Variant report

Variant	rs7247247
Chromosome Location	chr19:41156940-41156941
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 38 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:22)

rs_ID	r²[population]
rs11665867	0.85[LWK][hapmap]
rs11668501	0.89[ASW][hapmap];0.92[LWK][hapmap]
rs11673492	0.89[ASW][hapmap];1.00[CHB][hapmap]
rs11881578	0.84[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs12459415	0.93[EUR][1000 genomes]
rs12975396	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.96[LWK][hapmap];1.00[MEX][hapmap];0.88[MKK][hapmap];0.88[TSI][hapmap];0.83[AFR][1000 genomes];0.84[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs12984927	1.00[CEU][hapmap];1.00[CHB][hapmap];0.81[EUR][1000 genomes]
rs13343945	0.84[EUR][1000 genomes]
rs34433534	0.98[EUR][1000 genomes]
rs34547501	0.98[EUR][1000 genomes]
rs34605579	0.86[AFR][1000 genomes];0.88[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs34652347	0.81[AFR][1000 genomes];0.92[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs34689418	0.99[EUR][1000 genomes]
rs35172225	0.82[EUR][1000 genomes]
rs35625703	0.98[EUR][1000 genomes]
rs35687546	0.95[EUR][1000 genomes]
rs35735265	0.94[EUR][1000 genomes]
rs58429803	0.82[EUR][1000 genomes]
rs7253502	0.89[ASW][hapmap];0.85[LWK][hapmap]
rs7508466	0.82[EUR][1000 genomes]
rs8104739	0.82[EUR][1000 genomes]
rs8105009	0.88[ASW][hapmap];1.00[CHB][hapmap];0.83[LWK][hapmap]

Variant overlapped rSNPs/rCNVs (count:16 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv1830682	chr19:40880127-41270055	Weak transcription Strong transcription Enhancers Genic enhancers Active TSS Flanking Active TSS Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	139 gene(s)	inside rSNPs	diseases
2	nsv911714	chr19:41006426-41165252	Enhancers Weak transcription Active TSS Flanking Bivalent TSS/Enh Flanking Active TSS Bivalent Enhancer Strong transcription Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	33 gene(s)	inside rSNPs	diseases
3	nsv1057634	chr19:41019512-41174259	Enhancers Active TSS Strong transcription Genic enhancers Weak transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS Flanking Active TSS Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	37 gene(s)	inside rSNPs	diseases
4	nsv911720	chr19:41033109-41156940	Flanking Active TSS Enhancers Bivalent/Poised TSS Weak transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Strong transcription Active TSS Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	33 gene(s)	inside rSNPs	diseases
5	nsv911722	chr19:41040334-41176403	Bivalent Enhancer Enhancers Weak transcription Active TSS Strong transcription Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3' Flanking Active TSS Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	37 gene(s)	inside rSNPs	diseases
6	nsv911723	chr19:41075990-41195279	Active TSS Strong transcription Weak transcription Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Genic enhancers Enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	38 gene(s)	inside rSNPs	diseases
7	nsv1064699	chr19:41086506-41174259	Genic enhancers Bivalent Enhancer Enhancers Active TSS Flanking Active TSS Flanking Bivalent TSS/Enh Weak transcription Strong transcription Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	37 gene(s)	inside rSNPs	diseases
8	nsv911724	chr19:41089505-41165252	Bivalent/Poised TSS Strong transcription Enhancers Weak transcription Flanking Active TSS Flanking Bivalent TSS/Enh Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	33 gene(s)	inside rSNPs	diseases
9	nsv911727	chr19:41111069-41200511	Weak transcription Enhancers Genic enhancers Flanking Active TSS Strong transcription Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	38 gene(s)	inside rSNPs	diseases
10	nsv911728	chr19:41111069-41211056	Flanking Active TSS Weak transcription Transcr. at gene 5' and 3' Genic enhancers Enhancers Strong transcription Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	38 gene(s)	inside rSNPs	diseases
11	nsv870022	chr19:41113071-41178982	Strong transcription Enhancers Flanking Active TSS Weak transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Genic enhancers Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region miRNA target site	27 gene(s)	inside rSNPs	diseases
12	esv1800615	chr19:41127465-41270055	Weak transcription Active TSS Bivalent Enhancer Flanking Active TSS Enhancers Transcr. at gene 5' and 3' Genic enhancers Strong transcription ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	64 gene(s)	inside rSNPs	diseases
13	nsv2489	chr19:41145034-41182170	Enhancers Weak transcription Strong transcription Flanking Active TSS Genic enhancers Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	Chromatin interactive region miRNA target site	13 gene(s)	inside rSNPs	diseases
14	nsv1058707	chr19:41146147-41200820	Weak transcription Enhancers Active TSS Strong transcription Transcr. at gene 5' and 3' Flanking Active TSS ZNF genes & repeats Genic enhancers Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region miRNA target site	20 gene(s)	inside rSNPs	diseases
15	esv993784	chr19:41150978-41160426	Weak transcription Flanking Active TSS Enhancers Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
16	esv3509800	chr19:41152400-41158141	Flanking Active TSS Bivalent Enhancer Enhancers Weak transcription Active TSS	Chromatin interactive region	1 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs7247247	STRN4	cis	parietal	SCAN
rs7247247	LMTK3	cis	cerebellum	SCAN
rs7247247	EMP3	cis	parietal	SCAN

Chromatin state (count:37 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr19:41146800-41157000	Weak transcription	Spleen	Spleen
2	chr19:41152800-41157600	Weak transcription	Esophagus	oesophagus
3	chr19:41153000-41157400	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
4	chr19:41153000-41157600	Weak transcription	Hela-S3	cervix
5	chr19:41153000-41158000	Weak transcription	Left Ventricle	heart
6	chr19:41156000-41157000	Enhancers	Fetal Muscle Leg	muscle
7	chr19:41156000-41157800	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
8	chr19:41156000-41158400	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
9	chr19:41156200-41157000	Flanking Active TSS	Foreskin Fibroblast Primary Cells skin02	Skin
10	chr19:41156200-41157000	Enhancers	Fetal Adrenal Gland	Adrenal Gland
11	chr19:41156200-41157000	Enhancers	Skeletal Muscle Male	skeletal muscle
12	chr19:41156200-41157200	Enhancers	Lung	lung
13	chr19:41156200-41157800	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
14	chr19:41156200-41157800	Enhancers	Rectal Smooth Muscle	rectum
15	chr19:41156200-41157800	Enhancers	Right Atrium	heart
16	chr19:41156200-41157800	Enhancers	Stomach Smooth Muscle	stomach
17	chr19:41156200-41157800	Enhancers	NHLF	lung
18	chr19:41156200-41158000	Enhancers	Fetal Lung	lung
19	chr19:41156200-41158000	Enhancers	Osteobl	bone
20	chr19:41156200-41158200	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
21	chr19:41156200-41158200	Enhancers	Adipose Nuclei	Adipose
22	chr19:41156200-41158400	Enhancers	Colon Smooth Muscle	Colon
23	chr19:41156400-41157200	Enhancers	Colonic Mucosa	Colon
24	chr19:41156400-41157200	Enhancers	Ovary	ovary
25	chr19:41156400-41157200	Enhancers	HSMM	muscle
26	chr19:41156400-41158200	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
27	chr19:41156400-41158200	Enhancers	Fetal Stomach	stomach
28	chr19:41156400-41158200	Enhancers	Skeletal Muscle Female	skeletal muscle
29	chr19:41156600-41157000	Enhancers	Brain Hippocampus Middle	brain
30	chr19:41156600-41157600	Enhancers	Breast Myoepithelial Primary Cells	Breast
31	chr19:41156600-41157600	Weak transcription	GM12878-XiMat	blood
32	chr19:41156600-41158200	Enhancers	Muscle Satellite Cultured Cells	--
33	chr19:41156800-41157000	Enhancers	Fetal Intestine Small	intestine
34	chr19:41156800-41157200	Enhancers	Fetal Muscle Trunk	muscle
35	chr19:41156800-41157600	Weak transcription	HSMMtube	muscle
36	chr19:41156800-41158000	Enhancers	NHDF-Ad	bronchial
37	chr19:41156800-41158400	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived

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