Variant report

Variant	rs2296864
Chromosome Location	chr9:16415459-16415460
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr9:16409821..16411525-chr9:16413857..16415873,2	MCF-7	breast:

Extended variants
information (count: 36 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:34)

rs_ID	r²[population]
rs10511620	1.00[CEU][hapmap];0.87[TSI][hapmap];0.81[EUR][1000 genomes]
rs10511621	1.00[CEU][hapmap];0.83[JPT][hapmap];1.00[MEX][hapmap];0.94[TSI][hapmap];0.84[EUR][1000 genomes]
rs16934614	0.81[JPT][hapmap]
rs16934619	0.81[JPT][hapmap]
rs16934621	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.95[LWK][hapmap];1.00[MEX][hapmap];0.97[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.91[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs16934644	1.00[CEU][hapmap];0.82[TSI][hapmap];0.87[EUR][1000 genomes]
rs16934647	1.00[CEU][hapmap];0.87[TSI][hapmap];0.89[EUR][1000 genomes]
rs16934660	1.00[CEU][hapmap];0.87[TSI][hapmap];0.82[EUR][1000 genomes]
rs16934675	1.00[CEU][hapmap]
rs16934679	1.00[CEU][hapmap]
rs16934681	0.82[CEU][hapmap]
rs1927622	1.00[CEU][hapmap]
rs1927623	0.82[CEU][hapmap];0.81[EUR][1000 genomes]
rs1927624	0.83[EUR][1000 genomes]
rs1927625	1.00[CEU][hapmap]
rs2296862	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.94[TSI][hapmap];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2296863	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3739715	1.00[CEU][hapmap];0.85[MEX][hapmap];0.82[TSI][hapmap];0.85[EUR][1000 genomes]
rs3814110	1.00[CEU][hapmap];0.85[MEX][hapmap];0.82[TSI][hapmap];0.87[EUR][1000 genomes]
rs41313973	0.87[EUR][1000 genomes]
rs41313975	0.87[EUR][1000 genomes]
rs57010092	0.85[EUR][1000 genomes]
rs57310704	0.85[EUR][1000 genomes]
rs57937957	0.85[EUR][1000 genomes]
rs58105894	0.85[EUR][1000 genomes]
rs59049761	0.85[EUR][1000 genomes]
rs60573475	0.85[EUR][1000 genomes]
rs61393085	0.85[EUR][1000 genomes]
rs7021534	1.00[CEU][hapmap];0.88[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs7025750	0.80[AFR][1000 genomes];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs7041544	0.83[EUR][1000 genomes]
rs7851973	1.00[CEU][hapmap];0.83[JPT][hapmap];0.84[EUR][1000 genomes]
rs7867445	1.00[CEU][hapmap];0.85[MEX][hapmap];0.87[TSI][hapmap]
rs7871743	1.00[CEU][hapmap];0.87[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:2 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv530933	chr9:16251206-16830845	Enhancers Weak transcription Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh Strong transcription Genic enhancers Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	13 gene(s)	inside rSNPs	diseases
2	nsv530934	chr9:16281246-16779432	Strong transcription Active TSS Weak transcription Enhancers Flanking Active TSS Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	13 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:36 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr9:16405800-16416400	Weak transcription	HUVEC	blood vessel
2	chr9:16407200-16415800	Weak transcription	Fetal Muscle Leg	muscle
3	chr9:16407200-16417000	Weak transcription	HSMM	muscle
4	chr9:16407400-16415800	Weak transcription	Fetal Kidney	kidney
5	chr9:16411200-16418800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
6	chr9:16411200-16419000	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
7	chr9:16411400-16419000	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
8	chr9:16411600-16418800	Weak transcription	Fetal Muscle Trunk	muscle
9	chr9:16414000-16417000	Weak transcription	HUES6 Cell Line	embryonic stem cell
10	chr9:16414000-16417200	Enhancers	Fetal Lung	lung
11	chr9:16414000-16418800	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
12	chr9:16414200-16415600	Weak transcription	Rectal Smooth Muscle	rectum
13	chr9:16414200-16415600	Enhancers	NHLF	lung
14	chr9:16414200-16416600	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
15	chr9:16414200-16416800	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
16	chr9:16414200-16417200	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
17	chr9:16414200-16421200	Weak transcription	ES-I3 Cell Line	embryonic stem cell
18	chr9:16414400-16416400	Weak transcription	HUES64 Cell Line	embryonic stem cell
19	chr9:16414400-16416400	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
20	chr9:16414400-16416600	Weak transcription	Muscle Satellite Cultured Cells	--
21	chr9:16414400-16417200	Weak transcription	Adipose Nuclei	Adipose
22	chr9:16414400-16418600	Weak transcription	Fetal Intestine Large	intestine
23	chr9:16414400-16418800	Weak transcription	Placenta	Placenta
24	chr9:16414400-16421600	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
25	chr9:16414600-16415600	Weak transcription	Colon Smooth Muscle	Colon
26	chr9:16414600-16421200	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
27	chr9:16414800-16415800	Weak transcription	Ovary	ovary
28	chr9:16414800-16417000	Enhancers	A549	lung
29	chr9:16414800-16417200	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
30	chr9:16414800-16418800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
31	chr9:16415000-16416000	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
32	chr9:16415200-16416800	Weak transcription	iPS-18 Cell Line	embryonic stem cell
33	chr9:16415200-16420800	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
34	chr9:16415400-16415800	Genic enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
35	chr9:16415400-16416000	Enhancers	Fetal Stomach	stomach
36	chr9:16415400-16425600	Weak transcription	iPS-15b Cell Line	embryonic stem cell

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