Variant report

Variant	rs3772130
Chromosome Location	chr3:121344140-121344141
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr3:121344119..121346108-chr3:121348732..121350963,2	K562	blood:

Extended variants
information (count: 44 )
Associated
traits (count: 14 )

rSNPs within LD-proxies of this variant (count:36)

rs_ID	r²[population]
rs11706783	0.96[CEU][hapmap];0.82[CHB][hapmap];1.00[JPT][hapmap]
rs11707716	0.86[AFR][1000 genomes];0.84[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs11714406	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.83[AFR][1000 genomes];0.82[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs11716984	0.86[AFR][1000 genomes];0.95[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs11719458	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.90[LWK][hapmap];0.93[MEX][hapmap];1.00[MKK][hapmap];0.94[TSI][hapmap];1.00[YRI][hapmap];0.88[EUR][1000 genomes]
rs11720859	0.82[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs11721318	1.00[CEU][hapmap];1.00[YRI][hapmap];0.86[EUR][1000 genomes]
rs13072618	0.87[EUR][1000 genomes]
rs13074834	0.86[EUR][1000 genomes]
rs13077135	0.85[EUR][1000 genomes]
rs13083794	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap]
rs13087578	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.97[TSI][hapmap];0.82[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs13090660	0.84[EUR][1000 genomes]
rs17691170	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2070180	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs28660600	0.96[CEU][hapmap];0.82[CHB][hapmap];0.87[CHD][hapmap];0.94[GIH][hapmap];1.00[JPT][hapmap];0.93[MEX][hapmap];0.90[TSI][hapmap]
rs33988592	0.86[EUR][1000 genomes]
rs34086988	1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs34667636	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs35988617	0.86[EUR][1000 genomes]
rs36142735	0.88[EUR][1000 genomes]
rs3732408	0.86[EUR][1000 genomes]
rs3772128	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4280673	0.89[JPT][hapmap]
rs4311252	0.96[CEU][hapmap];0.82[CHB][hapmap];0.87[CHD][hapmap];0.94[GIH][hapmap];1.00[JPT][hapmap];0.93[MEX][hapmap];0.90[TSI][hapmap]
rs55643643	0.82[EUR][1000 genomes]
rs56314138	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs62268732	0.86[AFR][1000 genomes];0.82[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs66653099	0.82[EUR][1000 genomes]
rs6768621	0.96[CEU][hapmap]
rs6776670	0.96[CEU][hapmap];0.82[CHB][hapmap];0.87[CHD][hapmap];0.94[GIH][hapmap];1.00[JPT][hapmap];0.93[MEX][hapmap];0.90[TSI][hapmap]
rs6791046	0.83[EUR][1000 genomes]
rs7427165	0.86[AFR][1000 genomes];0.88[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs7631939	1.00[JPT][hapmap]
rs9839617	0.96[CEU][hapmap];0.82[CHB][hapmap];1.00[JPT][hapmap]
rs9883467	0.96[CEU][hapmap];0.82[CHB][hapmap];1.00[JPT][hapmap]

Variant overlapped rSNPs/rCNVs (count:8 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv998555	chr3:120700604-121348015	Weak transcription Strong transcription Enhancers Active TSS ZNF genes & repeats Flanking Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA	19 gene(s)	inside rSNPs	diseases
2	nsv591395	chr3:120970900-121501070	Flanking Active TSS Weak transcription Enhancers ZNF genes & repeats Strong transcription Transcr. at gene 5' and 3' Genic enhancers Active TSS Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	47 gene(s)	inside rSNPs	diseases
3	nsv591396	chr3:120970900-121557533	Strong transcription Active TSS Flanking Active TSS Enhancers Weak transcription Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	50 gene(s)	inside rSNPs	diseases
4	nsv591397	chr3:120977383-121505882	Strong transcription Weak transcription Enhancers Active TSS Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	47 gene(s)	inside rSNPs	diseases
5	nsv999335	chr3:121100283-121408766	Weak transcription Strong transcription Genic enhancers Flanking Active TSS Active TSS Enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	18 gene(s)	inside rSNPs	diseases
6	nsv1007522	chr3:121200563-121374051	Enhancers Weak transcription Strong transcription Active TSS Flanking Active TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	15 gene(s)	inside rSNPs	diseases
7	nsv999349	chr3:121253990-121360206	Enhancers Strong transcription Active TSS Flanking Active TSS Flanking Bivalent TSS/Enh Weak transcription Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	13 gene(s)	inside rSNPs	diseases
8	nsv998740	chr3:121289499-121390271	Strong transcription Weak transcription Genic enhancers Enhancers Active TSS Flanking Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	8 gene(s)	inside rSNPs	diseases

Variant related diseases (count:1)

Disease	PMID	Source
Cognitive performance	19734545	GWAS catalog

mRNA abundance (count:13)

SNP	Gene	Cis/trans	Tissue	Source
rs3772130	HEG1	cis	parietal	SCAN
rs3772130	IQCB1	cis	Whole Blood	GTEx
rs3772130	CCDC58	cis	parietal	SCAN
rs3772130	HCLS1	cis	Whole Blood	GTEx
rs3772130	SLC15A2	cis	cerebellum	SCAN
rs3772130	SLC15A2	Cis_1M	lymphoblastoid	RTeQTL
rs3772130	IQCB1	cis	parietal	SCAN
rs3772130	PARP9	cis	cerebellum	SCAN
rs3772130	EAF2	Cis_1M	lymphoblastoid	RTeQTL
rs3772130	IQCB1	cis	cerebellum	SCAN
rs3772130	IQCB1	Cis_1M	lymphoblastoid	RTeQTL
rs3772130	CHST13	cis	cerebellum	SCAN
rs3772130	EAF2	cis	cerebellum	SCAN

Chromatin state (count:20 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:121341800-121348400	Weak transcription	Spleen	Spleen
2	chr3:121342000-121350000	Weak transcription	Liver	Liver
3	chr3:121342200-121346200	Weak transcription	Right Ventricle	heart
4	chr3:121343200-121344200	Enhancers	HUES6 Cell Line	embryonic stem cell
5	chr3:121343200-121344400	Enhancers	ES-I3 Cell Line	embryonic stem cell
6	chr3:121343200-121344400	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
7	chr3:121343200-121344400	Enhancers	Fetal Heart	heart
8	chr3:121343200-121348400	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
9	chr3:121343400-121344200	Enhancers	iPS-18 Cell Line	embryonic stem cell
10	chr3:121343400-121348000	Weak transcription	Primary T cells fromperipheralblood	blood
11	chr3:121343600-121345800	Weak transcription	H9 Cell Line	embryonic stem cell
12	chr3:121343600-121346200	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
13	chr3:121343600-121348400	Weak transcription	Psoas Muscle	Psoas
14	chr3:121343800-121345000	Weak transcription	Skeletal Muscle Male	skeletal muscle
15	chr3:121343800-121345000	Strong transcription	Skeletal Muscle Female	skeletal muscle
16	chr3:121343800-121345600	Weak transcription	Left Ventricle	heart
17	chr3:121343800-121347200	Weak transcription	HUES48 Cell Line	embryonic stem cell
18	chr3:121343800-121347600	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
19	chr3:121343800-121353000	Weak transcription	H1 Cell Line	embryonic stem cell
20	chr3:121344000-121346200	Weak transcription	Right Atrium	heart

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