Variant report

Variant	rs6466028
Chromosome Location	chr7:104498130-104498131
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 28 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:27)

rs_ID	r²[population]
rs10226913	0.91[EUR][1000 genomes]
rs10226989	0.89[EUR][1000 genomes]
rs10252576	0.91[CEU][hapmap]
rs10267013	0.89[EUR][1000 genomes]
rs10953453	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];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11762138	0.90[CHB][hapmap];0.90[YRI][hapmap]
rs12055895	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12667640	0.81[CHB][hapmap]
rs12672828	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17706774	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2005888	0.82[EUR][1000 genomes]
rs2192931	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[YRI][hapmap];0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2385466	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[AMR][1000 genomes];0.92[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs3955473	0.88[AFR][1000 genomes];0.94[AMR][1000 genomes];0.92[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs4382394	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.89[AFR][1000 genomes];0.87[AMR][1000 genomes];0.91[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs4532541	0.90[CHB][hapmap];0.90[YRI][hapmap]
rs4571661	0.91[CEU][hapmap];0.82[EUR][1000 genomes]
rs4730052	1.00[CEU][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];0.99[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs4730053	1.00[CEU][hapmap];1.00[YRI][hapmap];0.93[AFR][1000 genomes];0.99[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs59264482	0.91[AMR][1000 genomes];0.91[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs59335487	0.85[EUR][1000 genomes]
rs59814386	0.97[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs62485395	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62485396	0.91[AMR][1000 genomes];0.92[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs6958846	0.95[CEU][hapmap];0.87[EUR][1000 genomes]
rs741323	0.90[CEU][hapmap];0.81[EUR][1000 genomes]
rs9885984	0.87[EUR][1000 genomes]

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

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv831086	chr7:104422503-104596766	Enhancers Weak transcription Flanking Active TSS Flanking Bivalent TSS/Enh Active TSS Bivalent Enhancer Genic enhancers Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	13 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:26 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr7:104476400-104503000	Weak transcription	Duodenum Mucosa	Duodenum
2	chr7:104481600-104514400	Weak transcription	Fetal Kidney	kidney
3	chr7:104493400-104500800	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
4	chr7:104493800-104498400	Weak transcription	Breast Myoepithelial Primary Cells	Breast
5	chr7:104494000-104502800	Weak transcription	Fetal Intestine Large	intestine
6	chr7:104496800-104500800	Strong transcription	Fetal Intestine Small	intestine
7	chr7:104497600-104499000	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
8	chr7:104497600-104499000	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
9	chr7:104497600-104499400	Enhancers	Primary hematopoietic stem cells short term culture	blood
10	chr7:104497600-104499400	Enhancers	Primary T helper naive cells fromperipheralblood	blood
11	chr7:104497600-104499400	Enhancers	Primary T helper cells PMA-I stimulated	--
12	chr7:104497800-104498600	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Female	--
13	chr7:104497800-104498800	Enhancers	Primary B cells from peripheral blood	blood
14	chr7:104497800-104498800	Enhancers	Primary T regulatory cells fromperipheralblood	blood
15	chr7:104497800-104499400	Enhancers	Primary T helper cells fromperipheralblood	blood
16	chr7:104498000-104498200	Flanking Active TSS	Primary hematopoietic stem cells	blood
17	chr7:104498000-104498400	Flanking Active TSS	Primary T killer naive cells fromperipheralblood	blood
18	chr7:104498000-104498600	Flanking Active TSS	Primary T cells from cord blood	blood
19	chr7:104498000-104498600	Bivalent Enhancer	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
20	chr7:104498000-104499000	Enhancers	Primary T helper 17 cells PMA-I stimulated	--
21	chr7:104498000-104499000	Enhancers	Primary T killer memory cells from peripheral blood	blood
22	chr7:104498000-104499000	Enhancers	Thymus	Thymus
23	chr7:104498000-104499000	Enhancers	Dnd41	blood
24	chr7:104498000-104499000	Flanking Active TSS	GM12878-XiMat	blood
25	chr7:104498000-104499200	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
26	chr7:104498000-104499200	Enhancers	Primary T helper naive cells from peripheral blood	blood

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