weak transcription	Breast Myoepithelial Primary Cells	Breast
36	chr12:56934800-56955800	Weak transcription	HUVEC	blood vessel
37	chr12:56935600-56959200	Weak transcription	Cortex derived primary cultured neurospheres	brain
38	chr12:56936000-56946000	Weak transcription	Adipose Nuclei	Adipose
39	chr12:56936000-56952600	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
40	chr12:56936200-56956000	Weak transcription	Fetal Lung	lung
41	chr12:56936200-56956200	Weak transcription	Small Intestine	intestine
42	chr12:56937200-56959200	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
43	chr12:56937600-56952000	Weak transcription	Fetal Stomach	stomach
44	chr12:56937800-56952000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
45	chr12:56938000-56952000	Weak transcription	Fetal Intestine Small	intestine
46	chr12:56939600-56947800	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
47	chr12:56939600-56956000	Weak transcription	Muscle Satellite Cultured Cells	--
48	chr12:56939600-56957800	Weak transcription	HMEC	breast
49	chr12:56940200-56946400	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
50	chr12:56941000-56945600	Weak transcription	Lung	lung

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