Variant report

Variant	rs6541389
Chromosome Location	chr1:94149081-94149082
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr1:93913059..93915471-chr1:94146480..94149352,2	MCF-7	breast:
2	chr1:94147624..94149289-chr1:94160364..94162854,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000137942	Chromatin interaction

Extended variants
information (count: 38 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:36)

rs_ID	r²[population]
rs1011903	1.00[CEU][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs1011904	0.98[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs11164961	0.98[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs11164962	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs11164963	1.00[CEU][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs12057736	0.87[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs12059154	0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs12079723	0.95[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs12084853	1.00[CEU][hapmap];0.86[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs12092517	0.87[CEU][hapmap];0.98[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs1292929	0.91[ASN][1000 genomes]
rs1567791	1.00[CEU][hapmap];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs236284	0.89[CEU][hapmap];0.86[ASN][1000 genomes]
rs236285	0.86[ASN][1000 genomes]
rs236287	0.89[CEU][hapmap];0.86[ASN][1000 genomes]
rs236288	0.91[ASN][1000 genomes]
rs236291	0.91[ASN][1000 genomes]
rs236292	0.88[ASN][1000 genomes]
rs236301	0.91[ASN][1000 genomes]
rs61781002	0.95[AFR][1000 genomes];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs6541386	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs6541387	1.00[CEU][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs6541388	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs6656270	1.00[CEU][hapmap];0.93[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs6657709	0.88[CEU][hapmap];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs6660740	1.00[CEU][hapmap];0.98[AMR][1000 genomes];0.95[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs6675484	0.98[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs6684568	0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs6694536	0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs6701871	0.88[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs6702036	1.00[CEU][hapmap];1.00[YRI][hapmap];0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6704479	1.00[CEU][hapmap];0.95[AMR][1000 genomes];0.95[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs7513130	0.88[CEU][hapmap]
rs7519952	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs955470	1.00[YRI][hapmap];0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9659100	0.83[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	nsv482370	chr1:94000799-94183692	Enhancers Weak transcription Flanking Bivalent TSS/Enh Strong transcription Flanking Active TSS Genic enhancers Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	16 gene(s)	inside rSNPs	diseases
2	esv2755338	chr1:94059579-94176079	Weak transcription Flanking Active TSS Enhancers Strong transcription Genic enhancers Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	14 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	chr1:94147800-94153200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
2	chr1:94148000-94151600	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
3	chr1:94148200-94150400	Weak transcription	Primary B cells from peripheral blood	blood
4	chr1:94148200-94150800	Weak transcription	Primary B cells from cord blood	blood
5	chr1:94148200-94151000	Weak transcription	GM12878-XiMat	blood
6	chr1:94148200-94151800	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
7	chr1:94148200-94151800	Weak transcription	A549	lung
8	chr1:94148200-94151800	Weak transcription	HepG2	liver
9	chr1:94148200-94152000	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
10	chr1:94148200-94152200	Weak transcription	HUVEC	blood vessel
11	chr1:94148200-94154600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
12	chr1:94148200-94154600	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
13	chr1:94148200-94155200	Weak transcription	ES-I3 Cell Line	embryonic stem cell
14	chr1:94148200-94156800	Weak transcription	Adipose Nuclei	Adipose
15	chr1:94148200-94156800	Weak transcription	NHLF	lung
16	chr1:94148200-94167200	Weak transcription	Right Atrium	heart
17	chr1:94148400-94150200	Weak transcription	Placenta	Placenta
18	chr1:94148400-94151800	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
19	chr1:94148400-94152200	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
20	chr1:94148400-94152200	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
21	chr1:94148400-94156200	Weak transcription	HSMM	muscle
22	chr1:94148400-94156600	Weak transcription	Breast Myoepithelial Primary Cells	Breast
23	chr1:94148400-94156800	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
24	chr1:94148600-94152200	Weak transcription	NHEK	skin
25	chr1:94148800-94151200	Weak transcription	Hela-S3	cervix
26	chr1:94148800-94156400	Weak transcription	HMEC	breast

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