Variant report

Variant	rs896629
Chromosome Location	chr16:80705399-80705400
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	chr16:80695632..80702044-chr16:80703955..80710409,7	MCF-7	breast:

Variant related genes	Relation type
ENSG00000265341	Chromatin interaction

Extended variants
information (count: 54 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:47)

rs_ID	r²[population]
rs10514505	0.95[CHB][hapmap];0.91[JPT][hapmap];0.82[AMR][1000 genomes];0.90[ASN][1000 genomes]
rs10514506	0.87[MEX][hapmap]
rs1077885	0.89[CEU][hapmap];0.95[CHB][hapmap];0.90[JPT][hapmap];0.92[AMR][1000 genomes];0.89[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs1077886	0.88[CEU][hapmap];0.95[CHB][hapmap];0.91[JPT][hapmap];0.88[AMR][1000 genomes];0.81[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs10871392	0.83[AMR][1000 genomes];0.88[ASN][1000 genomes]
rs10871393	0.87[CEU][hapmap];0.94[CHB][hapmap];1.00[JPT][hapmap];0.84[AMR][1000 genomes];0.87[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs10871394	0.82[AMR][1000 genomes];0.87[ASN][1000 genomes]
rs11150298	0.81[CEU][hapmap];0.83[GIH][hapmap];0.81[JPT][hapmap];0.83[MEX][hapmap]
rs11150299	0.82[CEU][hapmap];0.84[CHB][hapmap];0.90[JPT][hapmap];0.85[AMR][1000 genomes];0.84[ASN][1000 genomes]
rs11150300	0.84[CEU][hapmap];0.83[GIH][hapmap];0.85[JPT][hapmap];0.95[MEX][hapmap];0.84[TSI][hapmap];0.88[AMR][1000 genomes]
rs11150301	0.86[AMR][1000 genomes]
rs11150302	0.90[AMR][1000 genomes]
rs11643733	0.80[CEU][hapmap];0.95[CHB][hapmap];0.88[JPT][hapmap];0.82[AMR][1000 genomes];0.84[ASN][1000 genomes]
rs11859496	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.84[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs11863297	0.85[CEU][hapmap];0.90[CHB][hapmap];0.91[JPT][hapmap];0.83[AMR][1000 genomes];0.88[ASN][1000 genomes]
rs12447921	0.91[MEX][hapmap];0.81[AMR][1000 genomes]
rs1377119	0.81[CEU][hapmap]
rs16953809	0.81[CEU][hapmap]
rs17752269	1.00[CEU][hapmap];0.90[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.83[AFR][1000 genomes];0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2012766	0.81[CEU][hapmap];0.83[YRI][hapmap]
rs2084866	0.89[CEU][hapmap];0.95[CHB][hapmap];0.90[JPT][hapmap];0.90[AMR][1000 genomes];0.89[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2316148	0.89[AMR][1000 genomes]
rs2316152	1.00[CEU][hapmap];0.94[JPT][hapmap];0.85[YRI][hapmap];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs2873084	0.85[CEU][hapmap];0.85[GIH][hapmap];0.85[JPT][hapmap];0.95[MEX][hapmap];0.87[AMR][1000 genomes]
rs35732345	0.80[AMR][1000 genomes]
rs4889193	0.96[CEU][hapmap];0.85[YRI][hapmap];0.83[EUR][1000 genomes]
rs4889194	0.84[CEU][hapmap];0.82[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs6564779	0.84[CEU][hapmap];0.89[AMR][1000 genomes]
rs6564783	0.83[YRI][hapmap]
rs7187646	0.94[ASW][hapmap];0.96[CEU][hapmap];0.80[GIH][hapmap];0.95[JPT][hapmap];0.95[MEX][hapmap];0.89[MKK][hapmap];1.00[TSI][hapmap];0.86[YRI][hapmap];0.83[AFR][1000 genomes];0.98[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs7190973	1.00[CEU][hapmap];0.86[CHB][hapmap];0.86[JPT][hapmap];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs7192094	0.81[CEU][hapmap];0.85[AMR][1000 genomes]
rs7195952	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7200113	0.80[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs8047798	0.87[MEX][hapmap];0.83[AMR][1000 genomes]
rs8047993	0.81[CEU][hapmap];0.96[YRI][hapmap]
rs8048068	0.88[AMR][1000 genomes]
rs8049284	0.82[MEX][hapmap]
rs8052730	0.88[AMR][1000 genomes]
rs8055305	0.80[YRI][hapmap]
rs8057515	0.82[CEU][hapmap];0.85[JPT][hapmap];0.88[AMR][1000 genomes]
rs896627	0.87[AMR][1000 genomes];0.83[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs896628	0.89[CEU][hapmap];0.95[CHB][hapmap];0.93[CHD][hapmap];0.95[GIH][hapmap];0.91[JPT][hapmap];0.95[MEX][hapmap];0.84[TSI][hapmap];0.90[AMR][1000 genomes];0.88[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs930743	0.91[MEX][hapmap];0.81[AMR][1000 genomes]
rs930744	0.83[ASW][hapmap];0.84[CEU][hapmap];0.95[MEX][hapmap];0.89[AMR][1000 genomes]
rs9929220	0.81[AMR][1000 genomes]
rs9930141	0.81[CEU][hapmap]

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	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
5	esv3451298	chr16:80696935-80997389	Weak transcription Enhancers Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Active TSS Flanking Active TSS Bivalent Enhancer Genic enhancers Strong transcription Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	21 gene(s)	inside rSNPs	diseases
6	esv3350075	chr16:80696955-80997359	Strong transcription Enhancers Weak transcription Flanking Active TSS Flanking Bivalent TSS/Enh Active TSS Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	21 gene(s)	inside rSNPs	diseases
7	esv1815070	chr16:80697870-80725811	Bivalent Enhancer Enhancers Weak transcription Strong transcription Active TSS ZNF genes & repeats Flanking Active TSS	TF binding region CpG island Chromatin interactive region	3 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs896629	ADAT1	cis	cerebellum	SCAN

Chromatin state (count:33 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr16:80674400-80707600	Weak transcription	Placenta	Placenta
2	chr16:80687000-80716200	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
3	chr16:80689000-80751000	Weak transcription	Pancreas	Pancrea
4	chr16:80690600-80728000	Weak transcription	Gastric	stomach
5	chr16:80699400-80723000	Weak transcription	HUVEC	blood vessel
6	chr16:80701200-80706400	Strong transcription	Hela-S3	cervix
7	chr16:80701600-80717800	Weak transcription	Duodenum Mucosa	Duodenum
8	chr16:80703200-80707000	Enhancers	Primary B cells from peripheral blood	blood
9	chr16:80703400-80723400	Weak transcription	Esophagus	oesophagus
10	chr16:80703800-80713600	Weak transcription	Lung	lung
11	chr16:80704000-80706600	Enhancers	Primary B cells from cord blood	blood
12	chr16:80704400-80711400	Weak transcription	Primary T helper naive cells from peripheral blood	blood
13	chr16:80704600-80705400	Enhancers	Spleen	Spleen
14	chr16:80704600-80705600	Enhancers	iPS DF 19.11 Cell Line	embryonic stem cell
15	chr16:80704600-80706000	Enhancers	Monocytes-CD14+_RO01746	blood
16	chr16:80704600-80721000	Weak transcription	Primary T cells fromperipheralblood	blood
17	chr16:80704800-80707800	Weak transcription	Fetal Intestine Small	intestine
18	chr16:80705000-80705400	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
19	chr16:80705000-80705600	Enhancers	iPS-15b Cell Line	embryonic stem cell
20	chr16:80705000-80705600	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
21	chr16:80705000-80705800	Enhancers	iPS-18 Cell Line	embryonic stem cell
22	chr16:80705000-80705800	Enhancers	Primary monocytes fromperipheralblood	blood
23	chr16:80705000-80706000	Enhancers	Primary hematopoietic stem cells	blood
24	chr16:80705200-80705400	Flanking Active TSS	Primary hematopoietic stem cells short term culture	blood
25	chr16:80705200-80705600	Enhancers	ES-I3 Cell Line	embryonic stem cell
26	chr16:80705200-80705600	Enhancers	H1 Cell Line	embryonic stem cell
27	chr16:80705200-80705600	Enhancers	H9 Cell Line	embryonic stem cell
28	chr16:80705200-80705800	Flanking Active TSS	GM12878-XiMat	blood
29	chr16:80705200-80706000	Enhancers	HUES48 Cell Line	embryonic stem cell
30	chr16:80705200-80706000	Enhancers	HUES64 Cell Line	embryonic stem cell
31	chr16:80705200-80706000	Enhancers	iPS-20b Cell Line	embryonic stem cell
32	chr16:80705200-80706000	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
33	chr16:80705200-80706000	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--

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