Variant report

Variant	rs7625839
Chromosome Location	chr3:45908148-45908149
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 15 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:11)

rs_ID	r²[population]
rs1029732	0.80[ASN][1000 genomes]
rs1125823	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11712469	0.94[ASN][1000 genomes]
rs13065964	1.00[ASW][hapmap];0.96[CEU][hapmap];0.95[CHB][hapmap];1.00[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];0.93[LWK][hapmap];1.00[MKK][hapmap];0.98[TSI][hapmap];0.93[YRI][hapmap];0.94[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1386930	1.00[ASW][hapmap];0.96[CEU][hapmap];0.95[CHB][hapmap];0.95[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];0.93[LWK][hapmap];1.00[MKK][hapmap];0.95[TSI][hapmap];0.89[YRI][hapmap];0.92[AFR][1000 genomes];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1488369	1.00[ASW][hapmap];0.96[CEU][hapmap];0.95[CHB][hapmap];0.95[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];0.93[LWK][hapmap];1.00[MKK][hapmap];0.95[TSI][hapmap];0.89[YRI][hapmap];0.91[AFR][1000 genomes];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2064061	0.86[CHB][hapmap]
rs2129880	0.95[ASN][1000 genomes]
rs7614952	0.81[CHB][hapmap];0.80[ASN][1000 genomes]
rs952287	0.81[CHB][hapmap]
rs9855780	0.82[AFR][1000 genomes];1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv876734	chr3:45725031-46468467	Weak transcription Enhancers Active TSS Flanking Active TSS Genic enhancers Bivalent/Poised TSS Strong transcription Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	42 gene(s)	inside rSNPs	diseases
2	nsv498008	chr3:45733423-46319401	Strong transcription Active TSS Genic enhancers Enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Weak transcription Flanking Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	29 gene(s)	inside rSNPs	diseases
3	nsv834678	chr3:45804294-46010256	Enhancers Flanking Bivalent TSS/Enh Strong transcription Weak transcription Bivalent Enhancer Flanking Active TSS Genic enhancers Active TSS ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	11 gene(s)	inside rSNPs	diseases
4	nsv876736	chr3:45900621-46027410	Strong transcription Enhancers Transcr. at gene 5' and 3' Weak transcription Genic enhancers Bivalent Enhancer Flanking Active TSS ZNF genes & repeats Active TSS Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	8 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:19 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:45902600-45910200	Weak transcription	Gastric	stomach
2	chr3:45905400-45911000	Weak transcription	Esophagus	oesophagus
3	chr3:45906800-45912600	Enhancers	Fetal Thymus	thymus
4	chr3:45907000-45909800	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
5	chr3:45907000-45911200	Enhancers	Thymus	Thymus
6	chr3:45907200-45910400	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
7	chr3:45907400-45910200	Weak transcription	Primary T helper naive cells from peripheral blood	blood
8	chr3:45907400-45910200	Weak transcription	Primary T helper cells PMA-I stimulated	--
9	chr3:45907400-45910400	Weak transcription	Primary T helper cells fromperipheralblood	blood
10	chr3:45907400-45910400	Weak transcription	Primary T killer memory cells from peripheral blood	blood
11	chr3:45907600-45909400	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
12	chr3:45907600-45909800	Weak transcription	Duodenum Mucosa	Duodenum
13	chr3:45907600-45910200	Enhancers	GM12878-XiMat	blood
14	chr3:45907600-45910600	Weak transcription	Primary B cells from peripheral blood	blood
15	chr3:45907800-45908800	Weak transcription	Primary hematopoietic stem cells short term culture	blood
16	chr3:45907800-45909000	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
17	chr3:45907800-45909800	Weak transcription	Primary T cells from cord blood	blood
18	chr3:45907800-45910000	Weak transcription	Primary hematopoietic stem cells	blood
19	chr3:45908000-45908800	Enhancers	Dnd41	blood

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dbSNP/dbVar ID: rs12345 /nsv7879
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chromosomal regions: chr1:12345-34567

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