Variant report

Variant	rs16949854
Chromosome Location	chr12:120447892-120447893
allele	A/G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr12:120446709..120448766-chr12:120465189..120467335,2	K562	blood:
2	chr12:120447212..120449206-chr12:120452200..120454968,2	MCF-7	breast:
3	chr12:120443342..120446063-chr12:120447694..120450232,2	MCF-7	breast:

Extended variants
information (count: 32 )
Associated
traits (count: 0)

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

rs_ID	r²[population]
rs1054631	1.00[ASN][1000 genomes]
rs16949862	0.88[ASW][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];1.00[MKK][hapmap];1.00[TSI][hapmap];0.80[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs16949870	0.88[ASW][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];1.00[MKK][hapmap];1.00[TSI][hapmap];0.80[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs16949914	1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];0.85[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2286041	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.85[LWK][hapmap];1.00[MEX][hapmap];0.94[MKK][hapmap];1.00[TSI][hapmap];0.84[AFR][1000 genomes];1.00[AMR][1000 genomes];0.85[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28613380	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];0.85[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs56105460	1.00[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs56152568	0.83[AFR][1000 genomes];0.90[AMR][1000 genomes];0.94[ASN][1000 genomes]
rs56939014	1.00[AFR][1000 genomes];1.00[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs57155388	0.97[AFR][1000 genomes];0.81[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs57339959	0.83[AFR][1000 genomes];0.90[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs57458743	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];0.85[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs59868595	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];0.85[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs60106911	1.00[ASN][1000 genomes]
rs60223336	1.00[ASN][1000 genomes]
rs60590470	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs60742518	0.89[AMR][1000 genomes]
rs61514727	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];0.85[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6490279	0.88[ASW][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];1.00[MKK][hapmap];1.00[TSI][hapmap];0.80[YRI][hapmap];1.00[AFR][1000 genomes];1.00[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs6490282	0.88[ASW][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.95[LWK][hapmap];0.94[MKK][hapmap];1.00[TSI][hapmap];0.80[YRI][hapmap];0.87[AFR][1000 genomes];1.00[AMR][1000 genomes];0.85[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7132099	0.82[AFR][1000 genomes];1.00[AMR][1000 genomes];0.85[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs7139151	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs7297564	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];0.85[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7298081	0.88[ASW][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];1.00[MKK][hapmap];1.00[TSI][hapmap];0.80[YRI][hapmap];0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];0.85[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7304560	1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];0.85[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7956221	0.83[AFR][1000 genomes];0.89[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs7957325	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][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	esv3525916	chr12:120345352-120665045	Bivalent Enhancer Genic enhancers Enhancers Weak transcription Strong transcription Active TSS Flanking Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	99 gene(s)	inside rSNPs	diseases
2	esv3525917	chr12:120345352-120665045	Weak transcription Enhancers Genic enhancers Active TSS Bivalent/Poised TSS Strong transcription Flanking Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	99 gene(s)	inside rSNPs	diseases
3	nsv899554	chr12:120389613-120513625	Weak transcription Flanking Active TSS Bivalent Enhancer Enhancers Active TSS Flanking Bivalent TSS/Enh Strong transcription Transcr. at gene 5' and 3' Genic enhancers Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	14 gene(s)	inside rSNPs	diseases
4	esv1797666	chr12:120426666-120449259	Active TSS Weak transcription Flanking Active TSS Enhancers Bivalent/Poised TSS Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Strong transcription ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases
5	esv1807589	chr12:120426666-120449259	Weak transcription Enhancers Flanking Bivalent TSS/Enh Flanking Active TSS Active TSS Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Strong transcription ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:37 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:120428600-120449800	Weak transcription	Brain Anterior Caudate	brain
2	chr12:120428600-120453200	Weak transcription	H9 Cell Line	embryonic stem cell
3	chr12:120428800-120451400	Weak transcription	HMEC	breast
4	chr12:120428800-120451600	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
5	chr12:120429000-120450000	Weak transcription	Esophagus	oesophagus
6	chr12:120437800-120462400	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
7	chr12:120438800-120451400	Weak transcription	A549	lung
8	chr12:120442200-120451400	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
9	chr12:120444800-120451200	Weak transcription	Hela-S3	cervix
10	chr12:120444800-120451400	Weak transcription	NHEK	skin
11	chr12:120445000-120449200	Genic enhancers	Primary T helper 17 cells PMA-I stimulated	--
12	chr12:120445400-120448800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
13	chr12:120445400-120449000	Weak transcription	H1 Cell Line	embryonic stem cell
14	chr12:120445400-120450000	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
15	chr12:120445600-120451800	Weak transcription	ES-I3 Cell Line	embryonic stem cell
16	chr12:120445600-120453200	Weak transcription	HUES6 Cell Line	embryonic stem cell
17	chr12:120445800-120448400	Weak transcription	HUES64 Cell Line	embryonic stem cell
18	chr12:120445800-120448400	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
19	chr12:120445800-120449600	Weak transcription	GM12878-XiMat	blood
20	chr12:120445800-120449800	Weak transcription	Primary B cells from peripheral blood	blood
21	chr12:120446000-120448200	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
22	chr12:120446000-120451200	Weak transcription	HepG2	liver
23	chr12:120446000-120451600	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
24	chr12:120446400-120448600	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
25	chr12:120446600-120448400	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
26	chr12:120446600-120449000	Weak transcription	Pancreatic Islets	Pancreatic Islet
27	chr12:120447400-120449400	Transcr. at gene 5' and 3'	Primary T helper cells PMA-I stimulated	--
28	chr12:120447400-120449800	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
29	chr12:120447400-120454600	Enhancers	Primary T helper naive cells fromperipheralblood	blood
30	chr12:120447600-120449000	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
31	chr12:120447600-120449200	Strong transcription	Thymus	Thymus
32	chr12:120447600-120454200	Enhancers	Primary T helper cells fromperipheralblood	blood
33	chr12:120447600-120454200	Enhancers	Primary T killer memory cells from peripheral blood	blood
34	chr12:120447800-120448000	ZNF genes & repeats	Fetal Thymus	thymus
35	chr12:120447800-120449600	Enhancers	Primary T cells fromperipheralblood	blood
36	chr12:120447800-120449600	Enhancers	Primary T helper naive cells from peripheral blood	blood
37	chr12:120447800-120454200	Enhancers	Primary T cells from cord blood	blood

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