Variant report

Variant	rs7533902
Chromosome Location	chr1:98079228-98079229
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 19 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:14)

rs_ID	r²[population]
rs10783069	0.96[YRI][hapmap];0.94[AFR][1000 genomes]
rs10783070	1.00[ASW][hapmap];0.96[LWK][hapmap];0.93[MKK][hapmap];0.93[YRI][hapmap];0.92[AFR][1000 genomes]
rs10875098	0.83[ASW][hapmap];0.90[LWK][hapmap];0.86[MEX][hapmap];0.93[MKK][hapmap];0.96[YRI][hapmap];0.88[AFR][1000 genomes]
rs10875099	0.96[YRI][hapmap];0.94[AFR][1000 genomes]
rs10875100	0.80[YRI][hapmap];0.82[AFR][1000 genomes]
rs11165895	0.94[ASW][hapmap];0.81[LWK][hapmap];0.86[MEX][hapmap];0.86[MKK][hapmap]
rs12144462	0.85[CHB][hapmap];0.82[CHD][hapmap];0.82[ASN][1000 genomes]
rs1337522	0.88[ASW][hapmap]
rs1337523	0.94[ASW][hapmap];0.80[LWK][hapmap];0.80[MEX][hapmap];0.80[YRI][hapmap];0.81[AFR][1000 genomes]
rs2065943	1.00[ASW][hapmap];0.90[LWK][hapmap];0.86[MEX][hapmap];0.90[MKK][hapmap];0.90[YRI][hapmap];0.89[AFR][1000 genomes]
rs2811193	1.00[ASW][hapmap];0.81[LWK][hapmap];0.80[MEX][hapmap];0.80[YRI][hapmap];0.82[AFR][1000 genomes]
rs4949958	0.82[ASW][hapmap];0.87[LWK][hapmap];0.92[MKK][hapmap];0.96[YRI][hapmap];0.88[AFR][1000 genomes]
rs6663357	1.00[ASW][hapmap];0.96[LWK][hapmap];0.86[MEX][hapmap];0.93[MKK][hapmap];0.96[YRI][hapmap];0.94[AFR][1000 genomes]
rs7537165	1.00[ASW][hapmap];0.96[LWK][hapmap];0.86[MEX][hapmap];0.93[MKK][hapmap];0.96[YRI][hapmap];0.95[AFR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:5 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv491816	chr1:97266403-98223619	Enhancers Strong transcription ZNF genes & repeats Weak transcription Flanking Active TSS Genic enhancers Active TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	9 gene(s)	inside rSNPs	diseases
2	nsv533039	chr1:97665736-98343102	ZNF genes & repeats Weak transcription Enhancers Strong transcription Flanking Active TSS Genic enhancers Active TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	10 gene(s)	inside rSNPs	diseases
3	nsv530049	chr1:97883261-98384614	Weak transcription Enhancers Strong transcription ZNF genes & repeats Flanking Active TSS Active TSS Bivalent/Poised TSS Genic enhancers Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	10 gene(s)	inside rSNPs	diseases
4	nsv830703	chr1:97907708-98101144	Weak transcription Strong transcription Enhancers Active TSS ZNF genes & repeats Flanking Active TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
5	nsv830714	chr1:98025090-98229416	Enhancers Weak transcription Strong transcription ZNF genes & repeats Flanking Active TSS Active TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	2 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs7533902	DNTTIP2	cis	cerebellum	SCAN
rs7533902	LRRC39	cis	cerebellum	SCAN

Chromatin state (count:11 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:98009800-98112200	Weak transcription	HSMM	muscle
2	chr1:98051800-98096000	Weak transcription	Left Ventricle	heart
3	chr1:98060000-98087400	Weak transcription	Primary hematopoietic stem cells	blood
4	chr1:98060800-98092400	Weak transcription	Primary monocytes fromperipheralblood	blood
5	chr1:98063000-98111400	Weak transcription	Liver	Liver
6	chr1:98063400-98081000	Weak transcription	Primary T cells from cord blood	blood
7	chr1:98065200-98083000	Weak transcription	Monocytes-CD14+_RO01746	blood
8	chr1:98073000-98087600	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
9	chr1:98074600-98085800	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
10	chr1:98077400-98087400	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
11	chr1:98077400-98099400	Weak transcription	Primary B cells from cord blood	blood

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dbSNP/dbVar ID: rs12345 /nsv7879
a single nucleotide as 0-based coordinates: chr1:12345
chromosomal regions: chr1:12345-34567

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