Variant report

Variant	rs6493939
Chromosome Location	chr15:57936129-57936130
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr15:57921790..57923628-chr15:57933516..57936267,2	K562	blood:

Extended variants
information (count: 30 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:25)

rs_ID	r²[population]
rs10162772	0.85[CEU][hapmap];0.87[MEX][hapmap]
rs11071337	0.90[JPT][hapmap]
rs11071338	0.82[CHB][hapmap];0.90[JPT][hapmap]
rs11071339	0.85[CEU][hapmap];0.87[MEX][hapmap]
rs11629719	0.85[CEU][hapmap];0.80[CHB][hapmap];1.00[JPT][hapmap];0.85[ASN][1000 genomes]
rs1425948	0.85[CEU][hapmap];0.87[MEX][hapmap]
rs17240055	0.90[CHB][hapmap];1.00[CHD][hapmap];0.90[JPT][hapmap];0.85[ASN][1000 genomes]
rs2433196	0.85[CEU][hapmap];0.80[CHB][hapmap];1.00[JPT][hapmap];0.88[MEX][hapmap];0.93[ASN][1000 genomes]
rs2433197	0.92[CEU][hapmap];0.90[CHB][hapmap];1.00[JPT][hapmap];0.82[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2433198	1.00[JPT][hapmap];0.80[AFR][1000 genomes];0.89[AMR][1000 genomes];0.82[ASN][1000 genomes]
rs2470356	0.90[JPT][hapmap];0.89[EUR][1000 genomes]
rs2554026	1.00[JPT][hapmap]
rs2554040	0.88[JPT][hapmap]
rs2733598	0.90[JPT][hapmap]
rs2733601	0.90[JPT][hapmap]
rs2733602	0.80[CHB][hapmap];0.90[JPT][hapmap]
rs2733603	0.81[CHB][hapmap];0.81[JPT][hapmap]
rs2733604	0.87[MEX][hapmap]
rs4774277	0.90[JPT][hapmap]
rs4774979	0.81[CEU][hapmap];0.81[JPT][hapmap]
rs7169211	0.90[CHB][hapmap];1.00[CHD][hapmap];0.90[JPT][hapmap];0.87[ASN][1000 genomes]
rs7176042	0.81[JPT][hapmap];0.84[MEX][hapmap]
rs9302201	0.83[MEX][hapmap]
rs9806740	0.85[CEU][hapmap];0.87[MEX][hapmap]
rs986868	0.81[CEU][hapmap];0.87[MEX][hapmap]

Variant overlapped rSNPs/rCNVs (count:5 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1045611	chr15:57350965-58070807	Weak transcription Enhancers Strong transcription Genic enhancers Flanking Active TSS Active TSS ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	49 gene(s)	inside rSNPs	diseases
2	nsv1054547	chr15:57600488-57977659	Active TSS Weak transcription Enhancers Strong transcription Flanking Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	19 gene(s)	inside rSNPs	diseases
3	nsv530682	chr15:57912502-58108285	Weak transcription Flanking Active TSS Strong transcription Active TSS Enhancers Genic enhancers Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
4	nsv1038667	chr15:57933076-58481870	Flanking Active TSS Enhancers Genic enhancers Active TSS Weak transcription Flanking Bivalent TSS/Enh Strong transcription Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	22 gene(s)	inside rSNPs	diseases
5	nsv542400	chr15:57933076-58481870	Weak transcription Enhancers Flanking Active TSS ZNF genes & repeats Active TSS Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS Strong transcription Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	22 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs6493939	Gcom1	cis	multi-tissue	Pritchard
rs6493939	MYO1E	cis	cerebellum	SCAN
rs6493939	WDR72	cis	parietal	SCAN

Chromatin state (count:39 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:57894400-57938200	Weak transcription	Primary B cells from peripheral blood	blood
2	chr15:57900600-57941600	Weak transcription	Colonic Mucosa	Colon
3	chr15:57904600-57936400	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
4	chr15:57905000-57940800	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
5	chr15:57912200-57939200	Weak transcription	Placenta	Placenta
6	chr15:57919400-57946800	Weak transcription	Fetal Lung	lung
7	chr15:57919400-57959400	Weak transcription	Duodenum Smooth Muscle	Duodenum
8	chr15:57923600-57939200	Weak transcription	Fetal Muscle Trunk	muscle
9	chr15:57924000-57938200	Strong transcription	Adipose Nuclei	Adipose
10	chr15:57925400-57939200	Weak transcription	HUVEC	blood vessel
11	chr15:57927400-57939800	Weak transcription	Lung	lung
12	chr15:57928200-57938800	Weak transcription	Skeletal Muscle Male	skeletal muscle
13	chr15:57928400-57938800	Weak transcription	Primary B cells from cord blood	blood
14	chr15:57928600-57937000	Weak transcription	Ovary	ovary
15	chr15:57928800-57939000	Strong transcription	Fetal Intestine Large	intestine
16	chr15:57929000-57939400	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
17	chr15:57929400-57938200	Weak transcription	Psoas Muscle	Psoas
18	chr15:57929400-57939200	Weak transcription	Skeletal Muscle Female	skeletal muscle
19	chr15:57930000-57936400	Weak transcription	HMEC	breast
20	chr15:57930000-57936600	Strong transcription	Rectal Mucosa Donor 31	rectum
21	chr15:57932200-57936400	Strong transcription	Left Ventricle	heart
22	chr15:57932200-57936600	Weak transcription	Rectal Mucosa Donor 29	rectum
23	chr15:57932200-57939200	Weak transcription	Spleen	Spleen
24	chr15:57932200-57939600	Weak transcription	Sigmoid Colon	Sigmoid Colon
25	chr15:57932200-57942200	Weak transcription	Breast Myoepithelial Primary Cells	Breast
26	chr15:57932200-57967400	Weak transcription	Aorta	Aorta
27	chr15:57932400-57939200	Weak transcription	Pancreas	Pancrea
28	chr15:57933400-57937800	Weak transcription	Duodenum Mucosa	Duodenum
29	chr15:57933400-57938200	Weak transcription	Stomach Smooth Muscle	stomach
30	chr15:57933400-57939200	Weak transcription	Gastric	stomach
31	chr15:57933400-57982600	Weak transcription	Esophagus	oesophagus
32	chr15:57934400-57940800	Weak transcription	Brain Angular Gyrus	brain
33	chr15:57934800-57937000	Weak transcription	Fetal Heart	heart
34	chr15:57934800-57939400	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
35	chr15:57935200-57937000	Strong transcription	Fetal Intestine Small	intestine
36	chr15:57935400-57937000	Strong transcription	Fetal Stomach	stomach
37	chr15:57935400-57937000	Strong transcription	Right Ventricle	heart
38	chr15:57936000-57936200	Enhancers	Stomach Mucosa	stomach
39	chr15:57936000-57937200	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin

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