Variant report

Variant	rs7182060
Chromosome Location	chr15:58970805-58970806
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 27 )
Associated
traits (count: 3 )

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

rs_ID	r²[population]
rs10851639	0.92[LWK][hapmap];1.00[YRI][hapmap]
rs11071396	0.90[CHB][hapmap]
rs12437552	1.00[CHB][hapmap];1.00[CHD][hapmap];0.96[GIH][hapmap];0.95[JPT][hapmap];0.87[ASN][1000 genomes]
rs12438114	0.80[CHB][hapmap]
rs12439189	0.81[LWK][hapmap];0.94[YRI][hapmap]
rs12592302	0.82[ASN][1000 genomes]
rs1427280	1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[AMR][1000 genomes];0.94[ASN][1000 genomes]
rs17236243	0.91[CHB][hapmap];0.86[JPT][hapmap]
rs2114573	1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[ASN][1000 genomes]
rs2414606	0.95[CHB][hapmap];0.95[JPT][hapmap];0.84[ASN][1000 genomes]
rs2414607	0.95[CHB][hapmap];0.96[GIH][hapmap];0.95[JPT][hapmap]
rs28391588	0.93[GIH][hapmap]
rs3933541	0.84[ASN][1000 genomes]
rs394845	0.87[ASW][hapmap];0.95[CHB][hapmap];0.95[CHD][hapmap];0.96[GIH][hapmap];1.00[JPT][hapmap];0.92[LWK][hapmap];0.81[MEX][hapmap];1.00[YRI][hapmap]
rs4774309	0.90[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];1.00[YRI][hapmap];0.83[AFR][1000 genomes];0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs681711	0.95[CHB][hapmap];0.86[JPT][hapmap]
rs694335	0.95[CHB][hapmap];0.93[CHD][hapmap];0.93[GIH][hapmap];0.91[JPT][hapmap];0.81[YRI][hapmap]
rs7173286	0.95[CHB][hapmap];1.00[JPT][hapmap]
rs7176436	0.86[ASW][hapmap];0.91[CHD][hapmap];1.00[GIH][hapmap];0.95[JPT][hapmap];0.84[AMR][1000 genomes];0.97[ASN][1000 genomes]
rs7179724	1.00[CHB][hapmap];1.00[CHD][hapmap];0.96[GIH][hapmap];1.00[JPT][hapmap];0.87[ASN][1000 genomes]
rs8027998	0.93[GIH][hapmap]
rs8036097	0.87[ASW][hapmap];0.90[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.88[TSI][hapmap];0.94[AMR][1000 genomes];0.92[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs9646204	0.91[CHB][hapmap];0.89[CHD][hapmap];0.81[JPT][hapmap]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1051058	chr15:58519922-59092530	Strong transcription Weak transcription Enhancers Flanking Active TSS ZNF genes & repeats Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	50 gene(s)	inside rSNPs	diseases
2	nsv542401	chr15:58519922-59092530	Strong transcription Weak transcription Active TSS Flanking Active TSS Enhancers Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	50 gene(s)	inside rSNPs	diseases
3	nsv904269	chr15:58906145-58992591	Enhancers Strong transcription ZNF genes & repeats Weak transcription Flanking Active TSS Active TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
4	esv34110	chr15:58949991-59381634	Weak transcription Bivalent Enhancer Strong transcription Enhancers Active TSS Flanking Active TSS ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	87 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs7182060	DYX1C1	cis	parietal	SCAN
rs7182060	PYGO1	cis	parietal	SCAN
rs7182060	CCPG1	cis	cerebellum	SCAN

Chromatin state (count:106 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:58905000-58983200	Weak transcription	Esophagus	oesophagus
2	chr15:58905400-58971800	Weak transcription	Spleen	Spleen
3	chr15:58905600-58976400	Weak transcription	Gastric	stomach
4	chr15:58906400-58976400	Weak transcription	Small Intestine	intestine
5	chr15:58921600-58976600	Weak transcription	Right Ventricle	heart
6	chr15:58923400-58971800	Weak transcription	Pancreas	Pancrea
7	chr15:58923400-58982800	Weak transcription	Lung	lung
8	chr15:58933000-58987000	Weak transcription	Rectal Smooth Muscle	rectum
9	chr15:58934200-58976400	Weak transcription	Psoas Muscle	Psoas
10	chr15:58936000-58977000	Weak transcription	Skeletal Muscle Female	skeletal muscle
11	chr15:58936200-58991400	Weak transcription	HMEC	breast
12	chr15:58947800-58971800	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
13	chr15:58947800-58976400	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
14	chr15:58949400-58976400	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
15	chr15:58951200-58987000	Weak transcription	NHEK	skin
16	chr15:58951600-58976400	Weak transcription	GM12878-XiMat	blood
17	chr15:58951600-58981800	Weak transcription	Fetal Brain Male	brain
18	chr15:58955000-58971800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
19	chr15:58955200-58971800	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
20	chr15:58955200-58971800	Weak transcription	Fetal Muscle Leg	muscle
21	chr15:58955200-58971800	Weak transcription	Fetal Stomach	stomach
22	chr15:58955200-58971800	Weak transcription	Left Ventricle	heart
23	chr15:58955200-58976400	Weak transcription	Sigmoid Colon	Sigmoid Colon
24	chr15:58955200-58988400	Weak transcription	Fetal Muscle Trunk	muscle
25	chr15:58955400-58971200	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
26	chr15:58955400-58976200	Weak transcription	Primary T killer memory cells from peripheral blood	blood
27	chr15:58955800-58972000	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
28	chr15:58956600-58974800	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
29	chr15:58956600-58974800	Weak transcription	Adipose Nuclei	Adipose
30	chr15:58956600-58984400	Weak transcription	Duodenum Mucosa	Duodenum
31	chr15:58956600-58984600	Weak transcription	Breast Myoepithelial Primary Cells	Breast
32	chr15:58956600-58987400	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
33	chr15:58956800-58974200	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
34	chr15:58956800-58980000	Weak transcription	Primary T helper cells PMA-I stimulated	--
35	chr15:58956800-58982000	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
36	chr15:58957000-58972400	Weak transcription	Placenta	Placenta
37	chr15:58957000-58976600	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
38	chr15:58957400-58984400	Weak transcription	Rectal Mucosa Donor 31	rectum
39	chr15:58957600-58989200	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
40	chr15:58958800-58989000	Weak transcription	Placenta Amnion	Placenta Amnion
41	chr15:58959600-58976400	Weak transcription	NH-A	brain
42	chr15:58959800-58973800	Weak transcription	Muscle Satellite Cultured Cells	--
43	chr15:58960200-58971800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
44	chr15:58960200-58976400	Weak transcription	HSMMtube	muscle
45	chr15:58960400-58971800	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
46	chr15:58960400-58972200	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
47	chr15:58960400-58976400	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
48	chr15:58960400-58982800	Weak transcription	Aorta	Aorta
49	chr15:58960400-58989600	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
50	chr15:58960800-58972000	Weak transcription	Primary hematopoietic stem cells short term culture	blood

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