Variant report

Variant	rs16841889
Chromosome Location	chr1:197670799-197670800
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	chr1:197669252..197673459-chr1:197743220..197745341,4	MCF-7	breast:
2	chr1:197669335..197671287-chr1:197871295..197873038,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000213047	Chromatin interaction
ENSG00000203724	Chromatin interaction

Extended variants
information (count: 49 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:42)

rs_ID	r²[population]
rs11799366	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs11801895	1.00[AMR][1000 genomes]
rs11802251	1.00[AMR][1000 genomes]
rs11802844	1.00[AMR][1000 genomes]
rs11802940	1.00[AMR][1000 genomes]
rs11802964	1.00[AMR][1000 genomes]
rs11803371	1.00[AMR][1000 genomes]
rs11803914	1.00[AMR][1000 genomes]
rs11804057	1.00[AMR][1000 genomes]
rs11804072	1.00[AMR][1000 genomes]
rs11804259	1.00[AMR][1000 genomes]
rs11805327	1.00[AMR][1000 genomes]
rs11805755	1.00[AMR][1000 genomes]
rs11805812	1.00[AMR][1000 genomes]
rs11805909	1.00[AMR][1000 genomes]
rs11806117	0.86[ASW][hapmap];0.89[YRI][hapmap]
rs11806221	1.00[AMR][1000 genomes]
rs11806385	1.00[AMR][1000 genomes]
rs11806645	1.00[AMR][1000 genomes]
rs11806651	1.00[AMR][1000 genomes]
rs11806821	1.00[AMR][1000 genomes]
rs11807556	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs11807717	1.00[AMR][1000 genomes]
rs11809987	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs11811376	1.00[AMR][1000 genomes]
rs16841850	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs16841865	0.88[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs16841893	0.88[MKK][hapmap];0.90[YRI][hapmap];0.84[AFR][1000 genomes]
rs35781299	0.84[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs41418447	0.86[MKK][hapmap]
rs6657488	1.00[AMR][1000 genomes]
rs6666890	1.00[AMR][1000 genomes]
rs6667162	1.00[AMR][1000 genomes]
rs6667565	1.00[AMR][1000 genomes]
rs6703514	1.00[AMR][1000 genomes]
rs6703515	1.00[AMR][1000 genomes]
rs7522037	1.00[AMR][1000 genomes]
rs7533154	1.00[AMR][1000 genomes]
rs7535981	1.00[AMR][1000 genomes]
rs7543290	1.00[AMR][1000 genomes]
rs7554788	1.00[AMR][1000 genomes]
rs9661515	1.00[AMR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:7 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv873074	chr1:197464448-197698103	Weak transcription ZNF genes & repeats Enhancers Strong transcription Active TSS Flanking Active TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
2	nsv873075	chr1:197464448-197714851	Enhancers ZNF genes & repeats Weak transcription Strong transcription Flanking Active TSS Active TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
3	nsv873076	chr1:197529218-197689967	Weak transcription Active TSS Enhancers Strong transcription ZNF genes & repeats Flanking Active TSS Genic enhancers	TF binding region CpG island Chromatin interactive region	8 gene(s)	inside rSNPs	diseases
4	nsv437263	chr1:197599030-197722240	Enhancers Weak transcription Strong transcription Active TSS ZNF genes & repeats Flanking Active TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
5	nsv427908	chr1:197611569-197767362	ZNF genes & repeats Weak transcription Enhancers Flanking Active TSS Strong transcription Bivalent/Poised TSS Active TSS Flanking Bivalent TSS/Enh Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	12 gene(s)	inside rSNPs	diseases
6	nsv873077	chr1:197615391-197698103	Weak transcription ZNF genes & repeats Enhancers Flanking Active TSS Strong transcription Active TSS Genic enhancers	TF binding region Chromatin interactive region	8 gene(s)	inside rSNPs	diseases
7	nsv548873	chr1:197664905-197694037	Enhancers ZNF genes & repeats Weak transcription Active TSS	Chromatin interactive region	5 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:10 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:197657000-197677000	Weak transcription	Ovary	ovary
2	chr1:197659400-197674800	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
3	chr1:197659800-197674400	Weak transcription	Primary hematopoietic stem cells short term culture	blood
4	chr1:197665800-197675400	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
5	chr1:197665800-197693600	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
6	chr1:197666200-197671400	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
7	chr1:197666800-197675800	Weak transcription	Primary T helper cells fromperipheralblood	blood
8	chr1:197669800-197680400	Weak transcription	Sigmoid Colon	Sigmoid Colon
9	chr1:197670200-197675600	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
10	chr1:197670400-197670800	ZNF genes & repeats	Fetal Intestine Small	intestine

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