Variant report

Variant	rs3113881
Chromosome Location	chr4:48015035-48015036
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	POLR2A	chr4:48015021-48015052	HUVEC	blood vessel:	n/a	n/a
2	POLR2A	chr4:48014830-48015155	HL-60	blood:	n/a	n/a
3	ZNF384	chr4:48014852-48015107	K562	blood:	n/a	n/a

Variant related genes	Relation type
CNGA1	TF binding region
NIPAL1	TF binding region

Extended variants
information (count: 54 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:47)

rs_ID	r²[population]
rs10002500	0.83[CEU][hapmap];0.86[CHB][hapmap];0.95[JPT][hapmap];0.95[YRI][hapmap]
rs10461076	0.83[ASN][1000 genomes]
rs10517200	0.84[CEU][hapmap]
rs10517204	0.86[JPT][hapmap];0.91[YRI][hapmap];0.84[AFR][1000 genomes]
rs10805163	0.86[JPT][hapmap];0.91[YRI][hapmap];0.84[AFR][1000 genomes]
rs10938520	0.84[AFR][1000 genomes]
rs11733288	0.91[CHB][hapmap];1.00[JPT][hapmap];0.88[YRI][hapmap];0.91[AFR][1000 genomes];0.89[AMR][1000 genomes];0.81[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs12504018	0.86[YRI][hapmap]
rs12645164	0.85[CEU][hapmap]
rs12645245	0.91[CHB][hapmap];1.00[JPT][hapmap];0.88[YRI][hapmap];0.88[AFR][1000 genomes];0.89[ASN][1000 genomes]
rs12651301	0.86[YRI][hapmap]
rs1371729	0.90[YRI][hapmap]
rs1371732	0.95[CHB][hapmap];0.91[JPT][hapmap]
rs1396051	0.87[JPT][hapmap];0.91[YRI][hapmap];0.84[AFR][1000 genomes]
rs1440228	0.87[YRI][hapmap]
rs1507913	0.91[AFR][1000 genomes];0.97[AMR][1000 genomes];0.93[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs1507914	0.91[AFR][1000 genomes];0.94[AMR][1000 genomes];0.93[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs178650	0.92[AFR][1000 genomes];0.89[AMR][1000 genomes];0.82[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1837518	0.91[AMR][1000 genomes];0.91[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1866688	0.84[CEU][hapmap];0.86[CHB][hapmap]
rs1866689	0.86[YRI][hapmap]
rs188901	0.90[AFR][1000 genomes];0.98[AMR][1000 genomes];0.89[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs1899060	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];0.93[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs224800	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];0.89[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2352470	0.91[YRI][hapmap]
rs2581493	0.90[AFR][1000 genomes];0.92[AMR][1000 genomes];0.93[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2661513	0.83[JPT][hapmap];1.00[YRI][hapmap];0.86[AFR][1000 genomes];0.82[AMR][1000 genomes]
rs28642966	0.81[CHB][hapmap];0.80[JPT][hapmap]
rs28699496	0.89[ASN][1000 genomes]
rs3113882	0.91[AFR][1000 genomes];0.97[AMR][1000 genomes];0.93[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs321621	0.92[AFR][1000 genomes];0.89[AMR][1000 genomes];0.81[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs321623	0.90[CHB][hapmap];1.00[JPT][hapmap];0.95[YRI][hapmap];0.92[AFR][1000 genomes];0.89[AMR][1000 genomes];0.81[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs321633	0.86[CHB][hapmap];1.00[JPT][hapmap];0.89[AMR][1000 genomes];0.82[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs321642	0.82[AFR][1000 genomes];1.00[AMR][1000 genomes];0.93[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs321644	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];0.91[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs321646	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];0.91[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs3950558	0.90[CHB][hapmap];1.00[JPT][hapmap];0.80[AMR][1000 genomes];0.81[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs4694880	0.87[JPT][hapmap];0.87[YRI][hapmap];0.84[AFR][1000 genomes]
rs4695326	0.92[AFR][1000 genomes];0.89[AMR][1000 genomes];0.93[ASN][1000 genomes]
rs6447603	1.00[CHB][hapmap];0.91[JPT][hapmap]
rs6823184	0.87[YRI][hapmap]
rs6823698	0.86[YRI][hapmap]
rs6850603	0.92[AFR][1000 genomes];0.89[AMR][1000 genomes];0.81[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs6858440	0.86[YRI][hapmap]
rs7685636	0.84[AFR][1000 genomes]
rs978094	0.87[YRI][hapmap]
rs9995122	0.90[YRI][hapmap]

Variant overlapped rSNPs/rCNVs (count:7 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv3447039	chr4:47822266-48285222	Flanking Active TSS Enhancers Weak transcription Flanking Bivalent TSS/Enh Strong transcription Active TSS Bivalent/Poised TSS Genic enhancers Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	34 gene(s)	inside rSNPs	diseases
2	nsv1013947	chr4:47915527-48052824	Enhancers Weak transcription Flanking Active TSS Active TSS Strong transcription ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
3	nsv537082	chr4:47915527-48052824	Flanking Active TSS Active TSS Weak transcription Flanking Bivalent TSS/Enh Enhancers Bivalent/Poised TSS Bivalent Enhancer Strong transcription ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
4	nsv1006745	chr4:47935250-48052824	Strong transcription Enhancers Flanking Active TSS ZNF genes & repeats Bivalent/Poised TSS Weak transcription Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
5	nsv537083	chr4:47935250-48052824	Enhancers Active TSS Genic enhancers Weak transcription Strong transcription Bivalent Enhancer Flanking Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
6	nsv1013163	chr4:47977844-48022511	Enhancers Active TSS ZNF genes & repeats Weak transcription Flanking Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Strong transcription Bivalent Enhancer Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
7	nsv537084	chr4:47977844-48022511	Active TSS Enhancers ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer Weak transcription Flanking Active TSS Flanking Bivalent TSS/Enh Strong transcription Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs3113881	CORIN	cis	Whole Blood	GTEx
rs3113881	CNGA1	cis	Nerve Tibial	GTEx
rs3113881	CNGA1	cis	Muscle Skeletal	GTEx
rs3113881	NFXL1	cis	Whole Blood	GTEx

Chromatin state (count:23 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:48005400-48017400	Weak transcription	Placenta Amnion	Placenta Amnion
2	chr4:48008000-48017600	Weak transcription	Psoas Muscle	Psoas
3	chr4:48010200-48017200	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
4	chr4:48010200-48017600	Weak transcription	Rectal Mucosa Donor 31	rectum
5	chr4:48011000-48017400	Weak transcription	Colonic Mucosa	Colon
6	chr4:48011000-48017600	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
7	chr4:48011000-48017600	Weak transcription	Skeletal Muscle Female	skeletal muscle
8	chr4:48011200-48017600	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
9	chr4:48011400-48017600	Weak transcription	Esophagus	oesophagus
10	chr4:48011800-48017800	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
11	chr4:48011800-48018200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
12	chr4:48012800-48016600	Enhancers	iPS-15b Cell Line	embryonic stem cell
13	chr4:48012800-48017400	Weak transcription	ES-I3 Cell Line	embryonic stem cell
14	chr4:48013000-48016800	Weak transcription	Fetal Intestine Large	intestine
15	chr4:48013200-48017200	Weak transcription	Liver	Liver
16	chr4:48013800-48017800	Weak transcription	H1 Cell Line	embryonic stem cell
17	chr4:48014000-48015400	Enhancers	HUES6 Cell Line	embryonic stem cell
18	chr4:48014200-48017800	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
19	chr4:48014400-48015200	Enhancers	HUES64 Cell Line	embryonic stem cell
20	chr4:48014400-48017800	Weak transcription	iPS-20b Cell Line	embryonic stem cell
21	chr4:48014800-48015400	Enhancers	Primary monocytes fromperipheralblood	blood
22	chr4:48014800-48015600	Enhancers	Sigmoid Colon	Sigmoid Colon
23	chr4:48015000-48015200	Enhancers	Primary hematopoietic stem cells short term culture	blood

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