Variant report

Variant	rs1951242
Chromosome Location	chr4:74617282-74617283
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr4:74616341..74618099-chr4:74619715..74622030,2	K562	blood:
2	chr4:74613567..74615922-chr4:74616921..74619617,2	K562	blood:
3	chr4:74616774..74619634-chr4:74626803..74629633,2	K562	blood:
4	chr4:74613677..74615255-chr4:74615539..74617498,2	MCF-7	breast:
5	chr4:74609331..74611384-chr4:74617018..74619785,2	K562	blood:
6	chr4:74615686..74617847-chr4:74622511..74624521,2	K562	blood:
7	chr4:74613405..74615443-chr4:74615480..74619617,3	K562	blood:

Extended variants
information (count: 72 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:64)

rs_ID	r²[population]
rs10005565	0.84[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs10009462	0.85[AMR][1000 genomes];0.85[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs10009488	0.84[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs10010970	0.84[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs10012962	0.82[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs10015626	0.84[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs10019318	0.85[AMR][1000 genomes];0.85[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs10031141	0.96[CEU][hapmap];0.86[CHB][hapmap];0.84[TSI][hapmap];0.81[EUR][1000 genomes]
rs10938092	0.87[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs10938094	0.82[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs10938095	0.82[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs10938096	0.82[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs10938097	0.85[AMR][1000 genomes];0.85[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs10938100	0.85[AMR][1000 genomes];0.85[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs1126647	0.90[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs11730284	1.00[AFR][1000 genomes];0.99[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11730560	0.90[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs11730667	1.00[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];0.96[GIH][hapmap];0.94[JPT][hapmap];1.00[MEX][hapmap];0.93[TSI][hapmap];0.91[AMR][1000 genomes];0.95[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs11938389	0.81[AMR][1000 genomes];0.85[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs12503139	0.82[ASN][1000 genomes]
rs12644561	0.82[ASN][1000 genomes]
rs13106097	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13109146	0.86[AMR][1000 genomes];0.85[ASN][1000 genomes]
rs13109377	0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13112910	0.81[AMR][1000 genomes];0.92[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs13116536	0.90[AFR][1000 genomes];0.89[AMR][1000 genomes];0.84[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs13117876	1.00[CEU][hapmap];1.00[CHB][hapmap];0.94[JPT][hapmap];0.90[AMR][1000 genomes];0.84[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs13151869	0.82[ASN][1000 genomes]
rs16849928	0.82[AMR][1000 genomes];0.95[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs16849945	0.90[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs16849958	0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1951235	0.84[ASN][1000 genomes]
rs1951236	0.83[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1951240	0.90[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1957070	0.85[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs1957661	0.90[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2145617	0.84[CEU][hapmap];0.95[CHB][hapmap];0.86[GIH][hapmap];0.92[MEX][hapmap];0.86[AMR][1000 genomes];0.84[ASN][1000 genomes]
rs2224434	0.84[CEU][hapmap];0.95[CHB][hapmap];0.86[GIH][hapmap];0.89[JPT][hapmap];0.87[MEX][hapmap];0.84[AMR][1000 genomes];0.84[ASN][1000 genomes]
rs2227306	0.96[CEU][hapmap];0.90[CHB][hapmap];0.85[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs2227307	0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2227521	0.88[AMR][1000 genomes];0.89[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2227543	0.96[CEU][hapmap];0.90[CHB][hapmap];0.95[CHD][hapmap];0.81[GIH][hapmap];0.84[JPT][hapmap];0.84[TSI][hapmap];0.87[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2367276	0.85[AMR][1000 genomes];0.86[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs28609798	0.82[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs28612337	0.90[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2886920	0.84[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2886922	0.80[AMR][1000 genomes];0.85[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs4073	0.91[AFR][1000 genomes];0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4279174	0.82[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs4549349	0.81[AMR][1000 genomes];0.85[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs4694178	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4694636	0.87[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];0.98[GIH][hapmap];0.94[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.81[MKK][hapmap];0.91[TSI][hapmap];0.88[YRI][hapmap];0.93[AFR][1000 genomes];0.92[AMR][1000 genomes];0.91[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4694637	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4694639	0.85[CHB][hapmap];0.84[JPT][hapmap]
rs62312370	0.90[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs6446959	0.90[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs6446960	0.85[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs6446961	0.96[CEU][hapmap];0.90[CHB][hapmap];0.82[TSI][hapmap]
rs6820848	0.83[AMR][1000 genomes];0.83[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs6831029	0.80[EUR][1000 genomes]
rs6853679	0.85[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7689435	0.85[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs9999262	0.82[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs9999446	0.85[AMR][1000 genomes];0.85[EUR][1000 genomes];0.94[ASN][1000 genomes]

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	nsv1001725	chr4:74354050-74860924	Enhancers Weak transcription Active TSS Flanking Active TSS Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Strong transcription Transcr. at gene 5' and 3' ZNF genes & repeats Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	27 gene(s)	inside rSNPs	diseases
2	nsv530126	chr4:74376622-74843892	Bivalent Enhancer Enhancers Weak transcription ZNF genes & repeats Flanking Active TSS Bivalent/Poised TSS Genic enhancers Flanking Bivalent TSS/Enh Active TSS Strong transcription Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	22 gene(s)	inside rSNPs	diseases
3	nsv1008104	chr4:74468434-74621952	Enhancers Active TSS Weak transcription Flanking Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS Strong transcription Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	12 gene(s)	inside rSNPs	diseases
4	nsv1012198	chr4:74487793-74621952	Enhancers Weak transcription Active TSS Flanking Active TSS ZNF genes & repeats Bivalent Enhancer Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	12 gene(s)	inside rSNPs	diseases
5	nsv537139	chr4:74487793-74621952	Weak transcription Enhancers Flanking Active TSS Active TSS Bivalent Enhancer ZNF genes & repeats Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	12 gene(s)	inside rSNPs	diseases
6	nsv1005231	chr4:74555497-74680079	Enhancers Weak transcription Flanking Active TSS Active TSS Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	12 gene(s)	inside rSNPs	diseases
7	nsv980219	chr4:74603561-74618789	Enhancers Flanking Active TSS Weak transcription Active TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	3 gene(s)	inside rSNPs	diseases
8	esv275137	chr4:74613334-74617282	Weak transcription Enhancers	Chromatin interactive region	1 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs1951242	PF4V1	cis	multi-tissue	Pritchard
rs1951242	SDAD1	cis	cerebellum	SCAN
rs1951242	ALB	cis	cerebellum	SCAN

Chromatin state (count:4 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:74617000-74617400	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
2	chr4:74617000-74617400	Enhancers	K562	blood
3	chr4:74617200-74617600	Enhancers	GM12878-XiMat	blood
4	chr4:74617200-74618800	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast

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