Variant report

Variant	rs41461644
Chromosome Location	chr16:80690432-80690433
allele	A/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr16:80689193..80691677-chr16:80694873..80698122,4	MCF-7	breast:
2	chr16:80577485..80580342-chr16:80689346..80691790,2	MCF-7	breast:
3	chr16:80663419..80665671-chr16:80688492..80690813,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000168589	Chromatin interaction

Extended variants
information (count: 26 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:22)

rs_ID	r²[population]
rs10514504	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AMR][1000 genomes];0.95[ASN][1000 genomes]
rs11865226	1.00[CHB][hapmap]
rs16953755	1.00[CHB][hapmap];0.83[CHD][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs16953756	1.00[AMR][1000 genomes];0.95[ASN][1000 genomes]
rs16953758	1.00[CHB][hapmap];0.83[CHD][hapmap];0.83[AMR][1000 genomes];0.95[ASN][1000 genomes]
rs16953773	1.00[CHB][hapmap];1.00[AMR][1000 genomes]
rs1869191	0.93[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs41368550	1.00[CHB][hapmap];0.83[CHD][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[ASN][1000 genomes]
rs56969697	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs59138080	1.00[AMR][1000 genomes];0.95[ASN][1000 genomes]
rs59559356	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs6564777	1.00[CHB][hapmap];0.85[ASN][1000 genomes]
rs6564780	1.00[CHB][hapmap]
rs6564782	1.00[CHB][hapmap]
rs7186836	1.00[CHB][hapmap]
rs7190255	1.00[CHB][hapmap]
rs7191647	1.00[CHB][hapmap]
rs7195009	1.00[AMR][1000 genomes];0.95[ASN][1000 genomes]
rs7203749	1.00[AMR][1000 genomes];0.95[ASN][1000 genomes]
rs8046128	0.88[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs9928210	1.00[CHB][hapmap]
rs9933370	1.00[CHB][hapmap]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1060621	chr16:80532848-80980616	Weak transcription Active TSS ZNF genes & repeats Enhancers Flanking Active TSS Strong transcription Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	29 gene(s)	inside rSNPs	diseases
2	nsv542989	chr16:80532848-80980616	Enhancers Active TSS ZNF genes & repeats Strong transcription Flanking Bivalent TSS/Enh Flanking Active TSS Bivalent Enhancer Weak transcription Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	29 gene(s)	inside rSNPs	diseases
3	nsv1058764	chr16:80656966-80707848	Active TSS Flanking Active TSS Weak transcription Enhancers Strong transcription ZNF genes & repeats Bivalent Enhancer Genic enhancers	TF binding region Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
4	nsv1057357	chr16:80662770-80794945	Weak transcription Enhancers Flanking Active TSS Strong transcription Active TSS ZNF genes & repeats Bivalent Enhancer Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:43 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr16:80674400-80707600	Weak transcription	Placenta	Placenta
2	chr16:80685800-80691800	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
3	chr16:80686800-80690800	Weak transcription	Fetal Kidney	kidney
4	chr16:80687000-80716200	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
5	chr16:80687200-80692400	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
6	chr16:80688200-80692800	Weak transcription	Aorta	Aorta
7	chr16:80689000-80751000	Weak transcription	Pancreas	Pancrea
8	chr16:80689200-80690600	Weak transcription	Fetal Intestine Small	intestine
9	chr16:80689800-80700200	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
10	chr16:80690000-80690600	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
11	chr16:80690000-80690600	Flanking Active TSS	Primary T helper naive cells from peripheral blood	blood
12	chr16:80690000-80690600	Flanking Active TSS	Primary T regulatory cells fromperipheralblood	blood
13	chr16:80690000-80690600	Enhancers	Spleen	Spleen
14	chr16:80690000-80691600	Enhancers	Small Intestine	intestine
15	chr16:80690000-80694600	Weak transcription	Hela-S3	cervix
16	chr16:80690200-80690600	Enhancers	Primary B cells from peripheral blood	blood
17	chr16:80690200-80690600	Flanking Active TSS	Primary T cells fromperipheralblood	blood
18	chr16:80690200-80690600	Flanking Active TSS	Primary T helper cells PMA-I stimulated	--
19	chr16:80690200-80690600	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
20	chr16:80690200-80690600	Enhancers	Liver	Liver
21	chr16:80690200-80690600	Enhancers	Colonic Mucosa	Colon
22	chr16:80690200-80690600	Flanking Active TSS	Duodenum Mucosa	Duodenum
23	chr16:80690200-80690600	Enhancers	Fetal Thymus	thymus
24	chr16:80690200-80690800	Flanking Active TSS	Primary T helper 17 cells PMA-I stimulated	--
25	chr16:80690200-80690800	Enhancers	Brain Anterior Caudate	brain
26	chr16:80690200-80690800	Enhancers	Lung	lung
27	chr16:80690200-80691000	Flanking Active TSS	Primary T helper memory cells from peripheral blood 2	blood
28	chr16:80690200-80691000	Enhancers	Right Atrium	heart
29	chr16:80690200-80691200	Flanking Active TSS	Primary T helper cells fromperipheralblood	blood
30	chr16:80690200-80691600	Flanking Active TSS	GM12878-XiMat	blood
31	chr16:80690200-80691800	Enhancers	HUVEC	blood vessel
32	chr16:80690400-80690600	Enhancers	Primary hematopoietic stem cells short term culture	blood
33	chr16:80690400-80690600	Flanking Active TSS	Primary T helper naive cells fromperipheralblood	blood
34	chr16:80690400-80690600	Flanking Active TSS	Primary T helper memory cells from peripheral blood 1	blood
35	chr16:80690400-80690600	Flanking Active TSS	Primary T killer memory cells from peripheral blood	blood
36	chr16:80690400-80690600	Enhancers	Gastric	stomach
37	chr16:80690400-80690800	Flanking Active TSS	Primary mononuclear cells fromperipheralblood	Blood
38	chr16:80690400-80690800	Enhancers	Sigmoid Colon	Sigmoid Colon
39	chr16:80690400-80691000	Active TSS	Primary T cells effector/memory enriched fromperipheralblood	blood
40	chr16:80690400-80691000	Flanking Active TSS	Primary T killer naive cells fromperipheralblood	blood
41	chr16:80690400-80691000	Active TSS	Rectal Mucosa Donor 29	rectum
42	chr16:80690400-80691000	Enhancers	Thymus	Thymus
43	chr16:80690400-80691200	Flanking Active TSS	Primary T cells from cord blood	blood

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