Variant report

Variant	rs936175
Chromosome Location	chr3:46904708-46904709
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 36 )
Associated
traits (count: 3 )

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

rs_ID	r²[population]
rs1042973	1.00[CHB][hapmap];0.81[CHD][hapmap];0.89[GIH][hapmap];0.80[JPT][hapmap];0.84[MEX][hapmap];0.88[ASN][1000 genomes]
rs12106917	0.93[CHB][hapmap];0.81[CHD][hapmap];0.88[JPT][hapmap]
rs12107311	0.93[CHB][hapmap];0.81[CHD][hapmap];0.88[JPT][hapmap]
rs12486015	0.86[CHB][hapmap]
rs12492369	0.86[CHB][hapmap]
rs12493158	0.86[CHB][hapmap]
rs1531136	0.80[ASW][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];0.86[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs1869868	0.85[AMR][1000 genomes];0.93[ASN][1000 genomes]
rs2227294	0.80[ASW][hapmap];0.95[GIH][hapmap];1.00[TSI][hapmap];0.97[EUR][1000 genomes]
rs2385860	1.00[CHB][hapmap];0.97[CHD][hapmap];0.91[GIH][hapmap];1.00[JPT][hapmap];0.84[MEX][hapmap];1.00[TSI][hapmap];0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs3792558	0.87[ASW][hapmap];1.00[CHB][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.83[MEX][hapmap];0.83[MKK][hapmap];1.00[TSI][hapmap];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4683304	0.93[CHB][hapmap];0.81[CHD][hapmap];0.88[JPT][hapmap]
rs57459864	0.83[AMR][1000 genomes];0.91[ASN][1000 genomes]
rs6763438	0.86[CHB][hapmap]
rs6768252	0.86[CHB][hapmap];0.88[JPT][hapmap]
rs6777190	0.86[CHB][hapmap];0.88[JPT][hapmap]
rs67839338	0.81[AMR][1000 genomes]
rs6797059	0.85[CHB][hapmap]
rs6801048	0.85[CHB][hapmap];0.87[JPT][hapmap]
rs7614762	0.85[CHB][hapmap];0.88[JPT][hapmap]
rs7633581	0.87[ASW][hapmap];1.00[CHB][hapmap];0.94[CHD][hapmap];1.00[JPT][hapmap];0.97[ASN][1000 genomes]
rs877670	0.83[AMR][1000 genomes];0.92[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:14 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1007449	chr3:46652343-46986578	Bivalent Enhancer Weak transcription Transcr. at gene 5' and 3' Enhancers ZNF genes & repeats Genic enhancers Strong transcription Bivalent/Poised TSS Flanking Active TSS Flanking Bivalent TSS/Enh Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	30 gene(s)	inside rSNPs	diseases
2	nsv536554	chr3:46652343-46986578	Enhancers Weak transcription Bivalent Enhancer Genic enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Strong transcription Bivalent/Poised TSS ZNF genes & repeats Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	30 gene(s)	inside rSNPs	diseases
3	esv2757869	chr3:46680452-46972489	Enhancers Flanking Bivalent TSS/Enh Flanking Active TSS Strong transcription Weak transcription Active TSS Bivalent Enhancer Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	28 gene(s)	inside rSNPs	diseases
4	esv2759147	chr3:46680452-46972489	Genic enhancers Flanking Active TSS Enhancers Strong transcription Bivalent/Poised TSS Weak transcription Flanking Bivalent TSS/Enh Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	28 gene(s)	inside rSNPs	diseases
5	nsv536558	chr3:46706571-47024756	Enhancers Bivalent Enhancer Active TSS Strong transcription Weak transcription Flanking Active TSS Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	35 gene(s)	inside rSNPs	diseases
6	nsv915922	chr3:46768104-47009805	Enhancers Weak transcription Bivalent Enhancer Genic enhancers Flanking Active TSS Strong transcription Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh Active TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	18 gene(s)	inside rSNPs	diseases
7	nsv590205	chr3:46852679-46929546	Weak transcription Bivalent Enhancer Active TSS Enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Strong transcription Transcr. at gene 5' and 3' Flanking Active TSS Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
8	nsv1003979	chr3:46853374-46943854	Flanking Active TSS Bivalent Enhancer Active TSS Weak transcription Enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats Strong transcription Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	12 gene(s)	inside rSNPs	diseases
9	nsv590206	chr3:46873957-46935527	Enhancers Bivalent Enhancer Flanking Active TSS Flanking Bivalent TSS/Enh Weak transcription Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3' Genic enhancers ZNF genes & repeats Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
10	nsv876752	chr3:46879831-46967040	Bivalent/Poised TSS Genic enhancers Enhancers Weak transcription Bivalent Enhancer Flanking Active TSS Flanking Bivalent TSS/Enh Strong transcription ZNF genes & repeats Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	12 gene(s)	inside rSNPs	diseases
11	nsv876753	chr3:46884552-46957298	Weak transcription Enhancers Bivalent Enhancer Bivalent/Poised TSS Active TSS Flanking Bivalent TSS/Enh Flanking Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Strong transcription Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases
12	nsv876754	chr3:46884552-46967040	Enhancers Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh Weak transcription Flanking Active TSS Active TSS Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	12 gene(s)	inside rSNPs	diseases
13	nsv876755	chr3:46895109-47061183	Genic enhancers Bivalent Enhancer Enhancers Flanking Active TSS Strong transcription Weak transcription Active TSS Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	25 gene(s)	inside rSNPs	diseases
14	nsv590207	chr3:46903361-46919379	Enhancers Weak transcription Bivalent Enhancer Flanking Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs936175	LOC285456	trans	parietal	SCAN
rs936175	ZNF502	cis	cerebellum	SCAN
rs936175	HYAL2	cis	parietal	SCAN

Chromatin state (count:34 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:46888000-46908800	Weak transcription	Esophagus	oesophagus
2	chr3:46893800-46906200	Weak transcription	Placenta Amnion	Placenta Amnion
3	chr3:46894200-46905200	Weak transcription	Fetal Lung	lung
4	chr3:46897000-46908600	Weak transcription	Gastric	stomach
5	chr3:46898000-46904800	Transcr. at gene 5' and 3'	Skeletal Muscle Male	skeletal muscle
6	chr3:46898800-46908400	Weak transcription	Liver	Liver
7	chr3:46900600-46904800	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
8	chr3:46901000-46909000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
9	chr3:46902200-46908400	Weak transcription	Stomach Smooth Muscle	stomach
10	chr3:46902800-46904800	Flanking Active TSS	Fetal Muscle Trunk	muscle
11	chr3:46902800-46907000	Enhancers	Fetal Intestine Large	intestine
12	chr3:46903000-46906000	Active TSS	Left Ventricle	heart
13	chr3:46903000-46907200	Enhancers	Fetal Intestine Small	intestine
14	chr3:46903200-46905600	Active TSS	Fetal Heart	heart
15	chr3:46903200-46906200	Active TSS	Right Ventricle	heart
16	chr3:46903400-46905400	Weak transcription	Lung	lung
17	chr3:46903600-46904800	Flanking Active TSS	Fetal Muscle Leg	muscle
18	chr3:46903600-46904800	Active TSS	Right Atrium	heart
19	chr3:46903600-46908200	Weak transcription	Pancreas	Pancrea
20	chr3:46903800-46906000	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
21	chr3:46903800-46906200	Weak transcription	Ovary	ovary
22	chr3:46903800-46906200	Enhancers	HSMMtube	muscle
23	chr3:46904000-46906200	Weak transcription	Spleen	Spleen
24	chr3:46904200-46906000	Weak transcription	Breast Myoepithelial Primary Cells	Breast
25	chr3:46904400-46905200	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
26	chr3:46904400-46905800	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
27	chr3:46904400-46906000	Active TSS	Skeletal Muscle Female	skeletal muscle
28	chr3:46904400-46906800	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
29	chr3:46904600-46904800	Bivalent Enhancer	Foreskin Fibroblast Primary Cells skin01	Skin
30	chr3:46904600-46905400	Active TSS	Psoas Muscle	Psoas
31	chr3:46904600-46905600	Enhancers	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
32	chr3:46904600-46905800	Weak transcription	Adipose Nuclei	Adipose
33	chr3:46904600-46906600	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
34	chr3:46904600-46911600	Enhancers	Placenta	Placenta

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