Variant report

Variant	rs1042973
Chromosome Location	chr3:46899516-46899517
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	chr3:46896689..46901073-chr3:46902625..46907600,6	K562	blood:
2	chr3:46898224..46901202-chr3:46902129..46904254,2	K562	blood:

Variant related genes	Relation type
ENSG00000160808	Chromatin interaction

Extended variants
information (count: 35 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:21)

rs_ID	r²[population]
rs12106917	0.93[CHB][hapmap]
rs12107311	0.93[CHB][hapmap]
rs12486015	0.86[CHB][hapmap]
rs12492369	0.86[CHB][hapmap]
rs12493158	0.86[CHB][hapmap]
rs1531136	1.00[CHB][hapmap];0.81[CHD][hapmap];0.87[GIH][hapmap];0.80[JPT][hapmap];0.88[ASN][1000 genomes]
rs1869868	0.85[ASN][1000 genomes]
rs2227294	0.85[GIH][hapmap]
rs2385860	1.00[CHB][hapmap];0.81[GIH][hapmap];0.80[JPT][hapmap];1.00[MEX][hapmap]
rs3792558	1.00[CHB][hapmap];0.89[GIH][hapmap];1.00[MEX][hapmap];0.81[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs4683304	0.93[CHB][hapmap]
rs57459864	0.84[ASN][1000 genomes]
rs6763438	0.86[CHB][hapmap]
rs6768252	0.86[CHB][hapmap]
rs6777190	0.86[CHB][hapmap]
rs6797059	0.85[CHB][hapmap]
rs6801048	0.85[CHB][hapmap]
rs7614762	0.85[CHB][hapmap]
rs7633581	1.00[CHB][hapmap];0.80[JPT][hapmap];0.86[ASN][1000 genomes]
rs877670	0.84[ASN][1000 genomes]
rs936175	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]

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	nsv590204	chr3:46852679-46901654	Enhancers Transcr. at gene 5' and 3' Weak transcription Flanking Active TSS Active TSS Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Strong transcription Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
8	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
9	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
10	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
11	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
12	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
13	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
14	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

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs1042973	TSPAN12	trans	lymphoblastoid	seeQTL
rs1042973	LRRC2	cis	parietal	SCAN
rs1042973	SCAP	cis	parietal	SCAN

Chromatin state (count:16 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:46888000-46908800	Weak transcription	Esophagus	oesophagus
2	chr3:46891800-46901000	Weak transcription	Fetal Intestine Small	intestine
3	chr3:46893400-46900600	Weak transcription	Fetal Intestine Large	intestine
4	chr3:46893800-46906200	Weak transcription	Placenta Amnion	Placenta Amnion
5	chr3:46894200-46905200	Weak transcription	Fetal Lung	lung
6	chr3:46895000-46904400	Enhancers	Fetal Adrenal Gland	Adrenal Gland
7	chr3:46896400-46902800	Weak transcription	Ovary	ovary
8	chr3:46897000-46908600	Weak transcription	Gastric	stomach
9	chr3:46897800-46900400	Strong transcription	Left Ventricle	heart
10	chr3:46898000-46904800	Transcr. at gene 5' and 3'	Skeletal Muscle Male	skeletal muscle
11	chr3:46898600-46900600	Flanking Active TSS	Fetal Heart	heart
12	chr3:46898800-46899800	Enhancers	iPS DF 19.11 Cell Line	embryonic stem cell
13	chr3:46898800-46908400	Weak transcription	Liver	Liver
14	chr3:46899000-46899600	Genic enhancers	Right Ventricle	heart
15	chr3:46899200-46902800	Weak transcription	Adipose Nuclei	Adipose
16	chr3:46899400-46899800	Transcr. at gene 5' and 3'	Skeletal Muscle Female	skeletal muscle

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